Proteins
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Protein Structure, Secondary
Models, Molecular
Protein Conformation
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Databases, Protein
Sequence Analysis, Protein
Structural Homology, Protein
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Software
Algorithms
Computational Biology
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Amino Acid Sequence
Internet
Computer Simulation
Models, Chemical
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
User-Computer Interface
Nuclear Magnetic Resonance, Biomolecular
Crystallography, X-Ray
Hydrogen Bonding
Computer Graphics
Thermodynamics
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
Binding Sites
Amino Acids
Evolution, Molecular
Sequence Homology, Amino Acid
Molecular Dynamics Simulation
Structure-Activity Relationship
Protein Binding
Solvents
Hydrophobic and Hydrophilic Interactions
Magnetic Resonance Spectroscopy
Molecular Structure
Crystallography
Protein Structure, Quaternary
Databases, Factual
Extensive collections, reputedly complete, of facts and data garnered from material of a specialized subject area and made available for analysis and application. The collection can be automated by various contemporary methods for retrieval. The concept should be differentiated from DATABASES, BIBLIOGRAPHIC which is restricted to collections of bibliographic references.
Protein Denaturation
Muramidase
A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 3.2.1.17.
Enzymes
Ligands
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Knowledge Bases
Artificial Intelligence
Information Storage and Retrieval
Database Management Systems
Protein Engineering
Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes.
Amino Acid Motifs
Protein Stability
Circular Dichroism
Mutation
Membrane Proteins
Conserved Sequence
Myoglobin
Protein Interaction Domains and Motifs
Water
X-Ray Diffraction
The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Monte Carlo Method
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
Crystallization
Pattern Recognition, Automated
Models, Statistical
Peptides
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Cluster Analysis
A set of statistical methods used to group variables or observations into strongly inter-related subgroups. In epidemiology, it may be used to analyze a closely grouped series of events or cases of disease or other health-related phenomenon with well-defined distribution patterns in relation to time or place or both.
Temperature
Neural Networks (Computer)
A computer architecture, implementable in either hardware or software, modeled after biological neural networks. Like the biological system in which the processing capability is a result of the interconnection strengths between arrays of nonlinear processing nodes, computerized neural networks, often called perceptrons or multilayer connectionist models, consist of neuron-like units. A homogeneous group of units makes up a layer. These networks are good at pattern recognition. They are adaptive, performing tasks by example, and thus are better for decision-making than are linear learning machines or cluster analysis. They do not require explicit programming.
Solutions
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Entropy
Reproducibility of Results
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Chemistry, Physical
Physicochemical Phenomena
Base Sequence
Models, Theoretical
Disulfides
Amino Acid Substitution
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Automation
Pliability
Spectrophotometry, Infrared
Catalytic Domain
Cryoelectron Microscopy
Enzyme Stability
Mathematical Concepts
Hydrogen
The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight [1.00784; 1.00811]. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.
Mutagenesis, Site-Directed
Deuterium Exchange Measurement
Markov Chains
Tryptophan
An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.
Electrons
Stable elementary particles having the smallest known negative charge, present in all elements; also called negatrons. Positively charged electrons are called positrons. The numbers, energies and arrangement of electrons around atomic nuclei determine the chemical identities of elements. Beams of electrons are called CATHODE RAYS.
Hemerythrin
Synchrotrons
Molecular Sequence Annotation
Bacteriophage T4
Normal Distribution
Mass Spectrometry
Peptide Fragments
Cattle
Surface Properties
Scattering, Small Angle
Scattering of a beam of electromagnetic or acoustic RADIATION, or particles, at small angles by particles or cavities whose dimensions are many times as large as the wavelength of the radiation or the de Broglie wavelength of the scattered particles. Also know as low angle scattering. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Small angle scattering (SAS) techniques, small angle neutron (SANS), X-ray (SAXS), and light (SALS, or just LS) scattering, are used to characterize objects on a nanoscale.
Rubredoxins
Systems Integration
Online Systems
Quantum Theory
Drug Design
The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.
Spectroscopy, Fourier Transform Infrared
Data Interpretation, Statistical
Hydrogen-Ion Concentration
Ribonuclease, Pancreatic
Cloning, Molecular
Sequence Analysis
Bacteriorhodopsins
Crown Ethers
Macrocyclic polyethers with the repeating unit of (-CH2-CH2-O)n where n is greater than 2 and some oxygens may be replaced by nitrogen, sulfur or phosphorus. These compounds are useful for coordinating CATIONS. The nomenclature uses a prefix to indicate the size of the ring and a suffix for the number of heteroatoms.
Dimerization
Proline
Repetitive Sequences, Amino Acid
Apoproteins
Protein Multimerization
Databases as Topic
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Amides
Fourier Analysis
Analysis based on the mathematical function first formulated by Jean-Baptiste-Joseph Fourier in 1807. The function, known as the Fourier transform, describes the sinusoidal pattern of any fluctuating pattern in the physical world in terms of its amplitude and its phase. It has broad applications in biomedicine, e.g., analysis of the x-ray crystallography data pivotal in identifying the double helical nature of DNA and in analysis of other molecules, including viruses, and the modified back-projection algorithm universally used in computerized tomography imaging, etc. (From Segen, The Dictionary of Modern Medicine, 1992)
Motion
Ions
Point Mutation
Multiprotein Complexes
Triose-Phosphate Isomerase
Biochemistry
Energy Transfer
The transfer of energy of a given form among different scales of motion. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed). It includes the transfer of kinetic energy and the transfer of chemical energy. The transfer of chemical energy from one molecule to another depends on proximity of molecules so it is often used as in techniques to measure distance such as the use of FORSTER RESONANCE ENERGY TRANSFER.
Pyrococcus furiosus
Substrate Specificity
Metalloproteins
Protons
Models, Biological
Exons
Spectrum Analysis, Raman
Lipid Bilayers
National Institute of General Medical Sciences (U.S.)
Component of the NATIONAL INSTITUTES OF HEALTH. It conducts and supports basic biomedical research that is not targeted to specific diseases and funds studies on genes, proteins, and cells, as well as on fundamental processes like communication within and between cells and metabolism. It was established in 1962.
Data Display
Nitrogen Isotopes
Ubiquitin
A highly conserved 76-amino acid peptide universally found in eukaryotic cells that functions as a marker for intracellular PROTEIN TRANSPORT and degradation. Ubiquitin becomes activated through a series of complicated steps and forms an isopeptide bond to lysine residues of specific proteins within the cell. These "ubiquitinated" proteins can be recognized and degraded by proteosomes or be transported to specific compartments within the cell.
Solubility
Catalysis
Deuterium
Trypsin
Multigene Family
A set of genes descended by duplication and variation from some ancestral gene. Such genes may be clustered together on the same chromosome or dispersed on different chromosomes. Examples of multigene families include those that encode the hemoglobins, immunoglobulins, histocompatibility antigens, actins, tubulins, keratins, collagens, heat shock proteins, salivary glue proteins, chorion proteins, cuticle proteins, yolk proteins, and phaseolins, as well as histones, ribosomal RNA, and transfer RNA genes. The latter three are examples of reiterated genes, where hundreds of identical genes are present in a tandem array. (King & Stanfield, A Dictionary of Genetics, 4th ed)
Databases, Nucleic Acid
Genome
Spectrophotometry
Micelles
Particles consisting of aggregates of molecules held loosely together by secondary bonds. The surface of micelles are usually comprised of amphiphatic compounds that are oriented in a way that minimizes the energy of interaction between the micelle and its environment. Liquids that contain large numbers of suspended micelles are referred to as EMULSIONS.
Mutation, Missense
Glycosylation
Torsion, Mechanical
Protein Footprinting
A method for determining points of contact between interacting proteins or binding sites of proteins to nucleic acids. Protein footprinting utilizes a protein cutting reagent or protease. Protein cleavage is inhibited where the proteins, or nucleic acids and protein, contact each other. After completion of the cutting reaction, the remaining peptide fragments are analyzed by electrophoresis.
Sequence Analysis, DNA
Peptide Library
Oxidation-Reduction
A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).
Codon
A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE).
Electron Spin Resonance Spectroscopy
A technique applicable to the wide variety of substances which exhibit paramagnetism because of the magnetic moments of unpaired electrons. The spectra are useful for detection and identification, for determination of electron structure, for study of interactions between molecules, and for measurement of nuclear spins and moments. (From McGraw-Hill Encyclopedia of Science and Technology, 7th edition) Electron nuclear double resonance (ENDOR) spectroscopy is a variant of the technique which can give enhanced resolution. Electron spin resonance analysis can now be used in vivo, including imaging applications such as MAGNETIC RESONANCE IMAGING.
Metals
Protein Processing, Post-Translational
Any of various enzymatically catalyzed post-translational modifications of PEPTIDES or PROTEINS in the cell of origin. These modifications include carboxylation; HYDROXYLATION; ACETYLATION; PHOSPHORYLATION; METHYLATION; GLYCOSYLATION; ubiquitination; oxidation; proteolysis; and crosslinking and result in changes in molecular weight and electrophoretic motility.
Molecular Docking Simulation
Models, Structural
Electrophoresis, Polyacrylamide Gel
Allosteric Regulation
Neutrons
Electrically neutral elementary particles found in all atomic nuclei except light hydrogen; the mass is equal to that of the proton and electron combined and they are unstable when isolated from the nucleus, undergoing beta decay. Slow, thermal, epithermal, and fast neutrons refer to the energy levels with which the neutrons are ejected from heavier nuclei during their decay.
