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  • residues
  • 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)
  • 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)
  • Homology models contain sufficient information about the spatial arrangement of important residues in the protein and are often used in drug design for screening of large libraries by molecular docking techniques. (igi-global.com)
  • The computational methods for protein structure comparison usually represent a protein structure by atomic coordinates in the Euclidean space, as a distance matrix [ 1 ] whose entries represent the distances between two residues of the protein, or as a contact map [ 2 ], where a binary matrix is used to represent the distances between the residue pairs. (biomedcentral.com)
  • This means that 2 adjacent residues in the primary structure must form the same hydrogen bonding pattern. (wikipedia.org)
  • To guarantee the connectivity of the protein chain, adjacent residues on the backbone must be placed on adjacent vertices of the lattice. (wikipedia.org)
  • For the simple HP model, this is simply an enumeration of all the contacts between H residues that are adjacent in the structure but not in the chain. (wikipedia.org)
  • The reactivity is enhanced when the thiol is ionized, and cysteine residues in proteins have pKa values close to neutrality, so are often in their reactive thiolate form in the cell. (wikipedia.org)
  • Beyond the iron-sulfur proteins, many other metal cofactors in enzymes are bound to the thiolate substituent of cysteinyl residues. (wikipedia.org)
  • found in proteins
  • In cell biology, cystine (found in proteins) can only exist in non-reductive (oxidative) organelles, such as the secretory pathway (ER, Golgi, lysosomes, vesicles and ECM). (wikipedia.org)
  • In particular, the L-amino acids normally found in proteins can spontaneously isomerize at the C α {\displaystyle \mathrm {C^{\alpha }} } atom to form D-amino acids, which cannot be cleaved by most proteases. (wikipedia.org)
  • conformation
  • A general paradigm for de novo prediction involves sampling conformation space, guided by scoring functions and other sequence-dependent biases such that a large set of candidate ("decoy") structures are generated. (wikipedia.org)
  • Conformation analysis of proteins (PhD thesis). (wikipedia.org)
  • In particular, lattice models have been used to investigate the energy landscapes of proteins, i.e. the variation of their internal free energy as a function of conformation. (wikipedia.org)
  • synthesis
  • During protein synthesis the amino group of the amino acid being added is coupled to the carboxyl group of the prior amino acid, and two hydrogen atoms and one oxygen atom are removed as a water molecule (H 2 O) and the peptide bond is formed (see Figure 2). (encyclopedia.com)
  • biological
  • Since the vision is of a large collection of atoms with subgroupings of atoms that work together in a complex dynamic manner, a protein would be a collection of atoms, many of which are covalently bonded, that interact together to perform a specific biological function. (wikipedia.org)
  • Samudrala's work has thus focussed on proteins, which is the fundamental unit of biological function within the structeome. (wikipedia.org)
  • In biological systems, proteins are produced during translation by a cell's ribosomes. (wikipedia.org)
  • glycoprotein
  • Proteins (including their lipoprotein and glycoprotein forms) also constitute 10 percent of the weight of the blood plasma of living organisms, carrying various nutrients throughout the body and acting as signals to coordinate bodily functions between the different organs. (encyclopedia.com)
  • bind
  • No FAD binding is observed in oxalyl-CoA decarboxylase, but an excess of coenzyme A in the crystal structure has led to the hypothesis that the binding site was co-opted during OXC evolution to bind the CoA moiety of its substrate. (wikipedia.org)
  • Initially, a 55 kDa protein was isolated from the actomyosin complex of Dictyostelium discoideum, which was later shown to bind actin in vitro. (wikipedia.org)
  • Although coronin is present in almost all eukaryotic organisms and has different functions, these proteins have all been shown to bind F-actin and localize in the dynamic F-actin rich area of cells. (wikipedia.org)
  • Gene
  • 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)
  • 7 ] identified an outer member protein gene ( omp ) to differentiate isolates/strains of ' Ca . L. asiaticus' from different geographical origins, although each regions was represented by only one to three strains. (pubmedcentralcanada.ca)
  • Protein ubiquitination and subsequent proteolysis and degradation by the proteasome are important mechanisms in the regulation of the cell cycle, cell growth and differentiation, gene transcription, signal transduction and apoptosis. (wikipedia.org)
  • membrane
  • Chromosome The chromosome of a prokaryotic chamber is not surrounded on a atomic membrane, it has no explicit shape and no protein resources associated with it. (chelsi174.ru)
  • These inorganic phosphates are then bound to carrier proteins which deliver the inorganic phosphates to a specific high-affinity transport system, known as the Pst system, which transports phosphate across the cytoplasmic membrane. (wikipedia.org)
  • monomer
  • The conversion of a protein from a monomer to a large, ordered multimer could occur by several mechanisms, but the first step probably involves the formation of a seed. (elifesciences.org)
  • molecule
  • We have determined structures of two constructs of a Cu pump from Archaeoglobus fulgidus (CopA) by cryoelectron microscopy of tubular crystals, which reveal the overall architecture and domain organization of the molecule. (nih.gov)
  • Molecule that serves as the basic structural unit of proteins. (tolweb.org)
  • newly
  • Compared to related benchmarking techniques LiveBench and EVA, which run weekly against newly solved protein structures deposited in the Protein Data Bank, CAFASP generates much less data, but has the advantage of producing predictions that are directly comparable to those produced by human prediction experts. (wikipedia.org)
