MacromoleculesGlobular proteinsMembraneStructuresProtein'sFunctionalPeptides and proteinsStructuralAntibodiesAmino acidsInteractionsComplexesAffinityAntibodyBiologicallyResiduesMoleculesAlbuminDenaturationIntrinsicallyDifferent conformationsRNAsDynamicsConformersSolubleExtracellularValineAggregationAssembleTertiaryMolecularMyoglobinAtomsStabilityProcessesRibonucleasePrion proteinVivoTranscriptionFoldingHydrophobicFunctionAdoptsNucleic acidSequenceCellularLipidBiophysicalStructureCrystallographyDisulfideStructurallyPathogenicPolypeptidesPhysiologicallyInactiveEnzymesNativeReceptorsSynthesisFormInteractGeneticMRNATranslocation
Macromolecules8
- Large macromolecules, including proteins and their complexes, very often adopt multiple conformations. (biorxiv.org)
- Large macromolecules, including proteins and their complexes, are intrinsically flexible, and this flexibility is often linked with their function. (biorxiv.org)
- We proposed that a cell theoretically could in principle synthezise a big number of forms of [ 2 H]labeled macromolecules with somewhat different structures and conformations, so that a cell could easily select a preferable one from al these species in a course of adaptation to 2 H 2 O, that is the best suitable namely for that conditions. (o8ode.ru)
- RiboNucleic Acids (RNAs) are ubiquitous macromolecules within biological systems, capable of performing a wide range of regulatory and catalytic functions. (dagstuhl.de)
- Various interior dynamics including self organization of macromolecules, protein conformation, movement of human thoracic diaphragm, formation of logarithmic spiral in nature were discussed in the light of potential energy of self gravity and kinetic energy of metabolic energy. (webmedcentral.com)
- SANS is a ver important technique applied to many different systems: polymers, colloids, biological macromolecules, emulsions, pores in solids, aggregates in alloys, and even magnetic microstructures. (ill.eu)
- These include polymers, alloys, and biological macromolecules. (ill.eu)
- Most of the structure databases obtain the 3D structure of biological macromolecules from techniques like X-ray crystallography, NMR Spectroscopy, Small angle X-ray scattering, Electron microscopy etc. (amrita.edu)
Globular proteins3
- Partial hydrophobic collapse is an experimentally accepted model for the folding kinetics of many globular proteins, such as myoglobin, alpha-lactalbumin, barstar, and staphylococcal nuclease. (wikipedia.org)
- Globular proteins that are thought to fold by hydrophobic collapse are particularly amenable to complementary computational and experimental study using phi value analysis. (wikipedia.org)
- This is thought to make globular proteins stable and soluble in the watery environment of the cell. (anl.gov)
Membrane21
- MorphoSys , a biotechnology company focused on fully human antibodies, and Heptares Therapeutics , a developer of new medicines targeting G protein-coupled receptors (GPCRs), have signed an agreement to discover novel antibody therapeutics targeting GPCRs-membrane proteins involved in a broad range of biological processes and diseases. (centerwatch.com)
- StaRs enable antibody discovery by stabilizing the GPCR protein outside the cellular membrane in the correct conformation. (centerwatch.com)
- These proteins are synthesized in the bacterial cytoplasm and cross one membrane into the bacterial periplasm. (anl.gov)
- Autotransporter proteins then remain in an unfolded state in the periplasm until they pass through the outer bacterial membrane, folding properly along the way. (anl.gov)
- Periplasmic LptC and LptA proteins of the LPS transport system (Lpt) are responsible for LPS transfer between the Lpt inner and outer membrane complexes. (nih.gov)
- Here we present a new approach to incorporate single or multiple post-translational modifications or non-canonical amino acids into soluble and membrane proteins expressed in eukaryotic cells. (biorxiv.org)
- We thus sought to complement these approaches with a method that could incorporate synthetic peptides carrying multiple post-translational modifications (PTMs) or ncAAs into both cytosolic and membrane proteins in live eukaryotic cells. (biorxiv.org)
- Their unique hourglass-shaped architecture is highly conserved among different bacterial membrane proteins and other biological channels. (ibecbarcelona.eu)
- Thus the MHV model system divulges relatively stable CEACAM receptor-induced S conformations that are quite likely the intermediate structures on the way to membrane fusion (see Figure 2 for hypothetical illustration of receptor-induced generation of fusion intermediate S structures). (globaltechbiz.com)
- All-atom simulations of 4E10, PGZL1, 10E8 and LN01 docked onto HIV-like membranes consistently form phospholipid complexes at key complementarity-determining region loop sites, solidifying that stable and specific lipid interactions anchor bnAbs to membrane surfaces. (elifesciences.org)
- Simulations estimating protein-membrane interaction strength for PGZL1 variants along an inferred maturation pathway show bilayer affinity is evolved and correlates with neutralization potency. (elifesciences.org)
- The modeling platform developed here uncovers insights into lipid participation in antibodies' recognition of membrane proteins and highlights antibody features to prioritize in vaccine design. (elifesciences.org)
- Antibodies can target epitopes on integral membrane proteins very near to the lipid bilayer surface, even those partially embedded within the headgroup region. (elifesciences.org)