Mathematical Computing
Heme
Urea
Macromolecular Substances
Detergents
Plant Proteins
Asparagine
Melatonin biosynthesis: the structure of serotonin N-acetyltransferase at 2.5 A resolution suggests a catalytic mechanism. (1/55031)
Conversion of serotonin to N-acetylserotonin, the precursor of the circadian neurohormone melatonin, is catalyzed by serotonin N-acetyltransferase (AANAT) in a reaction requiring acetyl coenzyme A (AcCoA). AANAT is a globular protein consisting of an eight-stranded beta sheet flanked by five alpha helices; a conserved motif in the center of the beta sheet forms the cofactor binding site. Three polypeptide loops converge above the AcCoA binding site, creating a hydrophobic funnel leading toward the cofactor and serotonin binding sites in the protein interior. Two conserved histidines not found in other NATs are located at the bottom of the funnel in the active site, suggesting a catalytic mechanism for acetylation involving imidazole groups acting as general acid/base catalysts. (+info)Structural basis of Rab effector specificity: crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A. (2/55031)
The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of activated Rab3A/GTP/Mg2+ bound to the effector domain of rabphilin-3A was solved to 2.6 A resolution. Rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion. (+info)Crystal structures of two Sm protein complexes and their implications for the assembly of the spliceosomal snRNPs. (3/55031)
The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F, and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs (snRNAs). These proteins share a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Crystal structures of two Sm protein complexes, D3B and D1D2, show that these proteins have a common fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta sheet, and the D1D2 and D3B dimers superpose closely in their core regions, including the dimer interfaces. The crystal structures suggest that the seven Sm proteins could form a closed ring and the snRNAs may be bound in the positively charged central hole. (+info)A viral mechanism for inhibition of p300 and PCAF acetyltransferase activity. (4/55031)
Nucleosomal histone modification is believed to be a critical step in the activation of RNA polymerase II-dependent transcription. p300/CBP and PCAF histone acetyltransferases (HATs) are coactivators for several transcription factors, including nuclear hormone receptors, p53, and Stat1alpha, and participate in transcription by forming an activation complex and by promoting histone acetylation. The adenoviral E1A oncoprotein represses transcriptional signaling by binding to p300/CBP and displacing PCAF and p/CIP proteins from the complex. Here, we show that E1A directly represses the HAT activity of both p300/CBP and PCAF in vitro and p300-dependent transcription in vivo. Additionally, E1A inhibits nucleosomal histone modifications by the PCAF complex and blocks p53 acetylation. These results demonstrate the modulation of HAT activity as a novel mechanism of transcriptional regulation. (+info)Crystal structure of the cytoplasmic domain of the type I TGF beta receptor in complex with FKBP12. (5/55031)
Activation of the type I TGFbeta receptor (TbetaR-I) requires phosphorylation of a regulatory segment known as the GS region, located upstream of the serine/threonine kinase domain in the cytoplasmic portion of the receptor. The crystal structure of a fragment of unphosphorylated TbetaR-I, containing both the GS region and the catalytic domain, has been determined in complex with the FK506-binding protein FKBP12. TbetaR-I adopts an inactive conformation that is maintained by the unphosphorylated GS region. FKBP12 binds to the GS region of the receptor, capping the TbetaR-II phosphorylation sites and further stabilizing the inactive conformation of TbetaR-I. Certain structural features at the catalytic center of TbetaR-I are characteristic of tyrosine kinases rather than Ser/Thr kinases. (+info)Crystal structure of wild-type human procathepsin K. (6/55031)
Cathepsin K is a lysosomal cysteine protease belonging to the papain superfamily. It has been implicated as a major mediator of osteoclastic bone resorption. Wild-type human procathepsin K has been crystallized in a glycosylated and a deglycosylated form. The latter crystals diffract better, to 3.2 A resolution, and contain four molecules in the asymmetric unit. The structure was solved by molecular replacement and refined to an R-factor of 0.194. The N-terminal fragment of the proregion forms a globular domain while the C-terminal segment is extended and shows substantial flexibility. The proregion interacts with the enzyme along the substrate binding groove and along the proregion binding loop (residues Ser138-Asn156). It binds to the active site in the opposite direction to that of natural substrates. The overall binding mode of the proregion to cathepsin K is similar to that observed in cathepsin L, caricain, and cathepsin B, but there are local differences that likely contribute to the specificity of these proregions for their cognate enzymes. The main observed difference is in the position of the short helix alpha3p (67p-75p), which occupies the S' subsites. As in the other proenzymes, the proregion utilizes the S2 subsite for anchoring by placing a leucine side chain there, according to the specificity of cathepsin K toward its substrate. (+info)Tolerance of a protein to multiple polar-to-hydrophobic surface substitutions. (7/55031)
Hydrophobic substitutions at solvent-exposed positions in two alpha-helical regions of the bacteriophage P22 Arc repressor were introduced by combinatorial mutagenesis. In helix A, hydrophobic residues were tolerated individually at each of the five positions examined, but multiple substitutions were poorly tolerated as shown by the finding that mutants with more than two additional hydrophobic residues were biologically inactive. Several inactive helix A variants were purified and found to have reduced thermal stability relative to wild-type Arc, with a rough correlation between the number of polar-to-hydrophobic substitutions and the magnitude of the stability defect. Quite different results were obtained in helix B, where variants with as many as five polar-to-hydrophobic substitutions were found to be biologically active and one variant with three hydrophobic substitutions had a t(m) 6 degrees C higher than wild-type. By contrast, a helix A mutant with three similar polar-to-hydrophobic substitutions was 23 degrees C less stable than wild-type. Also, one set of three polar-to-hydrophobic substitutions in helix B was tolerated when introduced into the wild-type background but not when introduced into an equally active mutant having a nearly identical structure. Context effects occur both when comparing different regions of the same protein and when comparing the same region in two different homologues. (+info)Sequence specificity, statistical potentials, and three-dimensional structure prediction with self-correcting distance geometry calculations of beta-sheet formation in proteins. (8/55031)
A statistical analysis of a representative data set of 169 known protein structures was used to analyze the specificity of residue interactions between spatial neighboring strands in beta-sheets. Pairwise potentials were derived from the frequency of residue pairs in nearest contact, second nearest and third nearest contacts across neighboring beta-strands compared to the expected frequency of residue pairs in a random model. A pseudo-energy function based on these statistical pairwise potentials recognized native beta-sheets among possible alternative pairings. The native pairing was found within the three lowest energies in 73% of the cases in the training data set and in 63% of beta-sheets in a test data set of 67 proteins, which were not part of the training set. The energy function was also used to detect tripeptides, which occur frequently in beta-sheets of native proteins. The majority of native partners of tripeptides were distributed in a low energy range. Self-correcting distance geometry (SECODG) calculations using distance constraints sets derived from possible low energy pairing of beta-strands uniquely identified the native pairing of the beta-sheet in pancreatic trypsin inhibitor (BPTI). These results will be useful for predicting the structure of proteins from their amino acid sequence as well as for the design of proteins containing beta-sheets. (+info)
Domain combinations for Carbohydrate-binding domain superfamily in Proterospongia sp. ATCC 50818
Polbase - Structure of polymerase: Co(III)bleomycinB2 bithiazole/C-terminal tail domain bound to d(ATTTAGTTAACTAAAT) complexed...
Genetic Evidence that Transcription Activation by RhaS Involves Specific Amino Acid Contacts with Sigma 70 | Journal of...
Evolutionary classification of protein domain structures
Evolutionary classification of protein domain structures
The evolution of protein domain families | Biochemical Society Transactions
SMART: SAM domain annotation
SMART: SAM domain annotation
Signal peptide-binding domain superfamily
Auto-inhibition of Arabidopsis th... preview & related info | Mendeley
KH homology domain-containing protein elisa and antibody
CDD Conserved Protein Domain Family: PTK CCK4
CDD Conserved Protein Domain Family: NR LBD GR
CSF1R protein domain and mutation schematic. Schematic | Open-i
Domain combinations for 49899,55486, gap ,57535, gap ,57535,57535, gap superfamilies in groups of genomes
cc Domain Names Search - Verisign
cc Domain Names Search - Verisign
Forkhead-associated domain-containing protein elisa and antibody
Domain combination pairs containing Dcp2 domain-like and Nudix in all archaea
Transmembrane domain architecture, symmetry and couplin | Open-i
GTLD Domain Names | New Domain Extensions Available - GoDaddy PH
Method for producing and identifying soluble protein domains - Domainex Limited
Tuning the Flexibility of Glycine-Serine Linkers ToAllow Rational Design of Multidomain Proteins - BioNMR
http://www.peopleeraconsulting.in/
http://www.peopleeraconsulting.in/
Etk/Bmx, a tyrosine kinase with a pleckstrin-homology domain, is an effector of phosphatidylinositol 3-kinase and is involved...
NMR paper Solution NMR structures provide first structural coverage of the large protein domain family PF08369 and...
HOMER1 - Wikipedia
Heat shock protein 70kD (HSP70), peptide-binding domain superfamily
Genes | Free Full-Text | Reassessing Domain Architecture Evolution of Metazoan Proteins: Major Impact of Errors Caused by...
Modulation of Escherichia coli Cell Membrane by a Monotopic Lipid Glycosyltransferase - an Exploration of Potential Mechanisms
Mechanisms of membrane interaction and dimerization of K-Ras4B | NIH Research Festival
Zn2/Cys6 DNA-binding domain superfamily
ISMB 2006: Fortaleza, Brazil, August 6-10
Herb intracellular immune receptors comprise a large number of multi-domain proteins | immune-source.com
PROSITE
org.Rn.egSF @ dnet 1.1.2
Structures of the Sgt2/SGTA Dimerization Domain with the Get5/UBL4A UBL Domain Reveal an Interaction that Forms a Conserved...
1ira - Proteopedia, life in 3D
ILKBP Definition: Integrin-Linked Kinase-Binding Protein
Avoiding Adverse Effects on SEO through Domain Name Ownership History Checks
SVEP1 Gene - GeneCards | SVEP1 Protein | SVEP1 Antibody
Automated Recommendation of Related Model Elements for Domain Models | SpringerLink
Bacterial Protein Impairs Important Cellular Processes | The BioScientist
Purification and aggregation of the amyloid precursor protein intracellular domain<...
CT domain of CCN2/CTGF directly interacts with fibronectin and enhances cell adhesion of chondrocytes through integrin α5β1<...
How many ways protein protein interactions are regulated? - Biochemistry - BioForum
MAPPING THE TRANSCRIPTIONAL REGULATORY NETWORK OF THE AMYLOID PRECURSOR PROTEIN INTRACELLULAR DOMAIN (AICD) | [email protected]
Three-Dimensional Structure Of The Amyloid Precursor Protein Intracellular Domain (AICD) In Complex With Human FE65-PTB2 -...
BAR domains as sensors of membrane curvature: the amphiphysin BAR structure. - Nuffield Department of Surgical Sciences
Prediction of VH-VL domain orientation for antibody variable domain modeling
Charting the Landscape of Tandem BRCT Domain-Mediated Protein Interactions. - Science Exchange
nanoHUB.org - Resources: [Illinois] Beckman Graduate Seminar: Membrane Sculpting by F-BAR Domains Studied by Molecular Dynamics...
The structure of the Myo4p globular tail and its function in ASH1 mRNA localization | JCB
CATH: Protein Structure Classification Database at UCL
The Regulation of Cellulose Biosynthesis in Plants | Plant Cell
Interdomain association in fibronectin: insight into cryptic sites and fibrillogenesis. - Oxford Neuroscience
Thousands of rare mutations linked with cancer revealed in new analysis
SDSL-EPR Structural Studies of the Cytoplasmic Helix in Novel Full-Length Constructs of the Influenza A M2 Protein
Systematic domain-based aggregation of protein structures highlights DNA-, RNA- and other ligand-binding positions. |...
RNAiDB Tree View
TCDB » SEARCH
TCDB » SEARCH
Cytoplasmic domain requirements for Frazzled-mediated attractive axon turning at the Drosophila midline | Development
Protein
Structure determination. Discovering the tertiary structure of a protein, or the quaternary structure of its complexes, can ... which correlate with typical tertiary structures: globular proteins, fibrous proteins, and membrane proteins. Almost all ... Protein structure prediction. Most proteins fold into unique 3-dimensional structures. The shape into which a protein naturally ... Tertiary structure: the overall shape of a single protein molecule; the spatial relationship of the secondary structures to one ...
Destrin
The secondary and tertiary structures of destrin are similar to the gelsolin family which is another actin-regulating protein ... Structure[edit]. The tertiary structure of destrin was determined by the use of triple-resonance multidimensional nuclear ... "Tertiary structure of destrin and structural similarity between two actin-regulating protein families". Cell. 85 (7): 1047-55. ... Nuclear magnetic resonance determined configuration of the tertiary structure of Destrin.[1] ...
Conformational isomerism
Folding, including the secondary and tertiary structure of biopolymers (nucleic acids and proteins). ... Protein folding also generates stable conformational isomers which can be observed. The Karplus equation relates the dihedral ... The equation aids in the elucidation of protein folding as well as the conformations of other rigid aliphatic molecules.[13] ...
Alfred Goodman Gilman
The structure of the G protein heterotrimer Gi alpha 1 beta 1 gamma 2. Cell. 1995 Dec 15;83(6):1047-58. PMID 8521505. ... Tertiary and quaternary structural changes in Gi alpha 1 induced by GTP hydrolysis. Science. 1995 Nov 10;270(5238):954-60. PMID ... GAIP and RGS4 are GTPase-activating proteins for the Gi subfamily of G protein alpha subunits. Cell. 1996 Aug 9;86(3):445-52. ... Structures of active conformations of Gi alpha 1 and the mechanism of GTP hydrolysis. Science. 1994 Sep 2;265(5177):1405-12. ...
Alfred Gilman - Wikipédia, a enciclopédia livre
The structure of the G protein heterotrimer Gi alpha 1 beta 1 gamma 2. Cell. 1995 Dec 15;83(6):1047-58. PMID 8521505. ... Tertiary and quaternary structural changes in Gi alpha 1 induced by GTP hydrolysis. Science. 1995 Nov 10;270(5238):954-60. PMID ... GAIP and RGS4 are GTPase-activating proteins for the Gi subfamily of G protein alpha subunits. Cell. 1996 Aug 9;86(3):445-52. ... Authors' summary on the structure (Science) (Retrieved on 26 Nov. 2007). Referências. *↑ «Dallas Nobel Laureate Dr. Alfred G. ...
Cysteine
... disulfide bridges between cysteine residues within a polypeptide support the protein's tertiary structure. Insulin is an ... Roles in protein structure[edit]. In the translation of messenger RNA molecules to produce polypeptides, cysteine is coded for ... "The primary structure of proteins is the amino acid sequence". The Microbial World. University of Wisconsin-Madison ... Cysteine residues play a valuable role by crosslinking proteins, which increases the rigidity of proteins and also functions to ...
Cysteine
... disulfide bridges between cysteine residues within a polypeptide support the protein's tertiary structure. Insulin is an ... Roles in protein structure[edit]. In the translation of messenger RNA molecules to produce polypeptides, cysteine is coded for ... "The primary structure of proteins is the amino acid sequence". The Microbial World. University of Wisconsin-Madison ... Disulfide bonds play an important role in the folding and stability of some proteins, usually proteins secreted to the ...
