• The HBsAg amino acid sequence contains a highly base-pairing errors can be generated per day over the conformational, hydrophilic domain from positions 100 to 3,200-bp genome ( 6 ). (cdc.gov)
  • Such buried ionizable groups destabilize the protein and may trigger conformational changes in response to pH variations. (lu.se)
  • On the other hand, the MRD data are consistent with a local conformational change in response to ionization of the internal residues. (lu.se)
  • We proposed to utilise CIDNP kinetics in proteins to determine the paramagnetic nuclear relaxation times and use them for site-specific determination of correlation times of intramolecular mobility of residues in different conformational states on the nanosecond time scale. (europa.eu)
  • CABS-flex 2.0 implements an efficient simulation engine that allows for modeling of large-scale conformational transitions of protein systems. (edu.pl)
  • Assessing the conformational changes of pb5, the receptor-binding protein of phage T5, upon binding to its Escherichia coli receptor FhuA. (ibs.fr)
  • On the other hand, current computational molecular interaction prediction approaches are unsuitable for interactome prediction as they are either computationally intractable when attempted on large molecules such as proteins due to their inability to sample the entire conformational space or produce inaccurate results due to their inability to distinguish binding from non-binding protein pairs. (hhs.gov)
  • Its six backbone torsion angles and glycosidic bond between base and ribose provide conformational dynamics not afforded by the peptide bond of proteins and more flexibility than the DNA backbone. (datexis.com)
  • An Active Site Inhibitor Induces Conformational Penalties for ACE2 Recognition by the Spike Protein of SARS-CoV-2. (acs.org)
  • The structure of a peptide antigen corresponding to the subtype P1.7 variant of the porin PorA from the human pathogen Neisseria meningitidis was determined by solution of the X-ray crystal structure of the ternary complex of the peptide (ANGGASGQVK) in complex with a Fab fragment and a domain from streptococcal protein G to 1.95 A resolution. (rcsb.org)
  • The peptide adopted a beta-hairpin structure with a type I beta-turn between residues Gly4P and Gly7P, the conformation of the peptide being further stabilised by a pair of hydrogen bonds from the side-chain of Asn2P to main-chain atoms in Val9P. (rcsb.org)
  • Recognition was supplemented by hydrogen bonds from heavy chain residues Thr50H, Asp95H, Leu97H and Tyr100H to main-chain and side-chain atoms in the peptide. (rcsb.org)
  • Human alpha(2)-macroglobulin-proteinase complexes bind to their receptor, the lowdensity lipoprotein receptor-related protein (LRP), through a discrete138-residue C-terminal receptor binding domain (RBD), which also binds to thebeta-amyloid peptide. (embl.de)
  • Therefore, we attempt to check whether we'd elicit ligand-dependent behavioural reactions in em C. elegans /em by expressing mammalian GPCRs in the ASH and ADL gustatory neurons, because they are straight exposed to the surroundings allowing gain access to of proteins and peptide ligands towards the heterologous receptors. (exposed-skin-care.net)
  • Cambinol Our primary data reveal that while protein-peptide connections make better general use of user interface surface area pockets on the proteins partners in comparison to various other classes of relationship (Fig.?3a), connections between two globular protein Cambinol often utilize deep relationship sites (Fig.?3b), only if with a little pocket installing an individual residue also. (gasyblog.com)
  • This option has been used in protein-peptide docking to protein receptor with flexible regions of significant length. (edu.pl)
  • Functional recognition of the modified human tRNA(UUU)(Lys3) anticodon domain by HIV's nucleocapsid protein and a peptide mimic. (ncsu.edu)
  • The antibacterial peptide pyrrhocoricin inhibits the ATPase actions of DnaK and prevents chaperone-assisted protein folding. (research.com)
  • Structural Basis for Phosphotyrosine Peptide Recognition by Protein Tyrosine Phosphatase 1B. (molmovdb.org)
  • The strategy therefore promises reliable automated user- independent protein identification using peptide mass fingerprints. (lu.se)
  • The standard experiment is to separate the proteins, e.g. by 2D gel electrophoresis, digest the proteins with a highly specific enzyme, measure the masses of the peptide fragments with a mass spectrometer (typically a MALDI-TOF mass spectrometer) and then compare the peptide monoisotopic masses with expected monoisotopic masses from a database (protein or DNA database). (lu.se)