- The trimeric Sec61/SecY complex is a protein-conducting channel (PCC) for secretory and membrane proteins. (cipsm.de)
- As a test-case, the membrane protein FepA is investigated in its full environment, yielding a more precise description of the protein surface. (nature.com)
- Membrane proteins, such as those operating transport through the membrane in a controlled way, are prone to show interesting topological properties related to their function. (nature.com)
- Our study uses classical algorithms such as space partitions and Dijkstra paths search 9 , applied in an original and novel way by taking into account the full representation of a membrane protein including the solvent and the lipid bilayer (Fig. 1 ). (nature.com)
- The FepA membrane protein is surrounded by a lipid bilayer separating the extracellular medium and the periplasm. (nature.com)
- While many studies have been focused on the membrane structure, the dynamics of such systems are crucial for the function of the membrane including membrane bound proteins. (lu.se)
- Native membrane derived polymer-supported lipid bilayers (nSLBs) are poised to bridge the gap between live cell experiments and traditional model membrane architectures that by offering a combination of accessibility by surface sensitive analytical instrumentation and a composition which more closely resembles cellular membranes by displaying a diversity of endogenous membrane proteins, lipids, and carbohydrates. (lu.se)
- Due to the lack of detergent solubilization and reconstitution steps, the nSLBs created using this approach contain essentially all of the native lipids, as well as the membrane-associated proteins and carbohydrates from the donor membrane. (lu.se)
Structures14
- As a key biological building block, the stability and conformation of amides affect the structures of peptides and proteins as well as their biological function. (rwth-aachen.de)
- Current hypotheses on protein folding suggest that folding is initiated by formation of secondary structures followed by association of the hydrophobic regions of the emerging structure to orient them toward the interior of the protein in a process termed hydrophobic collapse. (anl.gov)
- Proteins from thermophilic organisms must retain their native structures under extreme conditions, where their homologues from mesophilic organisms denature. (berkeley.edu)
- RNAs with biological functions that depend on higher-order structures are vulnerable to forming inactive alternative structures. (utexas.edu)
- These alternative, misfolded structures can be stable enough to require intervention by proteins that promote conformational transitions. (utexas.edu)
- This review critically focuses on opportunities to employ protein-graphene oxide structures either as nanocomposites or as biocomplexes and highlights the effects of carbonaceous nanostructures on protein conformation and structural stability for applications in tissue engineering and regenerative medicine. (mdpi.com)
- For the first time crystal structures of wild-type bovine pancreatic ribonuclease A and its markedly less stable variant modified at position Ile106 were determined at different pressures. (udg.edu)
- The larger Rep proteins, Rep78 and Rep68, assemble into stable, hexameric oligomers on specific secondary structures on the 3' and 5' termini of the single stranded viral DNA. (utoledo.edu)
- Our studies are aimed at understanding how these proteins assemble on DNA structures and the specificity of their interaction with DNA. (utoledo.edu)
- I agree with you that we also want to examine the earlier, less stable structures. (alzforum.org)
- It adds missing hydrogen atoms to protein structures (PDB-format) and detects reasonable protonation states, tautomers, and hydrogen coordinates of both protein and ligand molecules. (proteins.plus)
- When one does any analysis like docking with the protein molecule, the structures have to be added with hydrogen and satisfy the bonds. (amrita.edu)
- Specialized cell structures called ribosomes are the cellular organelles that actually synthesize the proteins (RNA transcription). (cdc.gov)
- Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labeled chaperone Hsp104. (stanford.edu)
Protein's3
- Hydrophobic collapse is one of the main events necessary for reaching a protein's stable and functional conformation. (wikipedia.org)
- Qin explains that proteins absorb heat and convert it into a form of energy called enthalpy changes, which are associated with changes in a protein's conformation. (buffalo.edu)
- Upon co-incubation of GSH-MDI reaction products with human albumin, MDI was rapidly transferred to specific lysines of albumin, and the protein's native conformation/charge was altered, based on electrophoretic mobility. (cdc.gov)
Functional7
- In a second paper published in the Nov. 8 online issue of the journal Physical Review Letters, the scientists offer a detailed description of their novel device, an advanced version of the "optical trap," which uses infrared light to trap and control the forces on a functional protein, allowing researchers to monitor the molecule's every move in real time. (sciencedaily.com)
- Moreover, targeting protein functional motions bears a great potential to control and modulate proteins' activities and interactions in physio-pathological contexts. (biorxiv.org)