Chance and Necessity
Next Monod reviews the primary and tertiary structure of proteins. In reviewing the tertiary structure, what he calls the ... Allosteric interactions are mediated by discrete shifts in the proteins structure and this allows certain proteins to assume ... In regards to structure, all living beings are made up of proteins and nucleic acids and these are the same residues (twenty ... Finally, it is the primary structure of proteins that we shall consult for the "secret" to those cognitive properties thanks to ...
X-ray crystallography
For example, proteins and larger RNA molecules cannot be crystallized if their tertiary structure has been unfolded; therefore ... When a new protein structure is solved by X-ray crystallography and deposited in the Protein Data Bank, its authors are ... Levy ED (November 2007). "PiQSi: protein quaternary structure investigation". Structure. 15 (11): 1364-7. doi:10.1016/j.str. ... or the Protein Data Bank (for protein and sometimes nucleic acids). Many structures obtained in private commercial ventures to ...
Biochemistry
Tertiary structure is the entire three-dimensional shape of the protein. This shape is determined by the sequence of amino ... The structure of proteins is traditionally described in a hierarchy of four levels. The primary structure of a protein simply ... Finally, quaternary structure is concerned with the structure of a protein with multiple peptide subunits, like hemoglobin with ... Structures of some common lipids. At the top are cholesterol and oleic acid.[37] The middle structure is a triglyceride ...
Endospore
A reduction in these linkages has the potential to change the tertiary structure, causing the protein to unfold. This ... after further studies this group concluded that the structure of the spore coat protein was different from keratin.[10] When ... Small acid-soluble proteins (SASPs) are found in endospores. These proteins tightly bind and condense the DNA, and are in part ... An endospore is a dormant, tough, and non-reproductive structure produced by some bacteria in the phylum Firmicutes.[1][2] The ...
Hydrogen bond
... s also play a part in forming the tertiary structure of protein through interaction of R-groups. (See also protein ... Proteins[edit]. In the secondary structure of proteins, hydrogen bonds form between the backbone oxygens and amide hydrogens. ... Intramolecular hydrogen bonding is partly responsible for the secondary and tertiary structures of proteins and nucleic acids. ... The role of hydrogen bonds in protein folding has also been linked to osmolyte-induced protein stabilization. Protective ...
Michael Levitt Bahasa Melayu, ensiklopedia bebas
Xia, Y.; Huang, E. S.; Levitt, M.; Samudrala, R. (2000). "Ab initio construction of protein tertiary structures using a ... Daggett, V.; Levitt, M. (1993). "Protein Unfolding Pathways Explored Through Molecular Dynamics Simulations". Journal of ... "A refinement of the structure of lysozyme". Biochemical Journal. 125 (4): 92P. doi:10.1042/bj1250092Pa. PMC 1178298 . PMID ... "Evolutionarily consistent families in SCOP: Sequence, structure and function". BMC Structural Biology. 12: 27. doi:10.1186/ ...
Extracellular fluid
The tertiary structure of proteins is also affected by the pH of the bathing solution. In addition, the pH of the ECF affects ... or tertiary) structure of the protein is altered.[21][22] The normal shape, and therefore function of very many of the ... The proteins that are particularly sensitive to changes in the ECF ionized calcium concentration are several of the clotting ... Calcium ions have a great propensity to bind to proteins.[20] This changes the distribution of electrical charges on the ...
Lewis Joel Greene
... amino acid sequence predicted tertiary structure, carbohydrate recognition and analysis of the b-prims fold". Protein Science. ... Protein Expression and Purification. 21 (1): 134-140. doi:10.1006/prep.2000.1353. PMID 11162398.. ... where he is a full professor of cell and molecular biology and head of the Center for Protein Chemistry of Hemocentro de ... "Expression and the purification of a disulphide rich protein in a hydrophobic resin environment, bothropstoxin-I a Lys49- ...
Disulfide
... between thiol groups in two cysteine residues are an important component of the secondary and tertiary structure of proteins. ... Chemical structure. In biochemistry, a disulfide refers to a functional group with the structure R−S−S−R′. The linkage is also ... The in vivo oxidation and reduction of protein disulfide bonds by thiol-disulfide exchange is facilitated by a protein called ... The disulfide bond stabilizes the folded form of a protein in several ways: *It holds two portions of the protein together, ...
Rutgers University
This database is the authoritative research tool for bioinformaticists using protein primary, secondary and tertiary structures ... Rutgers is also home to the RCSB Protein Data bank,[117] 'an information portal to Biological Macromolecular Structures' ... "RCSB Protein Data Bank". Rcsb.org. Archived from the original on April 18, 2015. Retrieved March 11, 2013.. ... H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, P.E. Bourne: The Protein Data Bank. ...
Polyacrylamide gel electrophoresis
... thus overcoming some forms of tertiary protein folding, and breaking up quaternary protein structure (oligomeric subunits). ... By binding to the proteins the detergent destroys their secondary, tertiary and/or quaternary structure denaturing them and ... For proteins, sodium dodecyl sulfate (SDS) is an anionic detergent applied to protein samples to coat proteins in order to ... It is an anionic dye, which non-specifically binds to proteins. The structure of CBB is predominantly non-polar, and it is ...
Endospore
A reduction in these linkages has the potential to change the tertiary structure, causing the protein to unfold. This ... Small acid-soluble proteins (SASPs) are found in endospores. These proteins tightly bind and condense the DNA, and are in part ... StructureEdit. Variations in endospore morphology: (1, 4) central endospore; (2, 3, 5) terminal endospore; (6) lateral ... An endospore is a dormant, tough, and non-reproductive structure produced by some bacteria in the phylum Firmicutes.[1][2] The ...
Active site
... and tertiary structure. To maintain this defined three-dimensional structure, proteins rely on various types of interactions ... Alan Fersht, Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding. W. H. Freeman, 1998. ... "Comparison of protein active site structures for functional annotation of proteins and drug design". Proteins. 65: 124-135. doi ... while other amino acids within the protein are required to maintain the tertiary structure of the enzyme.[2] ...
Disease-modifying antirheumatic drug
... secondary and tertiary structure as an original (boDMARD) and possess similar efficacy and safety as the original protein ... a raised C-reactive protein level.[citation needed] More recently, the term has been used to indicate a drug that reduces the ... tsDMARDs are drugs that were developed to target a particular molecular structure ...
HH-suite
... such as methods to predict the secondary and tertiary structure of proteins, to predict their molecular functions or cellular ... proteins similar to the query protein. If such a template protein is found, the structure of the protein of interest can be ... HMMs for the protein data bank of protein structures, for the Pfam database of protein family alignments, the SCOP database of ... But for a large fraction of the approximately 20 000 human proteins the structures and functions remain unknown. Many proteins ...
Structural biology
... portal Primary structure Secondary structure Tertiary structure Quaternary structure Structural domain Structural motif Protein ... "tertiary structure" of molecules, depends in a complicated way on the molecules' basic composition, or "primary structures." ... 3D encyclopedia of proteins and other molecules. Protein structure prediction Banaszak, Leonard J. (2000). Foundations of ... See protein structure prediction. In the past few years it has become possible for highly accurate physical molecular models to ...
Protein microarray
... finding a surface and a method of attachment that allows the proteins to maintain their secondary or tertiary structure and ... Protein functional analysis is the identification of protein-protein interactions (e.g. identification of members of a protein ... protein-DNA, protein-RNA, protein-phospholipid, and protein-small-molecule interactions, to assay enzymatic activity and to ... A protein microarray (or protein chip) is a high-throughput method used to track the interactions and activities of proteins, ...
LSm
... proteins are characterized by a beta sheet (the secondary structure), folded into the LSm fold (the tertiary structure), ... Other proteins with very similar structures were subsequently discovered and named LSm proteins. New members of the LSm protein ... Proteins with similar structures are grouped into a hierarchy of protein families, superfamilies, and folds. The LSm protein ... Based on structure, the known LSm proteins divide into a group consisting of the bacterial LSm proteins (Hfq, YlxS and MscS) ...
Ribosomal protein
... binding to helical junctions is important for initiating the correct tertiary fold of RNA and to organize the overall structure ... Human protein. Pfam family with Human protein. 2. 40S ribosomal protein S2. RS2_HUMAN. PF03719 Ribosomal protein S5, C-terminal ... A ribosomal protein (r-protein or rProtein[1][2][3]) is any of the proteins that, in conjunction with rRNA, make up the ... 40S ribosomal protein S9. RS9_HUMAN. PF01479 S4 domain. 9. 40S ribosomal protein S9. RS9_HUMAN. PF00163 Ribosomal protein S4/S9 ...
List of protein structure prediction software
Protein tertiary structure predictions. server Selvita Protein Modeling Platform Package of tools for protein modeling. Free ... On-line server for peptide structure prediction. Server Secondary structure prediction[edit]. Main article: Protein structure ... This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction, ... Commercial protein structure prediction application. Home page I-TASSER Threading fragment structure reassembly. On-line server ...
Lactoferrin
Their tertiary structures are different; apolactoferrin is characterized by "open" conformation of the N-lobe and the "closed" ... The fraction of protein extracted from milk, contains 3.3% RNA, but, the protein preferably binds to double-stranded DNA rather ... Occurrence of iron-containing red protein in bovine milk was reported as early as in 1939; however, the protein could not be ... Lactoferrin: structure, function, and applications: proceedings of the 4th International Conference on Lactoferrin: Structure, ...
Denaturation (biochemistry)
When a protein is denatured, secondary and tertiary structures are altered but the peptide bonds of the primary structure ... Denaturation is a process in which proteins or nucleic acids lose the quaternary structure, tertiary structure, and secondary ... See also: Protein structure. *In quaternary structure denaturation, protein sub-units are dissociated and/or the spatial ... 3) Tertiary Structure : three-dimensional structure of alpha helixes and beta helixes folded 4) Quaternary Structure : three- ...
Structural Classification of Proteins database
These classes group structures with similar secondary structure composition, but different overall tertiary structures and ... The source of protein structures is the Protein Data Bank. The unit of classification of structure in SCOP is the protein ... Designed proteins [58788] (44): Experimental structures of proteins with essentially non-natural sequences. Not a true class ... coiled-coil proteins [57942] (7): Not a true class. *Low resolution protein structures [58117] (26): Peptides and fragments. ...
Food web
how community structure, function and stability is determined.[36][37]. Ecological pyramids[edit]. See also: Ecological pyramid ... Abbreviations: P=Producers, C1=Primary consumers, C2=Secondary consumers, C3=Tertiary consumers, S=Saprotrophs.[4] ... and proteins. These polymers have a dual role as supplies of energy as well as building blocks; the part that functions as ... Pyramid structure can vary across ecosystems and across time. In some instances biomass pyramids can be inverted. This pattern ...
Leaf
The concentration of photosynthetic structures in leaves requires that they be richer in protein, minerals, and sugars than, ... In turn, smaller veins branch from the secondary veins, known as tertiary or third order (or higher order) veins, forming a ... and flattened leaf stems called phyllodes which differ from leaves both in their structure and origin.[4][7] Some structures of ... Rudall, Paula J. (2007). Anatomy of flowering plants: an introduction to structure and development (3rd ed.). Cambridge: ...
Lentil
... protein itself is not lost).[16] Lentils have the second-highest ratio of protein per calorie of any legume, after soybeans. ... "Food Structure. 5: 241-246 - via digitalcommons.usu.edu.. *^ Bora, Pushkar Singh (2002). "Functional properties of native and ... Tertiary gene pool: L. lamottei and L. tomentosus. Crosses generally fail between members of different gene pools. However, ... Raw lentils are 8% water, 63% carbohydrates including 11% dietary fiber, 25% protein, and 1% fat (table). Lentils are a rich ...
Alkali metal
Structure of the octahedral n-butyllithium hexamer, (C4H9Li)6.[138] The aggregates are held together by delocalised covalent ... The balance between potassium and sodium is maintained by ion transporter proteins in the cell membrane.[231] The cell membrane ... and aryl ketones to tertiary carbinols (Ar'2C(Ar)OH). Finally, they may be used to synthesise other organometallic compounds ... Structure and Bonding. 21: 89-144. doi:10.1007/BFb0116498. ISBN 978-3-540-07109-9. . Retrieved 4 October 2013.. ...
Progesterone receptor
Available protein structures:. Pfam structures / ECOD PDB. RCSB PDB; PDBe; PDBj. PDBsum. structure summary. ... tertiary branching involved in mammary gland duct morphogenesis. Sources:Amigo / QuickGO. Orthologs. ... protein binding. • enzyme binding. • receptor binding. • lipid binding. • RNA polymerase II transcription factor activity, ... The progesterone receptor (PR), also known as NR3C3 or nuclear receptor subfamily 3, group C, member 3, is a protein found ...