  • Thus, the principle of protein or peptide haptenation could be used in in vitro assays to predict the sensitization potential of a new chemical entity. (cdc.gov)
  • Effective encoding of residue contact information is crucial for protein structure prediction since it has a unique role to capture long-range residue interactions compared to other commonly used scoring terms. (biomedcentral.com)
  • Among various structure-based terms, residue-residue contact potentials[ 21 - 23 ] are unique in that they capture long-range interactions in a protein structure[ 24 ]. (biomedcentral.com)
  • Trans- encoded sRNAs form imperfect base-pairing interactions with complementary sequences in their mRNA targets, which are often located at or near ribosome binding sites (RBS), but can also be located upstream of the translation start site as well as deep in the coding regions (CDS) [ 2 ]. (biomedcentral.com)
  • Such interactions generally result in a decrease in protein synthesis, either by stimulating mRNA degradation or by inhibiting translation. (biomedcentral.com)
  • The eponymous FinO protein was discovered as a regulator of F plasmid conjugation nearly 50 years ago, and acts to bind a single partner sRNA called FinP to stabilize FinP and facilitate its interactions with its antisense partner, the mRNA encoding the major F plasmid transcription factor, TraJ 5 . (nature.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)
  • The basic enzymatic activities and protein composition of these high-molecular mass complexes have been under intense study, but their specific protein interactions with functional pre-mRNA/gRNA substrates remains unknown. (tamu.edu)
  • All four interactions are stimulated by unpaired residues just 5' of the pre-mRNA/gRNA anchor duplex, but strongly inhibited by pairing of the editing site region. (tamu.edu)
  • This apparent structural selectivity suggests that the RNA-protein interactions we observe may be involved in recognition of editing sites and/or catalysis in assembled complexes. (tamu.edu)
  • Exploration of the supramolecular interactions involving tris-dipicolinate lanthanide complexes in protein crystals by a combined biostructural, computational and NMR study. (ibs.fr)
  • The D-loop is somewhat small and lacks the G residues at positions 18 and 19 that facilitate interactions with the T-loop in the tertiary structure. (ncsu.edu)
  • Because IgSF proteins function in immunity by specific trans-cellular noncovalent interactions between antigen-presenting cells and T cells, a molecular-level understanding of IgSF:IgSF binding interfaces would be of great aid to the design of novel immunomodulatory therapeutics. (hhs.gov)
  • Protein interactions of homeodomain proteins. (embl.de)
  • The recent structural determinations and biochemical analysis of several multimeric complexes have provided a better understanding of how protein interactions influence the DNA-binding activity of homeodomain proteins. (embl.de)
  • Marti, D. N. & Bosshard, H. R. Electrostatic interactions in leucine zippers: thermodynamic analysis of the contributions of Glu and His residues and the effect of mutating salt bridges. (uzh.ch)
  • Replacements that favored (Q44R) or impaired (Q44D) the polar interactions predicted between residues Q44 and D32 did not abolish dimer formation of transiently expressed 3A, indicating that these interactions are not critical for 3A dimerization. (asm.org)
  • Evolution of robustness in gene networks (Protein-DNA interactions, structure based prediction of DNA binding motifs. (einsteinmed.edu)
  • Target sequences cleaved by REases are recognized through protein-DNA interactions, and are intrinsic to the structure of each enzyme. (fredhutch.org)
  • The principal alpha-helix containstwo lysine residues on the outer face that are known to be essential for receptorbinding. (embl.de)
  • To examine the role of water penetration, we have measured the 17O and 2H magnetic relaxation dis- persions (MRD) for the V66E and V66K mutants of staphylococcal nuclease, where glutamic acid and lysine residues are buried in predominantly apolar environments. (lu.se)
  • Although protein structures have been solved by experiments at an increasing rate, a flood of new sequences have been determined even more rapidly due to the advance of sequencing technologies[ 6 , 7 ]. (biomedcentral.com)
  • For instance, analysis of proteins in the manner of displaying their structures. (projectguru.in)