- For many functional RNA families [11], decades of research have produced a deep understanding of the sequence and structural basis underlying their biological function(s). (dagstuhl.de)
- Typical applications of design include novel therapeutic strategies, control principles for existing biological systems, or sensors for the presence of small molecules [3], but designed sequences can also provide an objective experimental assessment of functional hypotheses, where designs are synthesized and their effect on the cellular context can be tested in vitro and, in turn, in vivo. (dagstuhl.de)
- This phenomenon can be explained if Cdcp4 has more than one essential function or, alternatively, if two mutant proteins assemble to form a functional complex. (ubc.ca)
- What we have found is that in order to achieve their high temperature sensitivity, the ion channel needs to undergo extreme structural changes in their functional state, and these extreme changes compromise protein stability," Qin explains. (buffalo.edu)
- Here we demonstrate that PSRP1 is not a bona fide ribosomal protein, but rather a functional homologue of the Escherichia coli cold-shock protein pY. (cipsm.de)
Peptides and proteins2
- The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS . (lookformedical.com)
- These covalent bonds are found in almost all classes of extracellular peptides and proteins. (lifetein.com)
Structural7
- Structural comparison to mesophilic acylphosphatases reveals significant differences in the conformation of the L5 loop connecting strands 4 and 5. (rcsb.org)
- How does an amino acid sequence that is unfolded when it leaves the ribosome manage to fold properly into a highly ordered, lightning-fast enzyme or sturdy structural protein? (anl.gov)
- This structural heterogeneity is not occasional and is frequently linked with specific biological function. (biorxiv.org)
- Other projects in the lab focus on the mechanism of protein misfolding, the structural and energetic mechanism of signaling, computational identification of folding modules, and the role of ligand binding. (berkeley.edu)
- The biological need - the strong temperature sensitivity of the receptors - apparently requires a larger energy than what reversible structural changes in the protein can afford," he says. (buffalo.edu)
- Some functions are performed by disordered protein structural parts. (alzforum.org)
- Cells depend on their DNA for coding information to make various classes of proteins that include enzymes, certain hormones, transport proteins, and structural proteins that support life. (cdc.gov)
Antibodies5
- We believe that by combining Heptares' unique StaR platform for generating stable GPCRs as antigens with our antibody discovery technology, we will be able to unlock the immense potential of therapeutic antibodies against GPCRs. (centerwatch.com)
- Heptares' StaRs offer a breakthrough solution to the main challenge associated with making antibodies against GPCRs, namely producing purified and properly folded protein for use as an antigen against which antibodies are raised. (centerwatch.com)
- Our data show that the stable knockdown of HIPK2 led to wtp53 misfolding, as detected by p53 immunoprecipitation with conformation-specific antibodies, and that p53 protein misfolding impaired p53 DNA binding and transcription of target genes. (aacrjournals.org)
- Storage These antibodies are stable for at least one (1) year at -20°C to -70°C. Store product in appropriate aliquots to avoid multiple freeze-thaw cycles. (qedbio.com)
- Here we report the selection of camelid-derived single-domain antibodies (nanobodies) that modulate the conformation and spectral properties of the green fluorescent protein (GFP). (cipsm.de)
Amino acids5
- However, previous work by this team of researchers from the University of Notre Dame and The University of Chicago has shown that, contrary to popular belief, intrinsically disordered proteins, which sample a variety of conformational forms the way the autotransporter proteins do, can remain quite extended in water even if they have high ratios of hydrophobic to charged amino acids. (anl.gov)
- This finding suggests that spacing of hydrophobic amino acids must be under selective pressure in bacterial proteins to facilitate their virulence functions. (anl.gov)
- Aminoacyl tRNA synthetases are a class of enzymes that ensure the fidelity of protein synthesis by attaching amino acids to their cognate tRNAs. (utoledo.edu)
- Twenty alpha-amino acids are the subunits which are polymerized to form proteins . (lookformedical.com)
- The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. (lookformedical.com)
Interactions9
- In this model, we do not consider the interactions of the peptide backbone as this maintains its stability in non-polar and polar environments as long as there is sufficient hydrogen bonding within the backbone, thus we will only consider the thermodynamic contributions of the side chains to protein stability. (wikipedia.org)
- These techniques provide valuable insights on proteins' functioning and interactions with their environment. (biorxiv.org)
- Based on the structure of Cdc4p, possible models for interallelic complementation including interactions with partner proteins and the formation of a myosin complex with Cdc4p fulfilling the role of both an essential and regulatory light chain are proposed. (ubc.ca)
- Moreover, iron interactions with N-terminally acetylated α S, the physiologically relevant form of the human protein, will be addressed to shed light on the current understanding of protein dynamics and the physiological environment in the disease state. (hindawi.com)