Reptile
This is because they lack a specialized structure called a loop of Henle, which is present in the nephrons of birds and mammals ... The albumin (9) further protects the embryo and serves as a reservoir for water and protein. The allantois (8) is a sac that ... mitogenomic phylogenetic analyses yield new insight into crocodylian evolution and their survival of the Cretaceous-Tertiary ... Geckos, skinks, and other lizards that are captured by the tail will shed part of the tail structure through a process called ...
Histone
Archaeal histone only contains a H3-H4 like dimeric structure made out of the same protein. Such dimeric structures can stack ... forming two nearly symmetrical halves by tertiary structure (C2 symmetry; one macromolecule is the mirror image of the other).[ ... The first step of chromatin structure duplication is the synthesis of histone proteins: H1, H2A, H2B, H3, H4. These proteins ... who believed that transcription was activated by protein-DNA and protein-protein interactions on largely naked DNA templates, ...
Nuclear magnetic resonance spectroscopy of nucleic acids
It was quickly realized that spectra of the low-field imino protons were providing clues to the tertiary structure of tRNA in ... NMR is also useful for probing the binding of nucleic acid molecules to other molecules, such as proteins or drugs. This can be ... Structure determinationEdit. The exchangeable and non-exchangeable protons are usually assigned to their specific peaks as two ... Nucleic acid NMR is the use of nuclear magnetic resonance spectroscopy to obtain information about the structure and dynamics ...
Cold Spring Harbor Laboratory
This section relies too much on references to primary sources. Please improve this section by adding secondary or tertiary ... James Watson, co-discoverer of structure of DNA, Nobel Laureate.. *Scott Lowe (currently at MSKCC), research on p53, Member of ... A.D. Hershey and Martha Chase, "Independent Functions of Viral Protein and Nucleic Acid in Growth of Bacteriophage," J. General ... RNA interference (RNAi) and small-RNA biology; DNA replication; RNA splicing; signal transduction; genome structure; non-coding ...
Glycogen phosphorylase
... results in small changes in tertiary structure at the subunit interface leading to large changes in quaternary structure.[8] ... Structure[edit]. The glycogen phosphorylase monomer is a large protein, composed of 842 amino acids with a mass of 97.434 kDa ... Residues 397-437 form this structure, which allows the protein to covalently bind to the glycogen chain a full 30 Å from the ... I. Isolation and characterization of the protein-glycogen complex". Journal of Biological Chemistry. 245 (24): 6642-6648. PMID ...
Amine
For chiral tertiary amines, NRR′R″ can only be resolved when the R, R′, and R″ groups are constrained in cyclic structures such ... which is one of the primary influences on the three-dimensional structures of proteins.[18] ... Tertiary (3°) amines-In tertiary amines, nitrogen has three organic substituents. Examples include trimethylamine, which has a ... StructureEdit. Alkyl aminesEdit. Alkyl amines characteristically feature tetrahedral nitrogen centers. C-N-C and C-N-H angles ...
Dentin
Tertiary dentin is only formed by an odontoblast directly affected by a stimulus; therefore, the architecture and structure ... which includes dentine-specific proteins), and 10% water (which is adsorbed on the surface of the minerals or between the ... Tertiary dentin (including reparative dentin or sclerotic dentin) - pathologicEdit. Tertiary dentin is dentin formed as a ... The structure of the dentinal tubules contributes to both its porosity and its elasticity. Elephant tusks are formed with a ...
Health in India
Protein-energy malnutrition (PEM), also known as protein-calorie malnutrition Iron deficiency: nutritional anaemia which can ... In planning health care structure for the future, it is desirable to move from a 'fee-for-service' mechanism, to address the ... secondary and tertiary care. In twelfth plan period entire Below Poverty Line(BPL) population will be covered through RSBY ... while also ensuring that there is no compromise in terms of standards of delivery and that the incentive structure does not ...
CLEC5A
tertiary granule membrane. • cytosol. • plasma membrane. Biological process. • cellular defense response. • myeloid cell ... GO:0001948 protein binding. Cellular component. • integral component of membrane. • integral component of plasma membrane. • ... Available structures. PDB. Ortholog search: PDBe RCSB List of PDB id codes. ... Structurally MDL-1 is a type II transmembrane protein with a short cytoplasmic tail and without signaling motifs, therefore it ...
Kallmann syndrome
Kisspeptin is a protein that regulates the release of GnRH from the hypothalamus, which in turn regulates the release of LH and ... The structure of GNRH1. (from PDB: 1YY1). The underlying cause of Kallmann syndrome or other forms of hypogonadotropic ...
Proteasome
... it is this structure that recognizes polyubiquitinated proteins and transfers them to the catalytic core.[15] An alternative ... but substantial tertiary structure, and in particular nonlocal interactions such as disulfide bonds, are sufficient to inhibit ... The protein degradation processEdit. Ribbon diagram of ubiquitin, the highly conserved protein that serves as a molecular tag ... Proteasomes are protein complexes which degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks ...
Epistasis
Proteins are held in their tertiary structure by a distributed, internal network of cooperative interactions (hydrophobic, ... Similarly, at the protein level, proteins that function as dimers may form a heterodimer composed of one protein from each ... In enzymes, the protein structure orients a few, key amino acids into precise geometries to form an active site to perform ... Horovitz A (1996). "Double-mutant cycles: a powerful tool for analyzing protein structure and function". Folding & Design. 1 (6 ...
Glossary of biology
A process in which proteins or nucleic acids lose the quaternary, tertiary, and secondary structure which is present in their ... especially proteins and nucleic acids, how they acquire the structures they have, and how alterations in their structures ... A cylindrical cell structure found in most eukaryotic cells, composed mainly of a protein called tubulin.. centrosome. An ... G protein. A family of proteins that act as molecular switches inside cells, and are implicated in transmitting signals from a ...
Paleontology
For example, the discovery by Luis Alvarez and Walter Alvarez of an iridium-rich layer at the Cretaceous-Tertiary boundary made ... by comparing sequences of DNA or proteins. The result of a successful analysis is a hierarchy of clades - groups that share a ... cells with complex internal structures, may have been present earlier, their evolution speeded up when they acquired the ... Although this early study compared proteins from apes and humans, most molecular phylogenetics research is now based on ...
David Eisenberg
Chapman, M. S.; Suh, S. W.; Curmi, P. M.; Cascio, D.; Smith, W. W.; Eisenberg, D. S. (1988). "Tertiary structure of plant ... Proteins[2]. Amyloid[3]. Structural biology[4][5][6]. Institutions. Howard Hughes Medical Institute. University of Oxford. ... His research group hosts the Database of Interacting Proteins.[16] Career[edit]. *Postdoctoral research, Princeton University ( ... Eisenberg, David J. (1965). Some problems in the electronic structure of molecules (PhD thesis). University of Oxford.. ...
Cathelicidin
OPM protein. 2k6o. Available protein structures:. Pfam. structures. PDB. RCSB PDB; PDBe; PDBj. ... tertiary granule lumen. Biological process. • positive regulation of interleukin-8 secretion. • defense response. • negative ... protein binding. Cellular component. • extracellular region. • specific granule. • intracellular. • extracellular exosome. • ... Cathelicidins range in size from 12 to 80 amino acid residues and have a wide range of structures.[8] Most cathelicidins are ...
PRNP
These mutations cause the cell to make prion proteins with an abnormal structure. The abnormal protein PrPSc accumulates in the ... The abnormal PrPSc isoform has a different secondary and tertiary structure from PrPC, but identical primary sequence. Circular ... ATP-dependent protein binding. • metal ion binding. • tubulin binding. • protein binding. • identical protein binding. • copper ... PRNP (prion protein) is the human gene encoding for the major prion protein PrP (proetase-resistant-protein, Pr for prion, and ...
CASS4
... within 432-591 residues of CASS4 and 449-610 residues of p130Cas/BCAR1 at the level of secondary and tertiary structures. Also ... "Entrez Gene: Cas scaffolding protein family member 4".. *^ a b Tikhmyanova N, Little JL, Golemis EA (April 2010). "CAS proteins ... Structure[edit]. Figure 1. Interaction network and domain structure scheme of Cass4. SH3 domain (SH3) preceded by a short ... Cas scaffolding protein family member 4 is a protein that in humans is encoded by the CASS4 gene.[5] ...
Food allergy
Proteins have unique properties that allow them to become allergens, such as stabilizing forces in their tertiary and ... A histamine, the structure shown, causes a person to feel itchy during an allergic reaction. A common medication to stop this ... The harmful proteins are those that do not break down due to the strong bonds of the protein. IgE antibodies bind to a receptor ... Are the transferred proteins resistant to digestion - a trait shared by many allergenic proteins?[115] Genes approved for ...
AKR1B1
Structure[edit]. Gene[edit]. The AKR1B1 gene lies on the chromosome location of 7q33 and consists of 10 exons. There are a few ... "Tonicity-responsive enhancer binding protein regulates the expression of aldose reductase and protein kinase C δ in a mouse ... Protein[edit]. AKR1B1 consists of 316 amino acid residues and weighs 35853Da. It does not possess the traditional dinucleotide ... stress-activated protein kinase signaling cascade. • cellular response to peptide. • daunorubicin metabolic process. • ...
Domperidone
J. Elks (14 November 2014). The Dictionary of Drugs: Chemical Data: Chemical Data, Structures and Bibliographies. Springer. pp ... "Audit of domperidone use as a galactogogue at an Australian tertiary teaching hospital". Journal of Human Lactation. 29 (1): 32 ... Protein binding. ~92%[1]. Metabolism. Hepatic (CYP3A4/5) and intestinal (first-pass)[1][4]. ...
Riboflavin
In whole milk, 14% of the flavins are bound noncovalently to specific proteins.[15] Egg white and egg yolk contain specialized ... July 2004). "High-dose riboflavin treatment is efficacious in migraine prophylaxis: an open study in a tertiary care centre". ... forms part of its structure) and "flavin", the ring-moiety which imparts the yellow color to the oxidized molecule (from Latin ... Free riboflavin is naturally present in foods along with protein-bound FMN and FAD. Bovine milk contains mainly free riboflavin ...
Cystine
Protein tertiary structure. *Sullivan reaction. *Cystinosis. ReferencesEdit. *^ Nelson, D. L.; Cox, M. M. (2000) Lehninger, ... a site of redox reactions and a mechanical linkage that allows proteins to retain their three-dimensional structure.[1] ... It was not recognized as being derived of proteins until it was isolated from the horn of a cow in 1899.[2] Human hair and skin ... In cell biology, cystine residues (found in proteins) only exist in non-reductive (oxidative) organelles, such as the secretory ...
Protein tertiary structure - Wikipedia
A number of tertiary structures may fold into a quaternary structure. The science of the tertiary structure of proteins has ... Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide ... The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary ... Contemporary methods are able to determine, without prediction, tertiary structures to within 5 Å (0.5 nm) for small proteins ( ...
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. - PubMed - NCBI
SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information.. Biasini M1, Bienert S1, ... SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014 Jul 1; ... SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Res. 2014 Jul 1; ... Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental ...
Prediction and Analysis of Surface Hydrophobic Residues in Tertiary Structure of Proteins
... Shambhu Malleshappa Gowder,1 Jhinuk ... The analysis of protein structures provides plenty of information about the factors governing the folding and stability of ... It is based on the nonredundant data set of 218 monomeric proteins. Solvent accessibility of each protein was determined using ... the preferred amino acids in the protein environment, the location of the residues in the interior/surface of a protein and so ...
Modelling Protein Structure from Remote Sequence Similarity: An Approach to Tertiary Structure Prediction | SpringerLink
... a molecular model can be constructed for one sequence provided that the tertiary structure of the other is known. This approach ... Given some similarity in sequence between two proteins, ... Modelling Protein Structure from Remote Sequence Similarity: An ... Taylor W.R. (1994) Modelling Protein Structure from Remote Sequence Similarity: An Approach to Tertiary Structure Prediction. ... Taylor, W. R. and Orengo, C. A. (1989b). Protein structure alignment. J. Molec. Biol., 208:1-22.CrossRefGoogle Scholar ...