  • If the observation-to-parameter ratio is small, for example when diffraction data only extend to low resolution, the Bayesian framework implemented in REFMAC 5 uses external restraints to inject additional information extracted from structures of homologous proteins, prior knowledge about secondary-structure formation and even data obtained using different experimental methods, for example NMR. (iucr.org)
  • The structures of the Drosophila Paired homodimer and the yeast a1/alpha2 heterodimer bound to DNA, along with a high-resolution study of a Drosophila eve-DNA complex, have deepened our understanding of how homeodomains locate their DNA targets. (embl.de)
  • Here, we investigate the structural basis for RNA recognition by ProQ/FinO proteins, through the crystal structure of the ProQ/FinO domain of the Legionella pneumophila DNA uptake regulator, RocC, bound to the transcriptional terminator of its primary partner, the sRNA RocR. (nature.com)
  • A pair of antiparallel β-strands is located between TM3 and TM10 and has an important role in structural organization and substrate recognition. (rhea-db.org)
  • The technique had high potential for determining the structural and magnetic resonance properties and the reactivity of the radicals of proteins, nucleic acids and their building blocks. (europa.eu)
  • Combining NMR and small angle X-ray and neutron scattering in the structural analysis of a ternary protein-RNA complex. (ibs.fr)
  • The structural and functional integrity of this overhang is based on its association with a constellation of specific proteins, some of them belonging to the shelterin complex [ 10 ]. (hindawi.com)
  • To accomplish this goal, we will first combine structural similarity-based and sequence-based approaches along with hidden Markov model profile-based functional sub-classification of the IgSF to identify the binding interfaces of IgSF proteins. (hhs.gov)
  • Crystal structure of a paired domain-DNA complex at 2.5 A resolution reveals structural basis for Pax developmental mutations. (embl.de)
  • The viral genome encodes four structural capsid proteins (VP1 to VP4) and seven nonstructural (NS) proteins, the leader Lb/ab protease, and proteins encoded in the P2 (2B and 2C) and P3 (3A, 3B, 3C, and 3D) regions ( 9 ). (asm.org)
  • To determine the structural organization of BbvCI, and the basis for asymmetric recognition and enzymatic activity, the authors identified its remaining catalytic site residues and crystalized the intact enzyme. (fredhutch.org)
  • We are moving on to structural analyses of far larger and more complex restriction-modification systems, including one that brings together multiple copies of several protein subunits harboring DNA recognition, DNA methylation, and DNA cleavage activities. (fredhutch.org)
  • For capturing contacts between neighboring β strands, considering the distance between Cα atoms is better than the Cβ−based distance because the side-chain of interacting residues on β strands sometimes point to opposite directions. (biomedcentral.com)
  • G-rich DNA strands are naturally involved in duplex-DNA architecture through association with their complementary C-rich DNA strands by the canonical Watson-Crick pairing [ 1 - 3 ]. (hindawi.com)
  • Indeed, given that four guanine residues can self-associate in a planar arrangement through a Hoogsteen-type hydrogen-bonding network [ 4 ] to form a structure called G-quartet, G-rich strands can adopt a peculiar three-dimensional arrangement called G-quadruplex DNA [ 5 - 9 ] resulting from the stacking of several contiguous G-quartets (Figure 1 ). (hindawi.com)
  • Analyses of PPI interfaces using brand-new computational equipment can identify crucial residues in interfaces mediating the proteinCprotein relationship (Pires et?al. (gasyblog.com)
  • Our goal is to develop a computational method that can be used to identify interacting IgSF receptor-ligand pairs. (hhs.gov)
  • We are developing a computational approach to model proteins for which a limited number of experimental restraints are available. (einsteinmed.edu)
  • To investigate the DNA-recognition ability of the enzyme, the authors performed homology-based modeling and computational docking utilizing mutation of specific residues. (fredhutch.org)
  • Conceptual parallels exist between bacterial and eukaryotic small-RNA (sRNA) pathways, yet relatively little is known about which protein may recognize and recruit bacterial sRNAs to interact with targets. (biomedcentral.com)
  • Like microRNAs (miRNAs) in eukaryotes, trans -acting bacterial sRNAs appear to recognize their targets by a seed-pairing mechanism using seeds as small as 6-7 nucleotides. (biomedcentral.com)
  • Insight into how these proteins recognize their cognate RNAs initiated with FinO. (nature.com)