- Furthermore, alternative conformations or overlapping entries that might be annotated in the original protein structure are removed, as they could disturb the analysis of molecular interactions. (proteins.plus)
- Protein conformation is critically linked to function and often controlled by interactions with regulatory factors. (cipsm.de)
- Some conserved cysteines within proteins are critical for protein-protein interactions. (lifetein.com)
- All or other nearby charged groups, the pKa shift of a buried pH-dependent properties of proteins are ultimately governed residue is dominated by the large electrostatic self-energy by the electrostatic interactions of ionizable side chains. (lu.se)
- 2004). The effect of electrostatic interactions is usually polarization effects in the protein are subsumed in an quantified in terms of the shift, DpKa, of the pKa value of an apparent dielectric constant, eP. (lu.se)
Complexes4
- RNasin is now utilized to preserve RNA during cDNA synthesis, in vitro transcription, in vitro translation, and the extraction and purification of mRNA-protein complexes, as well as to discover unique RNase activities. (yeasenbiotech.com)
- Protoss is a fully automated hydrogen prediction tool for protein-ligand complexes. (proteins.plus)
- Rarey, M., Fast automated placement of polar hydrogen atoms in protein-ligand complexes. (proteins.plus)
- Rarey, M., Protoss: a holistic approach to predict tautomers and protonation states in protein-ligand complexes. (proteins.plus)
Affinity4
- Hydrophobic collapse may also reduce the affinity of conformationally flexible drugs to their protein targets by reducing the net hydrophobic contribution to binding by self association of different parts of the drug while in solution. (wikipedia.org)
- To identify new candidates for this nonspecific RNA chaperone activity, we performed affinity purifications of budding yeast RNA-binding proteins, using an exogenous and non-orthologous RNA as bait: the highly structured ribozyme derived from the Tetrahymena thermophila Group I intron. (utexas.edu)
- Studies of the thermodynamics of binding of ligands to glycyl tRNAs suggest that the formation of glycyl adenylate, an obligate intermediate on the reaction pathway, is accompanied by a significant conformation change in the protein that alters the affinity of the enzyme for tRNA. (utoledo.edu)
- may not generate fusion-promoting S protein conformations protein receptors that bind S proteins at high affinity clearly do, as evidenced most extensively by studies with MHV. (globaltechbiz.com)
Antibody2
- We present evidence that zinc supplementation to HIPK2i cells increased p53 reactivity to conformation-sensitive PAb1620 (wild-type conformation) antibody and restored p53 sequence-specific DNA binding in vivo and transcription of target genes in response to Adriamycin treatment. (aacrjournals.org)
- Ancillary protein-lipid contacts reveal surprising contributions from antibody framework regions. (elifesciences.org)
Biologically2
- These RNA chaperone proteins are biologically critical, and they have long been hypothesized to possess nonspecific RNA binding as a general property - empowering a small collection of RNA chaperones to facilitate the folding of a large and diverse transcriptome. (utexas.edu)
- Biologically, all the protein molecules have hydrogen atom and all the bonds are satisfied to obtain a stable conformation. (amrita.edu)
Residues1
- The extreme thermostability of PhAcP can be attributed to an extensive ion-pair network consisting of 13 charge residues on the beta sheet of the protein. (rcsb.org)
Molecules5
- Hydrophobic collapse is a proposed process for the production of the 3-D conformation adopted by polypeptides and other molecules in polar solvents. (wikipedia.org)
- However, when the adaptive process goes continuously during the many generation, the population of cells can use a special genetic mechanisms for the adaptation to 2 H 2 O. For example, mutations of geens can be resulted in amino acid replacements in molecules of proteins, which in turn could cause a formation of a new isoenzymes, and in the special cases - even the anomal working enzymes of a newer structure type. (o8ode.ru)
- These biological nanopores have been designed to protect the interior of the bacterial cell from leakage of toxic compounds while selectively allowing the entry of the molecules needed for cell growth and function. (ibecbarcelona.eu)
- They are single-chain molecules present on host cellular membranes and belong to the complement control protein family. (medscape.com)
- The efficiency sential y uniform after whole-body izing (i.e. removing electrons from) in causing damage and subsequent exposure to being highly heteroge- atoms or molecules of the medium biological effects is related not only neous in the case of non-uniform to the amount of energy transferred being traversed. (who.int)
Albumin5
- The research of my laboratory is focused on nucleic acid enzymology, nucleic acid protein interaction and more recently on the development of modified human albumin for the treatment of shock. (utoledo.edu)
- The rationale behind using polyethylene glycol-modified albumin is that this modified protein has a sufficiently large hydrodynamic radius that precludes its passing through defects in capillaries that occur in shock and is thus retained within blood vessels to maintain the oncotic gradient. (utoledo.edu)