Protein Structure, Tertiary | Eukaryotic Cell
Gene triplication deduced from the tertiary structure of a muscle calcium binding protein. - PubMed - NCBI
FORCASP • View topic - Please Help: Tertiary Protein Structure Prediction
structure of a fluorescent protein with a sequence homology to know. fluorescent proteins, such as GFP and DsRed. The protein ... Re: Please Help: Tertiary Protein Structure Prediction. Posted: Thu Sep 16, 2010 12:12 am ... Please Help: Tertiary Protein Structure Prediction. Posted: Wed Oct 14, 2009 12:43 pm ... In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The ...
FORCASP • View topic - Please Help: Tertiary Protein Structure Prediction
structure of a fluorescent protein with a sequence homology to know. fluorescent proteins, such as GFP and DsRed. The protein ... Re: Please Help: Tertiary Protein Structure Prediction. by AlexanderSimmons on Thu Sep 16, 2010 12:12 am ... Please Help: Tertiary Protein Structure Prediction. by Proteinglow on Wed Oct 14, 2009 12:43 pm ... In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. But in nowadays The ...
Quantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments | SpringerLink
The publication of the crystallographic structure of calmodulin protein has offered an example leading us to believe that it is ... possible for many protein sequence segments to exhibit multiple 3D... ... Multi-structural segments protein structure protein structure comparison protein structure conservation URMSD ... Quantitative Analysis of the Conservation of the Tertiary Structure of Protein Segments. ...
Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method - McGuffin -...
Assessment of template based protein structure predictions in CASP9, Proteins: Structure, Function, and Bioinformatics, 2011, ... Automated tertiary structure prediction with accurate local model quality assessment using the intfold-ts method†. Authors. *. ... Next article in issue: Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio ... Next article in issue: Automated protein structure modeling in CASP9 by I-TASSER pipeline combined with QUARK-based ab initio ...
Going Beyond 'Lamarckism' in Protein Tertiary Structure Prediction
... more successful ones are those that rely either solely or partly on template/homology based modeling of full or sub-structures ... Several novel techniques are employed for protein tertiary structure prediction, but the ... in Protein Tertiary Structure Prediction Several novel techniques are employed for protein tertiary structure prediction, but ... Critical assessment of methods of protein structure prediction (CASP) - round IX. Proteins, Structure, Function & ...
De novo backbone and sequence design of an idealized α/β-barrel protein: evidence of stable tertiary structure - CaltechAUTHORS
Protein Structure: Tertiary; Scattering: Radiation; Molecular Sequence Data; Spectrophotometry: Ultraviolet; Structure-Activity ... De novo backbone and sequence design of an idealized α/β-barrel protein: evidence of stable tertiary structure ... De novo backbone and sequence design of an idealized α/β-barrel protein: evidence of stable tertiary structure. Journal of ... De novo Backbone and Sequence Design of an Idealized α/β-barrel Protein: Evidence of Stable Tertiary Structure, Journal of ...
Probing Secondary, Tertiary, and Quaternary Structure along with
Protein−Cofactor Interactions for a Helical Transmembrane...
... and Quaternary Structure along with Protein−Cofactor Interactions for a Helical Transmembrane Protein Complex through 1H Spin ... Helical Transmembrane Protein Complex 1 H Spin Diffusion magic angle Quaternary Structure helical transmembrane model protein ... Probing secondary, tertiary, and quaternary structure along with protein−cofactor interactions through ,sup,1,/sup,H spin ... Probing Secondary, Tertiary, and Quaternary Structure along with Protein−Cofactor Interactions for a Helical Transmembrane ...
ROSALIND | Glossary | Protein tertiary structure
Protein tertiary structure. The tertiary structure of a polypeptide (or protein containing only one polypeptide) refers to its ... inferring the tertiary structure of a protein from its primary structure poses a research problem of the first order for a wide ... the polypeptides tertiary structure follows uniquely from its primary structure (i.e., the order of amino acids). As a result ... The tertiary structure of a polypeptide will determine its chemical properties on a larger scale; however, ...
Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins | BMC...
Here we describe Bhageerath-H, a homology/ ab initio hybrid software/server for predicting protein tertiary structures with ... Despite significant progresses in the area of experimental protein structure determination, the sequence-structure gap is ... Data driven homology based computational methods have proved successful in predicting tertiary structures for sequences sharing ... Success of structure based drug discovery severely hinges on the availability of structures. ...
TCP: a tool for designing chimera proteins based on the tertiary structure information | BMC Bioinformatics | Full Text
We developed TCP, a tool for designing chimera proteins based on the tertiary structure information. TCP is robust and ... Although the designing the chimera proteins based on the tertiary structure information is required in such situations, there ... In light of the problem, we developed a tool named TCP (standing for a Tool for designing Chimera Proteins), which extracts ... The test results of our method indicate that the TCP is robust and applicable to various shapes of proteins. ...
Does secondary structure determine tertiary structure in proteins?<...
Does secondary structure determine tertiary structure in proteins? Proteins: Structure, Function and Genetics. 2005 Nov 1;61(2 ... Gong, Haipeng ; Rose, George D. / Does secondary structure determine tertiary structure in proteins?. In: Proteins: Structure, ... Gong, H., & Rose, G. D. (2005). Does secondary structure determine tertiary structure in proteins? Proteins: Structure, ... Gong, H & Rose, GD 2005, Does secondary structure determine tertiary structure in proteins?, Proteins: Structure, Function ...
Protein Structure, Tertiary
Crystal structure of theLeishmania majorMIX protein: A scaffold protein that mediates protein-protein interactions Academic ... BH3-only proteins: a 20-year stock-take Academic Article * Bax Crystal Structures Reveal How BH3 Domains Activate Bax and ... Structure of the BH3 Domains from the p53-Inducible BH3-Only Proteins Noxa and Puma in Complex with Mcl-1 Academic Article ... Structure of the heterodimer of human NONO and paraspeckle protein component 1 and analysis of its role in subnuclear body ...
GP4Rate 1.0.0 - Inference of Functionally Important Regions in Protein Tertiary Structures
GP4Rate is a C++ program which combines Gaussian processes and phylogenetics to infer conserved sites in protein tertiary ... Protein Protein Sequence Protein Structure RNA RNA-Seq Secondary Structure Sequence Sequencing Simulation SNP Structure Tool ... Posted by admin at 4:30 pm Tagged with: GP4Rate, Important Region, Protein Tertiary Structures 71 views. Sorry, the comment ... GP4Rate 1.0.0 - Inference of Functionally Important Regions in Protein Tertiary Structures. 3D molecular model ...
Specific recognition in the tertiary structure of beta-sheets of proteins. - Semantic Scholar
Specific recognition in the tertiary structure of beta-sheets of proteins. by Shneior Lifson et al. ... Specific recognition in the tertiary structure of beta-sheets of proteins.. @article{Lifson1980SpecificRI, title={Specific ... StrandPairsViewer: A Toolkit for Visualization and Analysis of Amino Acids Pairs in Protein Sheet Structures. Ning Zhang, Shan ... recognition in the tertiary structure of beta-sheets of proteins.}, author={Shneior Lifson and Christian Sander}, journal={ ...
What is protein tertiary structure?
The tertiary structure is determined by four interactions: hydrogen bonding,... ... The three-dimensional conformation of a polypeptide chain of a globular protein in its native folded state. ... What is protein tertiary structure?. 4 years ago by Pozzter Q&A 0 replies, read ~321197 times ... polypeptide chain of a globular protein in its. native folded state. The tertiary structure is. determined by four interactions ...
Protein Structure, Tertiary | Profiles RNS
"Protein Structure, Tertiary" by people in this website by year, and whether "Protein Structure, Tertiary" was a major or minor ... The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions ... "Protein Structure, Tertiary" is a descriptor in the National Library of Medicines controlled vocabulary thesaurus, MeSH ( ... Protein Structure, Tertiary*Protein Structure, Tertiary. *Tertiary Protein Structure. *Protein Structures, Tertiary ...
Browsing by Subject "Protein Structure, Tertiary"
Computational Protein Design (CPD) is a promising method for high throughput protein and ligand mutagenesis. Recently, we ... Computational protein design with a generalized born solvent model: Application to asparaginyl-tRNA synthetase Polydorides, ... Neuralized Encodes a Peripheral Membrane Protein Involved in Delta Signaling and Endocytosis Pavlopoulos, Elias; Pitsouli, ... Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular ...
Online Analysis Tools - Protein Tertiary Structure
PROTEIN TERTIARY STRUCTURE Sites are offered for calculating and displaying the 3-D structure of oligosaccharides and proteins ... Structures derived from NMR coordinates:. GeNMR (GEnerate NMR structure) - generates 3D protein structures using NOE-derived ... 3D-Match - Comparing 3D structures of two proteins (Softberry). iPBA - is a tool for comparison of protein structures based on ... With the two protein analysis sites the query protein is compared with existing protein structures as revealed through homology ...
Protein Structure, Tertiary | The Chopra Library
Newly described small molecules that inhibit BET proteins BRD2, BRD3, and BRD4 reduce proliferation of NUT (nuclear protein in ... Structures of KIX domain of CBP in complex with two FOXO3a transactivation domains reveal promiscuity and plasticity in ... Epigenetic proteins have recently emerged as novel anticancer targets. Among these, bromodomain and extra terminal domain (BET ... Hsp70, best known as a protein chaperone with well-defined peptide-refolding properties, is known to interact with ARE-like RNA ...
Structural Biochemistry/Proteins/Structures - Wikibooks, open books for an open world
Tertiary Structure[edit]. The tertiary structure of a protein is the three-dimensional structure of the protein. This three- ... Determination of Tertiary Structure[edit]. The tertiary structure of a protein is determined through X-Ray Crystallography and ... Tertiary structure is also the most important protein structure that is used in determining the enzymatic activity of proteins ... In order for a protein to be functional (except in food), it must have an intact tertiary structure. If a tertiary structure of ...
Protein Structures: Primary, Secondary, Tertiary, Quaternary | SchoolWorkHelper
... natively unstructured proteins) and exist in random conformations. The function of proteins depends on their structure,… ... and they show the greatest variety of structures. Many have intricate three-dimensional folding patterns that result in a ... Proteins are the largest and most varied class of biological molecules, ... Protein Folding. How and why do proteins naturally form secondary, tertiary, and quaternary structures? This question is a very ...
Secondary and Tertiary Protein Structure | SGS India
Gain a comprehensive view of secondary and tertiary protein structures in a biopharmaceutical formulation with SGS. Find out ... tertiary or 3D structure), folding (secondary structure) and proper subunit association (quaternary structure). Collectively, ... Life Sciences Secondary and Tertiary Protein Structure. SGS combines biophysical techniques with more sensitive orthogonal ... To gain accurate analysis of your secondary and tertiary protein structure, contact us today. ...
Protein Structure: Proteins are organized in tertiary Structure
This chapter explains the basics of tertiary organization of Proteins, It includes myoglobin ... Protein Structure-Proteins are organized in tertiary Structure- ... Protein Structure: How the Proteins are organized in tertiary ... Basic points on Tertiary Structure of Proteins:. The folding of a protein is connects to the Genomic function ... The best example of Tertiary Structure of Proteins are Myoglobin (Muscle Respiratory Pigment) and Ribunuclease. (RNA digestive ...
Rapid Detection of Positive Selection in Genes and Genomes Through Variation Clusters | Genetics
Clustering in the protein tertiary structure:. To determine whether a group of k amino acid replacements in a protein with ... To analyze protein tertiary structures, I first obtained a list of all human genes associated with a PDB structure file from ... Clustering of amino acid changes in protein tertiary structure. (a) The horizontal axis shows -log10(P3D), calculated only for ... They occur in well-defined domains of a proteins tertiary structure and show a large excess of amino acid replacement over ...