  • A remaining problem is certainly to recognize how better to utilise the depth utilized by PPI partner proteins in the introduction of chemical substance modulators. (gasyblog.com)
  • This modification may play a role in the unusual codon recognition requirements of this tRNA, which must recognize both AUG and AUA codons. (ncsu.edu)
  • The new paper in PLOS Genetics describes for the first time how PPR proteins recognize their RNA targets via an easy-to-understand code. (scitechdaily.com)
  • Most REases of its type are either homodimers (constructed of two identical enzyme subunits, that recognize and cleave a palindromic DNA target site) or gene-fused, pseudo-symmetric monomers (constructed of a single protein chain containing two consecutive, closely related enzyme domains, that recognize and cleave a non-palindromic DNA target). (fredhutch.org)
  • 1996 for mercury phytoremediation, with respect to its homologous protein sequences. (projectguru.in)
  • Not only does RNA translate the genetic code decoding it into protein, but it also has various catalytic and regulatory functions yet to be completely elucidated. (datexis.com)
  • Neural retina-specific leucine zipper proteins belong to this family. (wikipedia.org)
  • Marti, D. N., Jelesarov, I. & Bosshard, H. R. Interhelical ion pairing in coiled coils: solution structure of a heterodimeric leucine zipper and determination of pKa values of Glu side chains. (uzh.ch)
  • At neutral pH, where these residues are uncharged, we find no evidence of buried water molecules near the mutation site. (lu.se)
  • The defective aminoacylation of the 8U→C hmtRNAMet made it difficult to assess the effects of the mutation on additional steps in protein biosynthesis. (ncsu.edu)
  • A proton-coupled folate transporter mutation causing hereditary folate malabsorption locks the protein in an inward-open conformation. (einsteinmed.edu)
  • Search proteins in UniProtKB for this molecule. (rhea-db.org)
  • Because a uniform dielectric ionizable group in a protein relative to the pKa value of the continuum model is a very crude description of the highly same group in a small reference molecule in dilute aqueous heterogeneous protein interior, the dielectric coefficient, eP, solution. (lu.se)
  • A molecular model of a PPR protein recognizing a specific RNA molecule. (scitechdaily.com)
  • The identity of specific amino acid residues in the protein (colored sticks) determines the sequence of the RNA molecule it can bind. (scitechdaily.com)
  • Within this series, a HCL Salt rise in the overall hydrophobicity from the molecule improved the capability to stop the TRPM8 activation, permitting the recognition of substituents and amino acidity residues that resulted in selective modulators. (conferencedequebec.org)
  • The viral particle is composed of a protein capsid that contains a positive-sense RNA molecule of about 8,500 nucleotides that is infectious and encodes a single polyprotein, which is processed in infected cells by cis - and trans -acting viral proteases ( 55 ) to yield different polypeptide precursors and the mature viral proteins ( 9 , 62 ). (asm.org)
  • The tertiary structure of proteins provides crucial information for understanding molecular mechanisms of biological functions. (biomedcentral.com)
  • A proper encoding of residue contact information is crucial for structure prediction because in principle, a full distance map or a residue contact map has sufficient information for reconstructing the tertiary structure of a protein[ 25 ]. (biomedcentral.com)
  • One mutant (H238N) loses binding, which can be explained by a rearrangement of the Arg(222) and Asp(385) residues, which are crucial for specific collagen recognition. (uni-koeln.de)
  • NS proteins are involved in crucial aspects of the viral cycle and pathogenesis, such as rearrangements of intracellular membranes required for endomembrane recruitment and the lysis of host cells ( 1 , 12 , 14 , 18 , 73 ). (asm.org)
  • More recently, the application of RNA-seq technologies has enabled the elucidation of the biological partners and targets of several ProQ/FinO family proteins. (nature.com)
  • Key regulators identified in this context include the STAT1:STAT2 heterodimer and interferon regulatory factor family proteins. (bvsalud.org)
  • A conformation- and phosphorylation-dependent antibody recognizing the paired helical filaments of Alzheimer's disease. (research.com)
  • The morph shows the 334-residue sequence of the query (FtsZ) changing from the query conformation to the conformation of the superposed target (tubulin). (proteopedia.org)