  • form
  • Aggregates form when individual proteins stick together in repetitive patterns, much like the way a single Lego block might attach to another identical one. (elifesciences.org)
  • Normally folded tau proteins do not form aggregates. (elifesciences.org)
  • discovered that in the good form of tau the parts of the protein that allow it to stick to itself are hidden, folded inside. (elifesciences.org)
  • By contrast, the bad form of tau exposes the parts that allow it to aggregate, enabling the protein to build upon itself to form a large, toxic assembly. (elifesciences.org)
  • might apply to other proteins that form toxic aggregates. (elifesciences.org)
  • It is unknown how or why intracellular proteins such as tau transition from a relatively inert form to one that efficiently self-assembles into ordered structures in vivo. (elifesciences.org)
  • In contrast, the structure of the fully reduced Mo IV form of the active site showed S1 and S2 P-pterin and S1 Q-pterin maintained full coordination, however the S2 of the Q-pterin shifted away from the metal center, indicating decreased coordination. (wikipedia.org)
  • p53 binding correlates with inverted repeat sequences, such as the ones that help form cruciform DNA structures. (wikipedia.org)
  • Coronin belongs to the WD-repeat containing proteins, which form a beta propeller tertiary structure. (wikipedia.org)
  • cofactors
  • In R. sphaeroides, DMSOR is a single-subunit, water-soluble protein that requires no additional cofactors beyond pterin. (wikipedia.org)
  • accumulation
  • Subsequently, a compromised proteasome complex assembly and function lead to reduced proteolytic activities and the accumulation of damaged or misfolded protein species. (wikipedia.org)
  • Such protein accumulation may contribute to the pathogenesis and phenotypic characteristics in neurodegenerative diseases, cardiovascular diseases, inflammatory responses and autoimmune diseases, and systemic DNA damage responses leading to malignancies. (wikipedia.org)
  • bonds
  • The interactions and bonds of side chains within a particular protein determine its tertiary structure. (wikipedia.org)
  • Before 1991, ET in metalloproteins was thought to affect primarily the diffuse, averaged properties of the non-metal atoms forming an insulated barrier between the metals, but Beratan, Betts and Onuchic subsequently showed that the ET rates are governed by the bond structures of the proteins -- that the electrons, in effect, tunnel through the bonds comprising the chain structure of the proteins. (wikipedia.org)
  • Due to this, while ALP ultimately denatures at about 90 °C it has the added ability to accurately reform its bonds and return to its original structure and function once cooled back down. (wikipedia.org)
  • regulatory
  • Structure of a copper pump suggests a regulatory role for its metal-binding domain. (nih.gov)
  • We have built a pseudoatomic model by fitting existing crystallographic structures into the cryoelectron microscopy maps for CopA, which suggest a Cu-dependent regulatory role for the MBD. (nih.gov)
  • beta
  • Amyloids are ordered protein assemblies, typically rich in beta sheet, that underlie multiple disorders such as Alzheimer's disease (AD). (elifesciences.org)
  • domain
  • Crosslinks informed models of local peptide structure within the repeat domain which suggest relative inaccessibility of residues that drive aggregation (VQIINK/VQIVYK) in M i , and exposure in M s . (elifesciences.org)
  • binding domain present within the protein. (uniprot.org)
  • Both the cyclooxygenase and the peroxidase active sites are located in the catalytic domain, which accounts for approximately 80% of the protein. (wikipedia.org)
  • As for other members of DMSO reductase family, the tertiary structure of DMSOR is composed of Mo-surrounding domains I-IV, with domain IV heavily interacting with pyranopterindithiolene Mo-cofactor(s) (P- and Q-pterin) of the active site. (wikipedia.org)
  • These coordinates may refer either to a protein domain or to the entire tertiary structure. (wikipedia.org)
  • WD-40-domain -repeat proteins are defined by the presence of at least four WD repeats located centrally in the protein. (wikipedia.org)
  • binds
  • Lipid-binding protein that is able to promote the tubulation of the phosphatidic acid-containing membranes it preferentially binds. (uniprot.org)
  • A well-characterised example of this is the ribonuclease inhibitor, which binds to ribonucleases in one of the tightest known protein-protein interactions. (wikipedia.org)
  • domains
  • By comparing these structures, we localized its N-terminal MBD within the cytoplasmic domains that use ATP hydrolysis to drive the transport cycle. (nih.gov)
  • high
  • Cytodiagnostics 5nm NHS-activated Gold Nanoparticle Conjugation Kits have been optimized for high efficiency one-step conjugation of proteins and other primary amine-containing ligands to gold nanoparticles. (cytodiagnostics.com)
  • Haemodialysis is not recommended due to the high degree of protein binding with doxepin. (wikipedia.org)
  • different
  • p>When browsing through different UniProt proteins, you can use the 'basket' to save them, so that you can back to find or analyse them later. (uniprot.org)
  • mature
  • The use of alternative transcription starts causes dual targeting of the same mature MDAR protein to both mitochondria and chloroplast. (uniprot.org)
  • another
  • p>An evidence describes the source of an annotation, e.g. an experiment that has been published in the scientific literature, an orthologous protein, a record from another database, etc. (uniprot.org)
  • Contains
  • Contains enough reagents for conjugation of 2mg of protein. (cytodiagnostics.com)
  • The operon contains two heat-shock genes, encoding inclusion body binding proteins A and B (IbpA/B), and is the most drastically upregulated operon under heat-shock in Escherichia coli. (wikipedia.org)