PredictionNucleic AcidsInteractionsMolecularBiochemistryQuaternary structuresFoldResiduesChemistryBioinformaticsMoleculesSequencesPolypeptide chainsLipidsConformationMembrane proteinsGeneDisulfideStabilized conformationsHydrophobicPolypeptidesMetabolismMonomericConsistSecondary structuresGlobular proteinMoleculeCovalentDenaturationRecombinant proteinsPeptide bondsSolubleStructural ClassifiFingerprintSingle polypeptideInitioHelicalAmino acids and proteinsSolventSide chainsPeptidesRegionsMethodsBindingBiosynthesisBiologicalPatternsSubunitsHydrogen bondsMyoglobinProtein'sStableFunction of proteinsCellularFunctional proteinsBackboneSequence homologySynthesis
Prediction36
- Although Emil Fischer had suggested proteins were made of polypeptide chains and amino acid side chains, it was Dorothy Maud Wrinch who incorporated geometry into the prediction of protein structures. (wikipedia.org)
- Wrinch demonstrated this with the Cyclol model, the first prediction of the structure of a globular protein. (wikipedia.org)
- Taylor, W.R. (1991) Towards protein tertiary fold prediction using distance and motif constraints. (springer.com)
- In earlier stage the Tertiary Protein Structure Prediction is unsolved problem in molecular biology. (predictioncenter.org)
- At the same time, the remaining 2% of the sequences may pose problems for the sequence alignment based structure prediction methods. (springer.com)
- Several novel techniques are employed for protein tertiary structure prediction, but the more successful ones are those that rely either solely or partly on template/homology based modeling of full or sub-structures. (jbsdonline.com)
- It is quite apparent that efforts in tertiary structure prediction have saturated to a level where there is an immediate need for methodological innovations - beyond templates of folds to avoid falling into a trap of Lamarckism in protein folding. (jbsdonline.com)
- 2013) as incoporated in the continually evolving freely accessible Bhageerath-H webserver for protein tertiary structure prediction (http://www.scfbio-iitd.res.in/bhageerath/bhageerath_h.jsp) (Jayaram et al. (jbsdonline.com)
- 2012). We show that it is possible to push the accuracies in protein structure prediction beyond 60% even for tough targets. (jbsdonline.com)
- Bhageerath - Targeting the Near Impossible: Pushing the Frontiers of Atomic Models for Protein Tertiary Structure Prediction. (jbsdonline.com)
- Critical assessment of methods of protein structure prediction (CASP) - round IX. (jbsdonline.com)
- PHYRE 2 - P rotein H omology/analog Y R ecognition E ngine - this is my favourite site for the prediction of the 3D structure of proteins. (molbiol-tools.ca)
- ORION - is a web server for protein fold recognition and structure prediction using evolutionary hybrid profiles. (molbiol-tools.ca)
- I-TASSER was ranked as the No 1 server for protein structure prediction in recent CASP7 and CASP8 experiments. (molbiol-tools.ca)
- Robetta - is a protein structure prediction service that is continually evaluated through CAMEO. (molbiol-tools.ca)
- Motivation: Consensus structure prediction methods (meta-predictors) have higher accuracy than individual structure prediction algorithms (their components). (psu.edu)
- It is simple and offers a portable solution to improve the accuracy of other protein structure prediction protocols. (psu.edu)
- An alternative method is protein structure prediction, where structure is computationally predicted from amino acid sequence. (sjsu.edu)
- As opposed to x-ray crystallography and NMR spectroscopy, protein structure prediction is not encumbered by potential experimental problems. (sjsu.edu)
- In this research, we attempted to determine if certain protein structure features, known as tertiary contacts, can improve the prediction of protein three-dimensional structure. (sjsu.edu)
- From our calculations we were able to create a prediction filter based on our known literature-derived tertiary contacts of whether amino acid residues are buried or on the surface of a protein. (sjsu.edu)
- From our tertiary contact prediction filter, it was shown that approximately 80% of the amino acid residues in our protein learning set were correctly filtered to be on the surface of a protein. (sjsu.edu)
- From the tertiary contact prediction filter, we hope that tertiary contacts can be utilized in conjunction with other prediction approaches to more accurately predict where amino acids may be located in a protein. (sjsu.edu)
- This list of protein structure prediction software summarizes commonly used software tools in protein structure prediction , including homology modeling , protein threading , ab initio methods, secondary structure prediction , and transmembrane helix and signal peptide prediction. (wikipedia.org)
- Below is a list which separates programs according to the method used for structure prediction. (wikipedia.org)
- The present invention relates to drug design, and more particularly to drug design achieved rationally through the simulation and prediction of conformational features of selected oligopeptides or polypeptides for the purpose of predicting and making bioactive peptidomimetic compound structures. (google.com)
- Antigenicity of the protein was also evaluated by Chou & Fasman beta-turn prediction method. (ibbj.org)
- Explain why ab initio protein folding, or the prediction of tertiary structure from a sequence, is considered one of the most challenging problems in computational biology. (dal.ca)
- Efforts to predict tertiary structure from the primary structure are known generally as protein structure prediction. (bookin.org.ru)
- However, the environment in which a protein is synthesized and allowed to fold are significant determinants of its final shape and are usually not directly taken into account by current prediction methods. (bookin.org.ru)
- Automated protein tertiary structure prediction from sequence information alone remains an elusive goal to computational prescriptions. (ias.ac.in)
- secondary structure prediction, generation of plausible main chain loop dihedrals and side chain dihedral optimization, considerable progress has been achieved in our laboratory ( http://www.scfbio-iitd.res.in/bhageerath/index.jsp ) and elsewhere for proteins with less than 100 amino acids. (ias.ac.in)
- Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence-that is, the prediction of its secondary and tertiary structure from primary structure. (wikipedia.org)
- Structure prediction is different from the inverse problem of protein design. (wikipedia.org)
- the performance of current methods is assessed in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). (wikipedia.org)
- A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. (wikipedia.org)
Nucleic Acids3
- The key biological molecules are carbohydrates, lipids, proteins and nucleic acids. (hubpages.com)
- Like other biological macromolecules such as polysaccharides and nucleic acids , proteins are essential parts of organisms and participate in virtually every process within cells . (wikipedia.org)
- DNA sequences comprising nucleic acids encoding fusion proteins comprising an Fc portion of an antibody attached at the N-terminus of an OB protein moiety, vectors comprising such DNA sequences, host cells comprising such vectors or DNA sequences, and processes for preparing such fusion proteins, and. (google.com)
Interactions22
- The interactions and bonds of side chains within a particular protein determine its tertiary structure. (wikipedia.org)
- In the absence of a three-dimensional structure, the ability to predict surface accessibility of hydrophobic residues directly from the sequence is of great help in choosing the sites of chemical modification or specific mutations and in the studies of protein stability and molecular interactions. (hindawi.com)
- Finally, ^1H NMR spectra of the folded and unfolded proteins provided evidence for specific interactions in the folded protein. (caltech.edu)
- Exploring beta-sheet structure and interactions with chemical model systems. (semanticscholar.org)
- The tertiary structure is determined by four interactions: hydrogen bonding, electrostatic interactions (ionic), hydrophobic interactions and covalent cross-linkages. (pozzter.com)
- Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. (uchicago.edu)
- Protein structures are governed primarily by hydrophobic effects and by interactions between polar residues and other types of bonds. (wikibooks.org)
- This will eliminate many of the ionic interactions that were necessary for maintenance of the folded shape of the protein. (wikibooks.org)
- There is also the ionic interactions , the hydrophobic interaction (stronger in the center of the protein), the hydrogen bonds stabilizing folding, the forces Van der Waals , the disulfide bridges . (biochemden.com)
- The interactions between the side-chains of amino acids are responsible for the formation of the tertiary structure. (pediaa.com)
- The modulation of protein-protein interactions (PPIs) by means of creating or stabilizing secondary structure conformations is a rapidly growing area of research. (elsevier.com)
- Though there has been extensive analysis of coiled coil motifs, the interactions between pre-formed coiled coils and globular proteins have not been systematically analyzed. (elsevier.com)
- By calculating and analyzing sequence homology and related values, it was shown that tertiary contacts, which typically are long-range amino acid interactions separated by at least 10 amino acids in sequence length, generally have lower pair averaged sequence homology-based values. (sjsu.edu)
- It is the different interactions between the side chains of the amino acids that stabilize the tertiary structure. (encyclopedia.com)
- The third level of protein structure where side chain interactions dictate the direction of the folding. (sparknotes.com)
- In protein science , Protein Interaction Domains (Protein-Protein Interaction Domains) are recognition modules in proteins that mediate interactions between specific proteins involved in signal transduction pathways, which fold to form recognition pockets complementary to the short interaction sequence motifs on their ligands. (wellnessadvantage.com)
- Participants will be enabled to incorporate computer visualization and qualitative analysis of 3D structure of protein, DNA, RNA, and protein-ligand interactions into their teaching and research. (umass.edu)
- its structure resulting from interactions between amino acid side chains. (syvum.com)
- How side chain interactions can impact the tertiary structure of proteins. (wn.com)
- The completion of the human genome project has opened a new area for studying nucleic acid and protein interactions using nucleic acid cross-linking reagents, and advances have also been made in the area of biosensors and microarray biochips for the detection and analysis of genes, proteins, and carbohydrates. (routledge.com)
- Most isoforms share a common C-terminal domain, which contains two zinc finger motifs that are required for hetero- or homo-dimerization, and for interactions with other proteins. (cancerindex.org)
- Making the bend: DNA tertiary structure and protein-DNA interactions. (ebi.ac.uk)
Molecular11
- Given some similarity in sequence between two proteins, a molecular model can be constructed for one sequence provided that the tertiary structure of the other is known. (springer.com)
- Here we discuss our recent efforts, based on some newer sequence alignment protocols (Jayaram, 2008), quantum mechanical corrections to the molecular mechanics generated structures and structure/fold invariant metrics (Mittal et al. (jbsdonline.com)
- The function of proteins depends on their structure, and defining the structure of individual proteins is a large part of modern Biochemistry and Molecular Biology. (schoolworkhelper.net)
- Even such small proteins contain hundreds of atoms and have molecular weights of over 5000 Daltons (Da). (schoolworkhelper.net)
- Most proteins with a molecular weight greater than 50,000 consist of two or more noncovalently-linked monomers. (thoughtco.com)
- In addition to general chemistry texts, information about protein structure can be found in texts for biochemistry, organic chemistry, general biology, genetics, and molecular biology. (thoughtco.com)
- Organic compounds with the same molecular formula but different structures and, therefore, different properties. (brainscape.com)
- Here, we performed independently small-angle neutron and X-ray scattering experiments and unbiased molecular dynamics simulations to probe the solution structure of an IDP. (pnas.org)
- In silico gene reconstruction and molecular modelling indicate remarkable conservation of viral structure over a geologic timescale. (nature.com)
- Here we suggest a molecular mechanism for electromechanical coupling and gating polarity in non-domain-swapped K v channels on the basis of the cryo-electron microscopy structure of KAT1, the hyperpolarization-activated K v channel from Arabidopsis thaliana . (nature.com)
- This structure provides a molecular description of the core of the Tat translocation system and a framework for understanding the unique Tat transport mechanism. (biomedsearch.com)
Biochemistry1
- In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates. (bookin.org.ru)
Quaternary structures3
- By analysing these properties, we can provide you with valuable information on secondary, tertiary and quaternary structures of protein molecules, such as monoclonal antibodies, and provide evidence that the molecule maintains conformational stability. (sgsgroup.in)
- The primary structure of a polypeptide of protein determines its secondary, tertiary, and quaternary structures. (thoughtco.com)
- M2 - explain the tertiary and quaternary structures of proteins. (stuvia.co.uk)
Fold13
- A number of tertiary structures may fold into a quaternary structure. (wikipedia.org)
- The robust nature of the approach derives from the stability of the fold of the protein under mutational pressures. (springer.com)
- This is so conservative that, for two proteins, sequence similarity can be almost undetectable yet the overall fold can remain the same. (springer.com)
- Taylor, W.R. (1993) Protein fold refinement: building models from idealised folds using motif constraints and multiple sequence data. (springer.com)
- 2000). This saturation may show completeness of protein fold space - an unlikely possibility. (jbsdonline.com)
- Alternatively, it either implies the need for development of higly sensitive newer experimental methods to unveil the unexplored regions of protein fold space, or, beckons the development of more accurate, time efficient, non-template based computational strategies for unravelling the uniqueness and diversity of protein structures. (jbsdonline.com)
- Is highly approximate knowledge of a protein's backbone structure sufficient to successfully identify its family, superfamily, and tertiary fold? (elsevier.com)