  • As with mammalian systems, GPCRs play a significant part in the recognition of sensory 1062368-24-4 supplier indicators, and these indicators are relayed in the cell by heterotrimeric G protein. (exposed-skin-care.net)
  • They are members of the rBAT family of mammalian proteins (TC #8.A.9). (tcdb.org)
  • The hmtRNAMet serves both in translational initiation and elongation in human mitochondria making this tRNA of particular interest in mitochondrial protein synthesis. (ncsu.edu)
  • The mitochondrial genome encodes 13 proteins necessary for energy production, two rRNAs and all of the 22 tRNAs required for the synthesis of these proteins (1Attardi G. Int. Rev. Cytol. (ncsu.edu)
  • Aminoacylation is an early step required for the tRNA to be used in either the elongation or initiation phase of protein synthesis and is thus of central importance for protein synthesis in mitochondria. (ncsu.edu)
  • Specific modifications commonly found at the junction of the stems of the cloverleaf structure (Figure 1), referred to as the core, elbow or hinge in the three-dimensional structure of most tRNAs, are often associated with functional folding, allowing tRNAs to fold into the common L-shape form critical to ribosomal protein synthesis. (datexis.com)
  • The structure reveals specific recognition of the 3' nucleotide of the terminator by a conserved pocket involving a β-turn-α-helix motif, while the hairpin portion of the terminator is recognized by a conserved α-helical N-cap motif. (nature.com)
  • Unique Alzheimer's disease paired helical filament specific epitopes involve double phosphorylation at specific sites. (research.com)
  • Based on the statistical analysis, a set of frequently occurring sequence motifs, which GSK343 cost are different from the and (14), we found that in the promoter open complexes, these non-typical UP elements are located close to the C-terminal end of the CTD helix IV instead of the helix I for common UP element recognition. (mingsheng88.org)
  • Available at: https://www.projectguru.in/multiple-sequence-alignment-studies-mera-protein-sequence/ [Accessed 03 Dec. 2023]. (projectguru.in)
  • Kapagunta, Chandrika, and Priya Chetty "Multiple sequence alignment studies of merA protein sequence. (projectguru.in)
  • In this article, the protein sequence of merA enzyme is studied with respect to its closely related sequences found in NCBI database, through Multiple Sequence Alignment (MSA) . (projectguru.in)
  • The purpose of multiple sequence alignment is to characterize protein families. (projectguru.in)
  • It also determines the consensus sequence of the aligned sequences and reveals biological facts about proteins. (projectguru.in)
  • The minor loop is short lacking the usual G47, and the T-stem has two adjacent pyrimidine:pyrimidine pairs (U-U and U-:). Furthermore, the T-loop lacks the T:C sequence and contains only six nucleotides instead of the normal seven. (ncsu.edu)
  • Because a major determinant in the recognition of tRNAMet by the MetRS is thought to lie in the anticodon sequence that is unchanged (36Schulman L.H. Pelka H. Science. (ncsu.edu)
  • The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc. (embl.de)
  • A beta-hairpin comprising the nuclear localization sequence sustains the self-associated states of nucleosome assembly protein 1. (colorado.edu)
  • What's more, we can now design our own synthetic proteins to target any RNA sequence we choose - this should allow us to control the expression of genes in new ways that just weren't available before. (scitechdaily.com)
  • Crystallographic models of proteins with about 50% sequence identity differ by about 1 Å RMSD [3] [4] . (proteopedia.org)
  • was generated by FATCAT , which reported 3.02 Å RMSD for 298 superposed residues, and 10.2% sequence identity for the superposed residues. (proteopedia.org)
  • Isolation-induced decreases in PDE11A4 expression appear to be functional as social isolation elicited changes in PDE11A-relevant signal transduction cascades (i.e., decreased pCamKIIα and pS6-235/236) and behavior (i.e., increased remote long-term memory for social odor recognition). (frontiersin.org)
  • We hypothesize that each receptor interface can be characterized by a unique spatial fingerprint-an extended pharmacophore which we will call the residue-specific functional atom field (rsFAF)-which represents the energetically favorable positions of key functional atoms and can be used to identify cognate ligands. (hhs.gov)
  • The ability of RNA to form protonated base pairs and triples at acidic pH suggests that standard base pairing may not have been a dominant requirement of the early RNA world. (biomedcentral.com)