- To test this hypothesis, an occupationally relevant dose of MDI (0.1%w/v) was reacted with varying concentrations of GSH (10µM-10mM), and the reaction products were characterized with regard to mass/structure, and ability to carbamoylate human albumin, a major carrier protein for MDI in vivo. (cdc.gov)
- The "self"-protein albumin in mouse airway fluid was uniquely modified by GSH-MDI at position 414K, a preferred site of MDI reactivity on human albumin. (cdc.gov)
- The 414K-MDI conjugation appears to covalently cross- link GSH to albumin via GSH's NH2-terminus, a unique conformation possibly resulting from cyclized mono(GSH)-MDI or asymmetric ( S , N -linked) bis(GSH)-MDI conjugates. (cdc.gov)
Denaturation3
- Thermal and chemical denaturation data indicated the design was significantly more stable than was the wild-type protein. (rcsb.org)
- It has a disulfide bond in its structure, so it has the natural property of strong stability, is extremely difficult to inactivate, and can quickly restore its conformation after thermal denaturation. (yeasenbiotech.com)
- The protein denaturation may occur if the pH is lower than 3. (lifetein.com)
Intrinsically2
- Intrinsically disordered regions (IDRs) lacking a fixed three-dimensional protein structure are widespread and play a central role in cell regulation. (iucr.org)
- The major constituent of LBs is aggregated α -synuclein ( α S), an intrinsically unfolded protein predominantly localized in the presynaptic regions of dopaminergic neurons. (hindawi.com)
Different conformations3
- Proteins often exist in different conformations as they work. (cornell.edu)
- alpha1AC inhibits the activity of proteases such as cathepsin G from neutrophils and chymases from mast cells by cleaving them into different conformations. (qedbio.com)
- Furthermore, different conformations of phage tail fibers correlated with the aforementioned orientations of the tails. (stanford.edu)
RNAs2
- This versatility can be harnessed, and RNAs are increasingly utilized to accurately monitor and control biological processes [19], leading to RNA being found at the core of modern therapeutics [18]. (dagstuhl.de)
- Such studies, coupled with mature computational methods for structure prediction [23], have paved the way for a rational design of RNAs targeting a wide diversity of biological function [8, 2, 13]. (dagstuhl.de)
Dynamics4
- For instance, many proteins share the same native structure yet their cellular dynamics and function, in other words their energy landscapes, are different. (berkeley.edu)
- A three-year, million-dollar grant from the W.M. Keck Foundation will fund an ambitious project, led by Weill Cornell Medicine , to develop a next-generation, high-speed atomic-force microscope (AFM), capable of capturing the dynamics of proteins in unprecedented detail. (cornell.edu)
- This will allow us to record protein dynamics that cannot be seen with current technology but can be crucial to understanding how these proteins work and how to target them with drugs. (cornell.edu)
- Given the tight relation between protein structure and function, we present a set of methods to analyze protein topology, implemented in the VLDP program, relying on Laguerre space partitions built from series of molecular dynamics snapshots. (nature.com)
Conformers2
- Due to specific influence on the system equilibrium high pressure can act as a filter that enables to identify and investigate higher energy protein conformers. (udg.edu)
- Serpins fold to a metastable native state and are susceptible to undergoing spontaneous conformational change to more stable conformers, such as the latent form. (proteopedia.org)
Soluble2
- Soluble CEACAM receptors were then found to catalyze S1 release [30,56], and biological relevance was subsequently established when soluble receptors were found to support infectious MHV entry into CEACAM-negative cells [44]. (globaltechbiz.com)
- More recently, using an MHV2 MGCD-265 (Glesatinib) strain, soluble CEACAM receptors generated SDS-resistant S protein trimers with unique lipophilicities and protease susceptibilities [57]. (globaltechbiz.com)
Extracellular1
- Because the approach can introduce virtually any chemical modification into both intracellular and extracellular regions of target proteins, we anticipate that it will overcome some of the drawbacks of other semi-synthetic or ribosome-dependent methods to engineer proteins. (biorxiv.org)
Valine1
Aggregation3
- A tetrameric form of α S has also been identified in human tissues that has been postulated as the inactive storage form of this structurally dynamic protein due to its aggregation resistance [ 6 , 7 ]. (hindawi.com)
- See also David Thirumalai's Emerging Ideas on the Molecular Basis of Protein and Peptide Aggregation ' (.pdf). (alzforum.org)
- The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. (cipsm.de)
Assemble1
Tertiary1
- The polypeptide interacts with water, thus placing thermodynamic pressures on these regions which then aggregate or "collapse" into a tertiary conformation with a hydrophobic core. (wikipedia.org)
Molecular3
- DNA is often compared to a twisted ladder consisting of two strands connected by molecular rungs called "bases," which are known by the abbreviations A, T, G and C. Lengthier DNA sequences code for genes, which contain explicit instructions for building a specific protein. (sciencedaily.com)
- Identifying the molecular states relevant to protein functioning is necessary for our understanding of biological processes. (biorxiv.org)