- PEP-FOLD 3 is a de novo approach aimed at predicting peptide structures from amino acid sequences. (molbiol-tools.ca)
- Disulfide bonding can form within and between polypeptide chains as proteins fold to its native conformation. (wikibooks.org)
- Many have intricate three-dimensional folding patterns that result in a compact form, but others do not fold up at all ("natively unstructured proteins") and exist in random conformations. (schoolworkhelper.net)
- To understand how proteins fold, we will start with the basics of structure, and progress through to structures of increasing complexity. (schoolworkhelper.net)
- Many polypeptides fold into compact, globular structures in which amino acid residues that are distant from each other in primary structure come into close proximity in the folded structure. (encyclopedia.com)
- The second level of protein structure where the linear sequence of proteins begins to fold into regular repeating patterns. (sparknotes.com)
Residues13
- The analysis of protein structures provides plenty of information about the factors governing the folding and stability of proteins, the preferred amino acids in the protein environment, the location of the residues in the interior/surface of a protein and so forth. (hindawi.com)
- The present work depends on sequence as well as structural information of the protein and aims to understand nature of hydrophobic residues on the protein surfaces. (hindawi.com)
- Solvent accessibility of each protein was determined using NACCESS software and then obtained the homologous sequences to understand how well solvent exposed and buried hydrophobic residues are evolutionarily conserved and assigned the confidence scores to hydrophobic residues to be buried or solvent exposed based on the information obtained from conservation score and knowledge of flanking regions of hydrophobic residues. (hindawi.com)
- These encouraging results show that de novo design of an idealized protein structure of more than 200 amino acid residues is now possible, from construction of a particular backbone conformation to determination of an amino acid sequence with an automated sequence selection algorithm. (caltech.edu)
- Primary structure is simply the sequence of residues making up the protein. (schoolworkhelper.net)
- Thus primary structure involves only the covalent bonds linking residues together. (schoolworkhelper.net)
- So the primary structure of a small protein would consist of a sequence of 50 or so residues. (schoolworkhelper.net)
- There is no theoretical maximum size, but the largest protein so far discovered has about 30,000 residues. (schoolworkhelper.net)
- Deletions of 5 to 8 residues within predicted α- helices resulted in the failure of export of the mutant protein from the cell. (elsevier.com)
- Proteins are large biomolecules , or macromolecules , consisting of one or more long chains of amino acid residues . (wikipedia.org)
- Short polypeptides, containing less than 20-30 residues, are rarely considered to be proteins and are commonly called peptides , or sometimes oligopeptides . (wikipedia.org)
- The sequence of amino acid residues in a protein is defined by the sequence of a gene , which is encoded in the genetic code . (wikipedia.org)
- Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification , which alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins. (wikipedia.org)
Chemistry2
- Review of Protein Chemistry and Structure. (umass.edu)
- Since the publication of the first edition of Chemistry of Protein Conjugation and Cross-Linking in 1991, new cross-linking reagents, notably multifunctional cross-linkers, have been developed and synthesized. (routledge.com)
Bioinformatics4
- It progresses rapidly to powerful tools that will be of interest to specialists in protein structure and bioinformatics. (umass.edu)
- In this day of exploding bioinformatics information from genomics and proteomics, it is ever more important to be conversant with macromolecular three-dimensional structure, and how it relates to protein and nucleic acid function and drug design. (umass.edu)
- Experienced participants are encouraged to work at their own speed, ahead of the group -- there is plenty of power to discover within Protein Explorer and its connections to complementary structural bioinformatics resources! (umass.edu)
- The emphasis of the course is structural bioinformatics with focus on various computational methods to simulate, analyze and model protein structure, dynamics and function. (umb.edu)
Molecules10
- The tertiary structure of a polypeptide (or protein containing only one polypeptide) refers to its shape, or more precisely the complete description its molecules' positions in three-dimensional space. (rosalind.info)
- To obtain PDB coordinates for a protein of your interest, go to the Protein Data Bank or Molecules to Go or NCBI . (molbiol-tools.ca)
- The aggregation of nonpolar side chains in the interior of a protein is favored by the increase in Entropy of the water molecules that would otherwise form cages around the hydrophobic groups. (wikibooks.org)
- Proteins are the largest and most varied class of biological molecules, and they show the greatest variety of structures. (schoolworkhelper.net)
- This spatial configuration must meet those of other structures of other molecules, dimensional structure, biological role and stereo-specificity therefore are necessarily linked. (biochemden.com)
- Macromolecular Crystals: The Growth of Crystals Is Now the Key to Deducing the Structure of Large Molecules. (encyclopedia.com)
- Proteins perform a vast array of functions within organisms , including catalysing metabolic reactions , DNA replication , responding to stimuli , providing structure to cells and organisms , and transporting molecules from one location to another. (wikipedia.org)
- Pyrx with Autodock vina was used to screen the compounds from Drug bank and Protein Data Bank to find the molecules that can bind to the active site between 1 to 142 amino acids. (ibbj.org)
- This quiz is based on the various aspects of the structure of protein molecules and amino acids. (syvum.com)
- Any mixture of secondary, tertiary, or quaternary protein molecules which appear as clumps in or outside the cell. (bioportfolio.com)
Sequences13
- But in nowadays The evolutions in motif identification and side chain modeling present the prospect of nearly automatic model building for a large fraction of newly determined protein sequences. (predictioncenter.org)
- Liam J. McGuffin , Jennifer D. Atkins , Bajuna R. Salehe , Ahmad N. Shuid , Daniel B. Roche , IntFOLD: an integrated server for modelling protein structures and functions from amino acid sequences: Figure 1. (wiley.com)
- Decoding the design principles of amino acids and the chemical logic of protein sequences. (jbsdonline.com)
- However, these signature sequences have not so far been extensively investigated amongst orthologous Bcl-2 family proteins. (isharonline.org)
- They are linked by peptide sequences usually short and without secondary structure. (biochemden.com)
- can calculate comparative models for a large number of protein sequences, using many different template structures and sequence-structure alignments. (psu.edu)
- Protein primary structures can be directly sequenced , or inferred from DNA sequences . (wikipedia.org)
- Large sequence databases now exist that collate known protein sequences. (wikipedia.org)
- In protein science , Protein Interaction Motifs (Protein Interaction Binding Motifs) are short amino acid sequences which are the binding sites on the ligands of protein interaction domains. (wellnessadvantage.com)
- Two of the main sources for generating the new families added to release 27.0 were Protein Data Bank (PDB) structures =-=(8)-=- and human sequences. (psu.edu)
- We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. (psu.edu)
- Most such methods do rely on comparisons between the sequence to be predicted and sequences of known structure in the Protein Data Bank and thus account for environment indirectly, assuming the target and template sequences share similar cellular contexts. (bookin.org.ru)
- Ankyrin Repeat (ANK Repeat) is a protein interaction motif that contains a 33-amino acid long sequence that often occurs in tandem arrays (as amino acid repetitive sequences ). (wellnessadvantage.com)
Polypeptide chains1
- The secondary structure of proteins where the polypeptide chains are almost completely extended during the process of folding. (sparknotes.com)
Lipids1
- Carbohydrates, Lipids, and Proteins. (wikibooks.org)
Conformation8
- Using this coarse-grained mapping, protein conformation can be approximated by a linear sequence of mesostates. (elsevier.com)
- The three-dimensional conformation of a polypeptide chain of a globular protein in its native folded state. (pozzter.com)
- In order to maintain potency and activity, some of the most critical parameters to maintain are protein conformation (tertiary or 3D structure), folding (secondary structure) and proper subunit association (quaternary structure). (sgsgroup.in)
- However, analytical monitoring of the protein conformation has been frequently omitted due to time constraints, the complexity of techniques commonly employed and the inherent lack of sensitivity to subtle changes shown by some biophysical methods. (sgsgroup.in)
- The biologically active form of Globular Proteins are in Tertiary structure, which is in three-dimensional conformation. (biochemden.com)
- Secondary structure is the ordered arrangement or conformation of amino acids in localized regions of a polypeptide or protein molecule. (thoughtco.com)
- Only proline differs from this basic structure as it contains an unusual ring to the N-end amine group, which forces the CO-NH amide moiety into a fixed conformation. (wikipedia.org)
- A method of rational drug design includes simulating polypeptides in a way that predicts the most probable secondary and/or tertiary structures of a polypeptide, e.g., an oligopeptide, without any presumptions as to the conformation of the underlying primary or secondary structure. (google.com)
Membrane proteins2
- Structure determination of membrane proteins with magic angle spinning NMR is rapidly developing. (figshare.com)
- Bezanilla, F. How membrane proteins sense voltage. (nature.com)
Gene14
- Gene triplication deduced from the tertiary structure of a muscle calcium binding protein. (nih.gov)
- The protein of interest has four domains due to gene duplication. (predictioncenter.org)
- A synthetic gene coding for the designed sequence was constructed and the recombinant artificial protein was expressed in bacteria, purified and characterized. (caltech.edu)
- Its identification may point to functionally important regions of a gene and is thus of potential interest to protein engineers who alter proteins to produce new functions. (genetics.org)
- The codon sequence of the protein-coding gene determines the order of amino acids in the polypeptide chain. (pediaa.com)
- p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence. (uniprot.org)
- section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. (uniprot.org)
- This gene encodes a transcription factor that belongs to the family of zinc-finger DNA-binding proteins associated with chromatin remodeling. (cancerindex.org)
- What does this gene/protein do? (cancerindex.org)
- This gene encodes a member of the four-and-a-half-LIM-only protein family. (cancerindex.org)
- Also, this gene is down-regulated during transformation of normal myoblasts to rhabdomyosarcoma cells and the encoded protein may function as a link between presenilin-2 and an intracellular signaling pathway. (cancerindex.org)
- What pathways are this gene/protein implicaed in? (cancerindex.org)
- Tumorigenesis is frequently associated with activating mutations in β-catenin gene inducing nuclear expression of β-catenin protein. (cancerindex.org)
- The molcular biology lectures include topics like DNA structure and replication, RNA and transcription, protein synthesis, gene expression and basic recombinant DNA techniques. (rug.nl)
Disulfide5
- In some proteins, the linear polypeptide chain is cross-linked: Disulfide bonds. (wikibooks.org)
- Hydrogen bonds formed between amino acids are responsible for the formation of the secondary structure of a protein while disulfide and salt bridges form the tertiary structure. (pediaa.com)
- However, proteins can become cross-linked, most commonly by disulfide bonds , and the primary structure also requires specifying the cross-linking atoms, e.g., specifying the cysteines involved in the protein's disulfide bonds. (wikipedia.org)
- The primary structure of polypeptides and proteins is the sequence of amino acids in the polypeptide chain with reference to the locations of any disulfide bonds. (thoughtco.com)
- Tertiary structure is largely maintained by disulfide bonds. (thoughtco.com)
Stabilized conformations1
- Hydrogen bonds fine tune the tertiary structure by selecting the unique structure of a protein from among a relatively small number of hydrophobically stabilized conformations. (wikibooks.org)
Hydrophobic10
- Thermal unfolding monitored by near-UV CD revealed a cooperative transition with an apparent T_m of 65 °C. Moreover, the artificial protein did not exhibit any affinity for the hydrophobic fluorescent probe 1-anilinonaphthalene-8-sulfonic acid (ANS), providing additional evidence that the artificial barrel is not in the molten globule state, contrary to previously designed artificial a/ b-barrels. (caltech.edu)
- The hydrophobic effect is the major determination of original protein structure. (wikibooks.org)
- This is due to the exposure of hydrophilic, acidic ad basic amino acids to the outside and hiding of the hydrophobic amino acids such as aromatic amino acids and the amino acids with alkyl groups in the core of the protein structure. (pediaa.com)
- A major force stabilizing the tertiary structure is the hydrophobic interaction among nonpolar side chains in the core of the protein. (encyclopedia.com)
- Instead of a simple methyl group, the myristoyl group has a tail of 14 hydrophobic carbons, which make it ideal for anchoring proteins to cellular membranes . (wikipedia.org)
- Hydrophobic interaction is the main stabilizing force for subunits in quaternary structure. (thoughtco.com)
- The property of protein of being non-polar and hydrophobic, as well as having an increase in intensity from 200 to 219, indicates the protein folding. (ac.ir)
- The shift from 342 to 337 nm along with blue shift indicates hydrophobic properties and the removal of protein from the water environment. (ac.ir)
- The secondary structures are tightly packed in the protein core in a hydrophobic environment. (wikipedia.org)
- Other α helices buried in the protein core or in cellular membranes have a higher and more regular distribution of hydrophobic amino acids, and are highly predictive of such structures. (wikipedia.org)
Polypeptides4