  • These replacements also led to production of infective viruses that replaced the acidic residues introduced (E) by nonpolar amino acids, indicating that preservation of the hydrophobic interface is essential for virus replication. (asm.org)
  • Next using molecular dynamics simulations, we will sample the potential energy landscape of target receptor IgSF protein binding interfaces and design an optimal complementary ligand protein interface, which will then be evaluated to fit existing IgSF proteins. (hhs.gov)
  • Jelesarov, I. & Bosshard, H. R. Isothermal titration calorimetry and differential scanning calorimetry as complementary tools to investigate the energetics of biomolecular recognition. (uzh.ch)
  • Small angle neutron scattering for the study of solubilised membrane proteins. (ibs.fr)
  • Change of dynamics of raft-model membrane induced by amyloid-beta protein binding. (ibs.fr)
  • This includes the early recognition of these immunogenic membrane proteins that can serve as diagnostic markers, and the targeting of such markers for the destruction of the tumor, primarily thru ADCC. (jcancer.org)
  • The monoclonals (mAbs) that we have developed against specific immunogenic tumor membrane proteins have been studied in detail. (jcancer.org)
  • We were also able to define immunogenic membrane proteins from lung (squamous and adenoCa) as well as prostate neoplasms. (jcancer.org)
  • in poliovirus (PV), the interaction between the RNA replication complex and intracellular membranes appears to be accomplished by proteins 3A and 2C, which have membrane-binding properties ( 11 , 60 ). (asm.org)
  • CABS-flex method can be used as a component of methods for structure-based prediction of protein aggregation properties. (edu.pl)
  • Moreover, the evolutionary relationship of useful proteins and enzymes in bioremediation processes are identifiable across different species. (projectguru.in)
  • We've distinguished between connections of protein including enzymes with peptides on the main one hand, and heterologous and homologous globular relationship interfaces in the various other. (gasyblog.com)
  • Among them, macrocycles rapidly became popular for recognition of quadruplexes motivated by the fact that telomestatin is one of the most active known G-quadruplex ligands [ 33 ]. (hindawi.com)
  • RadA within a proteins oligomeric filament displaying the similarity from the user interface with that from the RAD51 BC4 complicated. (gasyblog.com)
  • Structure-guided mutagenesis reveals key RNA contact residues that are critical for RocC/RocR to repress the uptake of environmental DNA in L. pneumophila . (nature.com)
  • The nucleobase/ascorbate transporter (NAT) proteins, also known as nucleobase/cation symporter 2 (NCS2) proteins, are responsible for the uptake of nucleobases in all kingdoms of life and for the transport of vitamin C in mammals. (rhea-db.org)
  • 101: 15070-15075Crossref PubMed Scopus (205) Google Scholar).Normally, protein biosynthetic systems have two tRNAMet species. (ncsu.edu)
  • This discovery was made in plants but is applicable across many species as PPR proteins are found in humans and animals too," says Professor Bond. (scitechdaily.com)
  • Replacements L38E and L41E, involving charge acquisition at residues predicted to contribute to the hydrophobic interface, reduced the dimerization signal in the protein ligation assay and prevented the detection of dimer/multimer species in both transiently expressed 3A proteins and in synthetic peptides reproducing the N terminus of 3A. (asm.org)
  • The basis of hapten- molecular mechanisms of the sensitization pro- protein binding work is the hypothesis that upon cess will result in novel opportunities for the skin absorption, only protein-reactive chemicals development of alternative methods for assessing (or those that can be metabolically or chemically skin sensitization hazard and relative potency of converted to protein-reactive species) are able to chemicals. (cdc.gov)
  • The protein sample was dialyzed against 2 volumes of 500 ml of dialysis buffer (50 mm Tris-HCl, pH 7.6, 50 mm KCl, 2.5 mm MgCl2, 0.1 mm EDTA, 10% glycerol and 7 mm ;ME) for 1 h.Cells carrying a plasmid encoding the His6-tagged human mitochondrial MetRS were grown as described (23Spencer A.C. Heck A.H. Takeuchi N. Watanabe K. Spremulli L.L. Biochemistry. (ncsu.edu)
  • Upon binding of both Calcium ions to the structure, the two ion-binding loops in the structure move approximately 1.00 A together, while the pairs of helices in the structure move approximately 0.45 A together. (molmovdb.org)
  • CABS-flex 2.0 applications include modeling flexibility of globular proteins, proteins with disordered regions of significant length, loop flexibility and dynamics of selected protein fragments (where the allowed degree of protein flexibility is defined by user with distance restraints). (edu.pl)