- Among the process, the degree of hydrolysis (DH) and molecular weight distribution (MWD) of protein hydrolysates are two important parameters that need to be monitored. (bvsalud.org)
Myoglobin1
- The reason why Peter Lansbury and others used the term 'natively unfolded' for a-synuclein and other proteins, especially peptides, is that they do not exist, to a significant degree, in the same kind of stable structure that larger native proteins like myoglobin do. (alzforum.org)
Atoms3
- A Stanford University research team has designed the first microscope sensitive enough to track the real-time motion of a single protein down to the level of its individual atoms. (sciencedaily.com)
- We model a protein as a network of atoms connected by springs and deform it along the least-energy directions. (biorxiv.org)
- Stable carbon atoms that have the same atomic number as the element carbon, but differ in atomic weight. (lookformedical.com)
Stability3
- This maintains the stability of the structure within localized segments of the protein. (wikipedia.org)
- We have found that although protein stability can be altered by single amino acid substitution, evolution for optimal function requires more subtle and delocalized mechanisms.Recent results implicate structure in the unfolded state as playing an important and novel role for the thermostability of these proteins. (berkeley.edu)
- Disulfides in proteins play an important role in the maintenance of biological activity and conformational stability. (lifetein.com)
Processes3
- The GPCR superfamily plays a central role in many biological processes and is linked to a wide range of disease areas. (centerwatch.com)
- Such non-native states on the energy landscape are thought to play a determining function in many cellular processes such as translocation, protein synthesis, degradation, signaling and allostery. (berkeley.edu)
- For example, ion-channel proteins, which are fundamentally important in many biological processes, have multiple conformations including "open" and "closed" conformations. (cornell.edu)
Ribonuclease1
- Our use of different hydrogen exchange methods to study three different types of intermediates of E. coli ribonuclease H (the acid molten globule, the higher energy conformations of the native state and a kinetic folding intermediate) has been particularly powerful. (berkeley.edu)
Prion protein2
- Before clinical signs were noted, we detected a non-type 2B signature, indicating the existence of atypical prion protein during the incubation period. (cdc.gov)
- Schematic diagram of the mature nonglycosylated prion protein and below amino acid sequences of the human and the simian prion polypeptide chain. (cdc.gov)
Vivo3
- Here, we describe further development of an in vivo library selection platform based on self-assembling protein nanoparticles encapsulating their own mRNA genomes (synthetic nucleocapsids or synNCs). (uw.edu)
- Here, using a monomeric E. coli LptA mutant, we first show in vivo that a stable LptA oligomeric form is not strictly essential for bacteria. (nih.gov)
- Our findings suggest that Lhp1 may rely on other proteins in vivo to rescue activity after cycles of duplex unwinding. (utexas.edu)
Transcription1
Folding13
- Correct protein folding is integral to proper functionality within biological systems. (wikipedia.org)
- The driving force behind protein folding is not well understood, hydrophobic collapse is a theory, one of many, that is thought to influence how a nascent polypeptide will fold into its native state. (wikipedia.org)
- Hydrophobic collapse can be visualized as part of the folding funnel model which leads a protein to its lowest kinetically accessible energy state. (wikipedia.org)
- The polypeptide will continue folding into lower energy states as long as these conformations are kinetically accessible. (wikipedia.org)
- Protein folding is one of the fascinating unanswered questions in biology. (anl.gov)
- This highly specialized protein folding process has attracted the attention of a team of researchers who have used this bacterial system as a model to determine what allows these unique proteins to maintain their disordered state in the periplasm. (anl.gov)
- The authors believe their work will provide important information toward understanding basic questions of protein folding and tests long-held theories about how this remarkable biological process works. (anl.gov)
- Going forward, the team will test the extent of collapse in an even wider range of sequences, to more fully understand the importance of maintaining a highly expanded conformation prior to folding. (anl.gov)
- Understanding the sequence determinants of the energy landscape is therefore fundamental to the biological process that proteins carry out as well as protein folding itself. (berkeley.edu)
- This hypothesis unites a lot of work in the field of and has also provided insight and experimental tests for current theoretical work on protein folding. (berkeley.edu)
- Our studies on the mechanism of folding include investigating the role of topological complexity using permuted proteins, the nature and function of folding intermediates, and studies on the role of mechanical unfolding using single molecule measurements. (berkeley.edu)
- Protein Folding and Neurodegeneration: Biophysics to the Rescue? (alzforum.org)
- This does not change our view of protein folding in the least. (alzforum.org)
Hydrophobic2