- In the natural course of making a protein, polypeptides are elongated by the addition of amino acids to the C-terminal end of the growing chain. (schoolworkhelper.net)
- Long chains of amino acids, called polypeptides, make up the multicomponent, large complexes of protein. (encyclopedia.com)
- In general, polypeptides are unbranched polymers, so their primary structure can often be specified by the sequence of amino acids along their backbone. (wikipedia.org)
- There are four levels of structure found in polypeptides and proteins . (thoughtco.com)
Metabolism3
- Many proteins are enzymes that catalyse biochemical reactions and are vital to metabolism . (wikipedia.org)
- Digestion breaks the proteins down for use in the metabolism. (wikipedia.org)
- Part of an enzyme needed for energy, and protein metabolism. (prezi.com)
Monomeric2
- It is based on the nonredundant data set of 218 monomeric proteins. (hindawi.com)
- Hemoglobin's quaternary structure is the package of its monomeric subunits. (thoughtco.com)
Consist4
- Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure. (uchicago.edu)
- consist of a sufficient and balanced supply of both essential and nonessential amino acids in order to ensure high levels of protein production. (encyclopedia.com)
- The templates used for model building consist of representative multiple structure al. (psu.edu)
- Most proteins consist of linear polymers built from series of up to 20 different L -α- amino acids . (wikipedia.org)
Secondary structures8
- The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. (wikipedia.org)
- Far-UV CD spectra with prominent bands at 222 nm and 208 nm revealed the presence of α-helix secondary structures (50%) in fairly good agreement with the model. (caltech.edu)
- Various types of secondary structures have been discovered, but by far the most common is the orderly repeating forms known as the a-helix and the b sheet. (schoolworkhelper.net)
- This is very compact three-dimensional structure, the wound has previously viewed and secondary structures of the segments without secondary structure . (biochemden.com)
- The two main secondary structures are the alpha helix and the anti-parallel beta-pleated sheet. (thoughtco.com)
- A single polypeptide or protein may contain multiple secondary structures. (thoughtco.com)
- Meets the grading criterias: P3 - describe the primary and secondary structures of proteins. (stuvia.co.uk)
- In these secondary structures regular patterns of H bonds are formed between neighboring amino acids, and the amino acids have similar Φ and Ψ[clarification needed] angles. (wikipedia.org)
Globular protein1
- These areas are almost "independent" from the rest of the tertiary structure of the globular protein . (biochemden.com)
Molecule4
- Serving as the basic structural molecule of all the tissues in the body, protein makes up nearly 17 percent of the total body weight. (encyclopedia.com)
- Also, for a protein composed of a single polypeptide molecule, tertiary structure is the highest level of structure that is attained. (thoughtco.com)
- Suppose that when drawing a Lewis structure for a molecule, you end up with a structure in which the central at. (bartleby.com)
- its structure resulting from the union of more than one protein molecule, called subunit proteins. (syvum.com)
Covalent2
- Elucidation of the Covalent and Tertiary Structures of Biologically Active Ts3 Toxin. (uchicago.edu)
- The primary structure may be thought of as a complete description of all of the covalent bonding in a polypeptide chain or protein. (thoughtco.com)
Denaturation4
- This process of destroying the three-dimensional protein structure is called denaturation. (encyclopedia.com)
- We will conclude this section of the course with a consideration of denaturation and renaturation -- the forces involved in loss of a macromolecule's native structure (that is, its normal 3-dimensional structure), and how that structure, once lost, can be regained. (utah.edu)
- what structure does denaturation destroy? (brainscape.com)
- Reversible and irreversible denaturation of proteins. (unibo.it)
Recombinant proteins1
- The secondary structure of recombinant proteins can change through complex formation with other proteins. (ac.ir)
Peptide bonds1
- Proteins are chains of amino acids joined together by peptide bonds. (wikipedia.org)
Soluble1
- Tertiary structure or the globular form of proteins is water-soluble under physiological conditions. (pediaa.com)
Structural Classifi1
- 1994). SCOP: Structural Classification of Proteins. (jbsdonline.com)
Fingerprint2
- Fingerprint Dive into the research topics of 'Does secondary structure determine tertiary structure in proteins? (elsevier.com)
- Fingerprint Dive into the research topics of 'Erythropoietin structure-function relationships. (elsevier.com)
Single polypeptide1
- The tertiary structure of a polypeptide or protein is the three-dimensional arrangement of the atoms within a single polypeptide chain. (thoughtco.com)
Initio1
- It also incorporates a n ew ab initio folding simulation called Poing to model regions of your proteins with no detectable homology. (molbiol-tools.ca)
Helical5
- H spin diffusion with MAS NMR is demonstrated for a helical transmembrane model protein complex. (figshare.com)
- An example of a protein with many a-helical structures is the keratin that makes up human hair. (schoolworkhelper.net)
- tertiary structure The folding of the helical coil of a polypeptide chain. (encyclopedia.com)
- We present the GMPPCP-bound structures of the truncated human dynamin 1 helical polymer at 12.2 Å and a fusion protein, GG, linking human dynamin 1's catalytic G domain to its GTPase effector domain (GED) at 2.2 Å. (nih.gov)
- The simulated annealing procedure rapidly and frequently generates native-like structures for small helical proteins and better than random structures for small b sheet containing proteins. (psu.edu)
Amino acids and proteins1
- Do you want more information on amino acids and proteins? (thoughtco.com)
Solvent2
- The side chains project outward and contact any solvent, producing a structure something like a bottle brush or a round hair brush. (schoolworkhelper.net)
- Most of the simulated structures have native-like solvent accessibility and secondary structure patterns, and thus ensembles of these structures provide a particularly challenging set of decoys for evaluating scoring functions. (psu.edu)
Side chains3
- A pronounced absorption band in the near-UV CD region, arising from immobilized aromatic side-chains, showed that the artificial protein is folded in solution. (caltech.edu)
- Also, ionic bonds called salt bridges form between positively- and negatively-charged side-chains of amino acids, further stabilizing the tertiary structure. (pediaa.com)
- The process whereby water-fearing protein side chains interact more favorably with themselves than with water to create a hydrophilic exterior. (sparknotes.com)
Peptides3
- Self-assembling peptides that can form supramolecular structures such as fibrils, ribbons, and nanotubes are of particular interest to modern bionanotechnology and materials science. (ucy.ac.cy)
- Chemical methods typically synthesise peptides in the opposite order to biological protein synthesis (starting at the C-terminus). (wikipedia.org)
- TatC captures substrate proteins by binding their signal peptides. (biomedsearch.com)
Regions7
- Phylogenetic Gaussian process model for the inference of functionally important regions in protein tertiary structures. (mybiosoftware.com)
- The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. (uchicago.edu)
- The detection of positive selection can also help identify functionally important protein regions and thus guide protein engineering. (genetics.org)
- As a part of our on-going efforts in this direction and to facilitate tertiary structure selection/rejection in containing the combinatorial explosion of trial structures for a specified amino acid sequence, we describe here a web-enabled tool ProRegIn (Protein Regularity Index) developed based on the regularity in the 𝛷, Ψ dihedral angles of the amino acids that constitute loop regions. (ias.ac.in)
- We have analysed the dihedrals in loop regions in a non-redundant dataset of 7351 proteins drawn from the Protein Data Bank and categorized them as helix-like or sheet-like (regular) or irregular. (ias.ac.in)
- This allows for the easy identification of regions and types of structural flexibility present in a protein of interest. (rcsb.org)
- The interacting regions may be adjacent, with a short loop in between, or far apart, with other structures in between. (wikipedia.org)
Methods4
- The two most common methods for determining protein structure are x-ray crystallography and Nuclear Magnetic Resonance (NMR) spectroscopy. (sjsu.edu)
- In conclusion, compared with existing methods for in vivo testing of protein function, this complementation assay provides a rapid method for investigating protein structure/function relationships in plants. (osti.gov)
- Methods commonly used to study protein structure and function include immunohistochemistry , site-directed mutagenesis , X-ray crystallography , nuclear magnetic resonance and mass spectrometry . (wikipedia.org)
- Improved methods for building protein models in electron density maps and the location of errors in these models. (psu.edu)
Binding3
- In protein science , Protein Interaction Domains and Motifs are protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in signal transduction pathways and the specific binding sites of their cognate protein ligands. (wellnessadvantage.com)
- M. Bradford, "A Rapid and Sensitive Method for the Quantitation of Microgram Quantities of Protein Utilizing the Principle of Protein-Dye Binding", Anal. (freepatentsonline.com)
- Inhibition of apoptosis and NF-κB activation by vaccinia protein N1 occur via distinct binding surfaces and make different contributions to virulence. (biomedsearch.com)
Biosynthesis1
- Protein biosynthesis is most commonly performed by ribosomes in cells. (wikipedia.org)
Biological3
- As a result, inferring the tertiary structure of a protein from its primary structure poses a research problem of the first order for a wide range of biological applications, and one that is still far from fully understood. (rosalind.info)
- In biological systems, proteins are produced during translation by a cell's ribosomes . (wikipedia.org)
- p>This section provides any useful information about the protein, mostly biological knowledge. (uniprot.org)
Patterns3
- Though it may not be immediately obvious, proteins do follow certain recognisable folding patterns. (nottingham.ac.uk)
- Examination of protein structures resolved by X-ray diffraction and NMR has revealed a variety of folding patterns common to many different proteins. (nottingham.ac.uk)
- The present study analysed the role of transforming growth factor-β1 (TGF-β1) and four-and-a-half LIM domain protein 2 (FHL2) in pilomatricoma in synopsis with their expression patterns in human anagen hair. (cancerindex.org)
Subunits2
- Because there are two different subunits, hemoglobin exhibits heteroquaternary structure. (thoughtco.com)
- The fourth level of protein structure that refers to the spatial arrangement of the subunits within the protein. (sparknotes.com)
Hydrogen bonds6
- This level of structure describes the local folding pattern of the polypeptide backbone and is stabilized by hydrogen bonds between N-H and C=O groups. (schoolworkhelper.net)
- In a b sheet, the polypeptide chain folds back on itself so that polypeptide strands like side by side, and are held together by hydrogen bonds, forming a very rigid structure. (schoolworkhelper.net)
- Again, the polypeptide N-H and C=O groups form hydrogen bonds to stabilize the structure, but unlike the a-helix, these bonds are formed between neighbouring polypeptide (b) strands. (schoolworkhelper.net)
- In addition, hydrogen bonds also help in stabilizing the 3D-structure. (pediaa.com)
- Explanations of structural biology terms and concepts , e.g. asymmetric unit, Protein Data Bank, hydrogen bonds, temperature value, etc. all at About Macromolecular Structure . (umass.edu)
- its structure resulting from hydrogen bonds between the C=O and N-H groups of different amino acids. (syvum.com)
Myoglobin1
- A representation of the 3D structure of the protein myoglobin showing turquoise α-helices . (wikipedia.org)
Protein's2
- They occur in well-defined domains of a protein's tertiary structure and show a large excess of amino acid replacement over silent substitutions. (genetics.org)
- To understand protein's role and function in the human body, it is important to understand its basic structure and composition. (encyclopedia.com)
Stable4
- Taken together, the results indicate that the de novo designed α/β-barrel protein adopts a stable three-dimensional structure in solution. (caltech.edu)
- Indeed, they have their own and are stable tertiary structure independently of the rest of the polypeptide chain. (biochemden.com)
- The components of the assay include (1) construction of test vectors that drive expression of epitope-tagged PpCESA5 carrying engineered mutations, (2) transformation of a ppcesa5 knockout line that fails to produce gametophores with test and control vectors, (3) scoring the stable transformants for gametophore production, (4) statistical analysis comparing complementation rates for test vectors to positive and negative control vectors, and (5) analysis of transgenic protein expression by Western blotting. (osti.gov)
- Proteins can also work together to achieve a particular function, and they often associate to form stable protein complexes . (wikipedia.org)
Function of proteins1
- D2 - discuss the relationship between the structure and function of proteins. (stuvia.co.uk)
Cellular2
- Observing the structures of proteins within the cell and tracking structural changes under different cellular conditions are the ultimate challenges for structural biology. (ed.ac.uk)
- serves as a blueprint for proteins and, through the actions of proteins, for all cellular structures and activities. (brainscape.com)
Functional proteins1
- The assay distinguished mutations that generate fully functional, nonfunctional, and partially functional proteins. (osti.gov)
Backbone1
- To explore this question, backbone dihedral angles were extracted from the known three-dimensional structure of 2,439 proteins and mapped into 36 labeled, 60° × 60° bins, called mesostates. (elsevier.com)
Sequence homology1
- I am using Swiss-PdbViewer to determine the structure of a fluorescent protein with a sequence homology to know fluorescent proteins, such as GFP and DsRed. (predictioncenter.org)
Synthesis2
- Mad Cow Disease is a great way to get the students to pay attention before you lunge into the difficult lecture on protein synthesis (you start with prions, then work backwards). (scienceblogs.com)
- Studies on the enzymatic synthesis of optically pure tertiary alcohols. (bookin.org.ru)