  • In simulations of flexibility of globular proteins, the CABS-flex was shown to be a computationally efficient alternative to all-atom molecular dynamics - a classical simulation approach. (edu.pl)
  • The crystal structure of OsExo70F2 in complex with AVR-Pii reveals hydrophobic residues dominate the interaction interface. (phys.org)
  • Using protein structure analysis, the study reveals a tight binding mechanism in which a significant proportion of the effector surface is involved in the interaction with the host target. (phys.org)
  • Alanine scanning of MS2 coat protein reveals protein-phosphate contacts involved in thermodynamic hot spots. (colorado.edu)
  • Although understanding the molecular mechanisms underlying kin recognition is a fundamental biological question, such efforts are blocked by the inherent complexity of animal systems, which typically involve the five senses and cognition. (nature.com)
  • MSA refers to the alignment of three or more biological sequences, protein or nucleic acid of similar length. (projectguru.in)
  • In the case of proteins, structure superposition is often performed without reference to the sequences of the proteins. (proteopedia.org)
  • We also found that effective contact definitions differ from fold to fold, suggesting that using different residue contact definition specific for each template will lead to improvement of the performance of threading. (biomedcentral.com)
  • Heat shock protein 47 (HSP47) is an endoplasmic reticulum (ER)-resident collagen-specific chaperone and essential for proper formation of the characteristic collagen triple helix. (uni-koeln.de)
  • Monoclonal antibodies developed against immunogenic proteins (Tumor Specific Antigens/TSA's) that are expressed in human cancers, display a unique behavioral pattern. (jcancer.org)
  • Monoclonals that we were able to develop from tumor specific proteins derived from colon and pancreas cancer were found capable of targeting those tumors to induce apoptosis. (jcancer.org)
  • Milev, S., Bosshard, H. R. & Jelesarov, I. Enthalpic and entropic effects of salt and polyol osmolytes on site-specific protein-DNA association: the integrase Tn916-DNA complex. (uzh.ch)
  • The ProQ/FinO family of RNA binding proteins mediate sRNA-directed gene regulation throughout gram-negative bacteria. (nature.com)
  • and the X protein (X gene). (cdc.gov)
  • Homeodomain proteins play key roles in development and gene regulation in eukaryotes. (embl.de)
  • If a gene is defective, its RNA copy and the proteins made from this will also be defective. (scitechdaily.com)
  • bZIP Maf is a domain found in Maf transcription factor proteins. (wikipedia.org)
  • Small Maf proteins heterodimerize with Fos and may act as competitive repressors of the NF2-E2 transcription factor. (wikipedia.org)
  • The involvement of viral DNA-binding proteins in the regulation of virulence genes, transcription, DNA replication, and repair make them significant targets. (mdpi.com)
  • TFBSs are typically located upstream of target genes, within a few thousand base pairs of the transcription start site. (bvsalud.org)
  • It regulates cytokine inducible transcription networks by facilitating promoter recognition of target transcription factors. (thermofisher.com)
  • We are developing algorithms that take advantage of NMR chemical shift information to identify a subset of Smotifs that form a protein and setting up optimization approaches that will rapidly assemble overlapping Smotifs into compact folds. (einsteinmed.edu)
  • In this review, we consider some of the theoretical aspects of protein haptenation, how mechanisms of protein haptenation can be investigated experimentally and how we can use such knowledge in the development of novel, alternative approaches for predicting skin sensitization potential in the future. (cdc.gov)
  • These motifs are termed the Maf recognition element (MARE) and is 13 or 14 base pairs long. (wikipedia.org)
  • One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed. (embl.de)
  • The structure of calbindin is characteristic of an EF-hand protein, with two helix-loop-helix calcium binding motifs joined by a flexible linker, and a short anti-parallel beta-type interaction between the two ion-binding sites. (molmovdb.org)
  • The ordinate procedures how deep the neighborhood pocket environment across the residue is certainly, assessed as the deepest partner proteins atom discovered within 5? (gasyblog.com)