- The formation of amyloid fibrils, insoluble aggregates of hydrophobic protein can lead to a myriad of diseases including Parkinson's and Alzheimer's disease. (wikipedia.org)
- This observation has led them to try and understand how proteins with high hydrophobic ratios can maintain these extended conformations. (anl.gov)
Function11
- More generally, RNA design addresses the generation of sequences of nucleotides targeting a given biological function. (dagstuhl.de)
- Therefore, the function of the N terminus in tengpin resembles protein cofactors that prevent mammalian serpins from spontaneously adopting the latent conformation. (proteopedia.org)
- Homeodomain-interacting protein kinase-2 (HIPK2) is a positive regulator of p53 oncosuppressor function. (aacrjournals.org)
- The Schizosaccharomyces pombe Cdc4 protein is required for the formation and function of the contractile ring, presumably acting as a myosin light chain. (ubc.ca)
- Manipulation of proteins by chemical modification is a powerful way to decipher their function or harness that function for therapeutic purposes. (biorxiv.org)
- We insert synthetic peptides into proteins of interest via tandem protein trans-splicing using two orthogonal split intein pairs and validate our approach by investigating different aspects of GFP, Na V 1.5 and P2X2 receptor function. (biorxiv.org)
- Chemical or genetic engineering of proteins provides great potential to study protein function and pharmacology or to generate proteins with novel properties. (biorxiv.org)
- This would fundamentally change our conventional thinking about protein structure-function relationship, no? (alzforum.org)
- I do not think there is a contradiction to the conventional thinking of protein structure-function relation. (alzforum.org)
- An unnatural amino acid that is used experimentally to study protein structure and function. (lookformedical.com)
- Biological Function Although its physiological function is unclear, it can inhibit neutrophil cathepsin G and mast cell chymase, both of which can convert angiotensin-1 to the active angiotensin-2. (qedbio.com)
Adopts2
- The systematic description of the variety of shapes a protein adopts under particular environmental conditions, upon post-translational modifications and/or partner binding still remains out of reach. (biorxiv.org)
- Deletion of this domain creates a variant--tengpinDelta51--which folds past the native state and readily adopts the latent conformation. (proteopedia.org)
Nucleic acid1
- Nucleic acid having higher density finds place as 'core', medium denser protein in intermediate and least dense fat in the periphery. (webmedcentral.com)
Sequence5
- Our goal was to compute a stable, full-sequence design of the Drosophila melanogaster engrailed homeodomain. (rcsb.org)
- A single misplaced letter in gene's DNA sequence--a G substituted for a T, for example--can produce a defective protein that may cause a serious disease. (sciencedaily.com)
- Proteins undergo an incredible transformation from one-dimensional sequence information into complex three-dimensional shapes that carry out intricate cellular functions. (berkeley.edu)
- In addition to the native conformation, a protein sequence populates small fluctuations around the native state, partially unfolded forms and even the globally unfolded conformation. (berkeley.edu)
- The smaller replication proteins, Rep40 and Rep52, require ATP to bind DNA, show no sequence specificity in DNA binding and lack the N-terminal nuclease domains. (utoledo.edu)
Cellular2
- The etiology of Parkinson's disease (PD) is linked with cellular inclusions in the substantia nigra pars compacta region of the brain that are enriched in the misfolded presynaptic protein α -synuclein ( α S) and death of the dopaminergic neurons. (hindawi.com)
- They have a wide cellular and tissue distribution, and play a major role in the mediation of biological responses. (medscape.com)
Lipid1
- Recent years have seen strong research efforts on the lipid component of biological membranes. (lu.se)
Biophysical2
- We have taken a proteomic and biophysical approach to understand how a protein fine-tunes its landscape to control this feature. (berkeley.edu)
- Hydrostatic pressure in range 0.1-1.5 GPa is used to modify biological system behaviour mostly in biophysical studies of proteins in solution. (udg.edu)
Structure9
- Proteins perform extremely specific functions which are dependent on their structure. (wikipedia.org)
- Our method guaranties preservation of the protein structure during the transition and allows to access conformations that are unreachable with classical normal mode analysis. (biorxiv.org)
- This allows us to produce a wide range of motions, some of them previously inaccessible, and to preserve the structure of the protein during the motion. (biorxiv.org)
- Nevertheless, experimental protein structure determination remains a time consuming and costly process. (biorxiv.org)
- DoGSiteScorer is a grid-based method that uses a Difference of Gaussian filter to detect potential binding pockets 1 - solely based on the 3D structure of the protein - and splits them into subpockets. (proteins.plus)
- This is referred to as the primary structure of proteins . (lookformedical.com)
- So the coordinates for quaternary structure of a protein should calculate from the coordinate of the subunit. (amrita.edu)
- Disulfide bonds are an integral component of the three-dimensional structure of many proteins. (lifetein.com)
- Modification of the cysteine using Acm blocks disulfide bond formation, but retains the cysteine and preserves the primary structure of the protein. (lifetein.com)
Crystallography1
- While X-ray crystallography captures single stable states, cryo-EM allows observing conformational ensembles in solution. (biorxiv.org)
Disulfide1
- A disulfide bridge is created when a sulfur atom from one cysteine forms a single covalent bond with another sulfur atom from a second cysteine residue located in a different part of the protein. (lifetein.com)
Structurally2
- A molecule in solution can be viewed as a structurally heterogeneous ensemble, where a finite number of conformational states ( e.g . active-inactive, bound-unbound) may become stable under certain conditions to perform specific tasks. (biorxiv.org)
- By using NMR spectroscopy, we demonstrate that purified Cdc4p is a monomeric protein with two structurally independent domains, each exhibiting a fold reminiscent of the EF-hand class of calcium-binding proteins. (ubc.ca)
Pathogenic2
- The system involves the study of what are termed autotransporter proteins, which pathogenic bacteria secrete as virulence factors for infection. (anl.gov)
- This study tests the hypothesis that glutathione (GSH) reacts with MDI to form quasi-stable conjugates, capable of mediating the formation of MDI-conjugated "self" protein antigens, which may participate in pathogenic inflammatory responses. (cdc.gov)
Polypeptides1
- Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. (lookformedical.com)
Physiologically1
- When we're taught biochemistry, we see proteins in their physiologically active forms. (alzforum.org)
Inactive1
- The experiments showed that in the inactive form, the two ends of the protein form a sheet that closes a key site on the protein and prevents it from changing into its active form. (elifesciences.org)
Enzymes1
- The stable nature of these enzymes makes them resistant to numerous decontamination methods, often requiring aggressive chemical methods to eliminate RNases from surfaces and solutions. (yeasenbiotech.com)
Native3
- In this case, a native conformation does not have to be at the lowest energy trough of the diagram as shown, it must simply exist in its natural and kinetically accessible conformation in biological systems. (wikipedia.org)
- This assembly results in a spontaneous, essentially traceless splicing reaction that covalently links the two flanking protein segments through native chemical ligation 9 . (biorxiv.org)
- Shortly after SARS-CoV emerged at the turn of the 21st century, the spike (S) protein (particularly in its native conformation) was identified as the immunodominant antigen of the virus3. (who.int)
Receptors4
- Effector proteins interacting with the Fc portion of immunoglobulin M (IgM) include complement and complement receptors. (medscape.com)
- Partial or complete deficiencies of the components of the complement system, including its receptors and regulatory proteins, are now described in humans and may be of a genetic or familial origin or acquired. (medscape.com)
- Defects in the expression of complement or complement receptors may result in loss of tolerance to self-proteins and the development of immune complex-mediated autoimmune diseases such as systemic lupus erythematosus (SLE). (medscape.com)
- Among healthy individuals, the number of CR1 receptors on the red blood cells varies widely, yet the phenotypic expression, regulated by 2 codominant alleles, is stable. (medscape.com)
Synthesis1
- A transfer RNA which is specific for carrying leucine to sites on the ribosomes in preparation for protein synthesis. (lookformedical.com)
Form4
- form, usually the most stable one. (equimount.com)
- The protein then switches to an active form when DNA damage is detected to trigger the process of cell self-destruction. (elifesciences.org)
- However, this closed form can be thought of as being like a spring-loaded trap - it doesn't take much energy to spring the trap and open the protein into its active form. (elifesciences.org)
- This means that once the switch to the active form is triggered there is no delay waiting for other proteins to be made, which makes oocytes extremely sensitive to DNA damage. (elifesciences.org)
Interact1
- Due to their large surface area and ability to interact with proteins and peptides, graphene oxides offer valuable physiochemical and biological features for biomedical applications and have been successfully employed for optimizing scaffold architectures for a wide range of organs, from the skin to cardiac tissue. (mdpi.com)
Genetic3
- In the Nature study, Block and his colleagues tackled a fundamental principal of biology known as the central dogma, which states that in living organisms, genetic information flows from DNA to RNA to proteins. (sciencedaily.com)
- The events in signal transduction that govern MMP expression and activity and expression of inhibitory proteins are crucial for understanding wound healing, tumorigenesis, and certain genetic diseases. (stanford.edu)
- Mounting evidence suggests that the genetic disorders/mutation and diseases change not only the protein expression patterns but also membranes themselves. (lu.se)
MRNA1
Translocation1
- Preexisting antivector immunity can severely compromise the ability of Salmonella enterica serovar Typhimurium live vaccines to induce protective CD8 T-cell frequencies after type III secretion system-mediated heterologous protein translocation in orally immunized mice. (cipsm.de)