  • OsExo70F2 is presented as a solid surface, with the effector as cartoon ribbons and side chains displayed as a cylinder for AVR-Pii-interacting residues (Asp45, Tyr48, His49, Tyr64, Phe65, and Asn66) in addition to the residues coordinating the Zn 2+ atom (Cys51, Cys54, His67, and Cys69). (phys.org)
  • 3. modelling of non-enzymatic Deoxyribonucleic acid (DNA) repair via electron transfer from amino acids to the oxidised purine nucleotides that we recently found as a prototype of fast chemical repair of radiation induced damages of DNA and extending the findings to systems with increased complexity within the frame of proteomic research on peculiarities of recognition and processing of DNA substrate. (europa.eu)
  • Histidine residues have been suggested as triggers due to their approximate textbook pK(a) value of 6.1 for their side chains. (uni-koeln.de)
  • The ionizable amino acid side chains of proteins are usually located at the surface. (lu.se)
  • Most ionizable side chains reside at the protein surface, parent physical significance. (lu.se)
  • Each true point represents a residue contributed with the shortest chains in each interface pair. (gasyblog.com)
  • Because the superposition is about 300 residues long (and the protein chains are longer), it is hard to see details of this superposition in the complexity. (proteopedia.org)
  • However, in some proteins an ionizable group is embedded in an apolar internal region. (lu.se)
  • Compulsorily, this reversal selectivity ought to be attributed to the current presence of the excess stereogenic center (from the L-Asp or L-Glu residues) which should regulate the preferential development from the 4isomer. (conferencedequebec.org)
  • Our long-term goal is to understand the principles underlying molecular recognition and selectivity at the immunological synapse. (einsteinmed.edu)
  • Similarly, a minimal ProQ/FinO domain protein, NMB1681, has been shown to bind a range of structured RNAs in Neisseria meningitidis 15 . (nature.com)
  • HBV mutant tase activity of the HBV polymerase protein lacks a proof- surveillance and understanding of HBV mutant impact on reading function, random mis-incorporation of bases into disease diagnosis will pose a challenge to global health the replicating DNA strand occurs. (cdc.gov)
  • The C-terminal area (CTD) downstream from residue 235 of RNA polymerase subunit is involved with recognition from the promoter UP element. (mingsheng88.org)
  • Two particular useful domains (locations 2.4 and 4.2) from the 70 subunit, the promoter reputation device of RNA polymerase, connect to two canonical series components (indicators C10 and C35), each GSK343 cost comprising six nucleotide pairs long, from the promoter (1). (mingsheng88.org)
  • Many organisms regulate their social life through kin recognition, but the underlying mechanisms are poorly understood. (nature.com)
  • Basic Sciences member Dr. Barry Stoddard and his laboratory have long been fascinated by REases and bacterial restriction-modification systems, both in terms of their evolutionary history and their mechanisms of DNA recognition and fidelity. (fredhutch.org)
  • Juan Carlos De la Concepcion et al, A blast fungus zinc-finger fold effector binds to a hydrophobic pocket in host Exo70 proteins to modulate immune recognition in rice, Proceedings of the National Academy of Sciences (2022). (phys.org)
  • A molecular model of the FMDV 3A protein, derived from the nuclear magnetic resonance (NMR) structure of the poliovirus 3A protein, predicted a hydrophobic interface spanning residues 25 to 44 as the main determinant for 3A dimerization. (asm.org)
  • Foot-and-mouth disease virus (FMDV) nonstructural protein 3A plays important roles in virus replication, virulence, and host range. (asm.org)
  • In particular, the two residues at the beginning of helix H2 are positioned to recognise the flanking region of the DNA. (wikipedia.org)
  • In the case of threading, alignment accuracy strongly influences the fraction of common contacts identified among proteins of the same fold, which eventually affects the fold recognition accuracy. (biomedcentral.com)
  • In the resulting aM-protease complex, the active site of the protease is sterically shielded, thus substantially decreasing access to protein substrates. (embl.de)
  • We will also look at the combination of mAbs with immunostimulants such as GMCSF and IL-2 (fusion proteins) and eventual conjugation of the mAbs with alpha and possibly B -emitters to help in targeting bystander cells. (jcancer.org)
  • Furthermore, the ASH and ADL neurons communicate a large selection of G subunits [3], raising the probability of GPCR-G proteins conversation. (exposed-skin-care.net)