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  • disulfide bond
  • Post-translational modification such as disulfide bond formation, phosphorylations and glycosylations are usually also considered a part of the primary structure, and cannot be read from the gene. (wikipedia.org)
  • It belongs to the CRISP (cysteine-rich secretory protein) glycoprotein subfamily, which are single chain polypeptides containing strictly conserved cysteines (cysteines not oxidised to cystine and thus not providing disulfide bond support to tertiary protein structure). (wikipedia.org)
  • folds
  • At present, some of the most successful methods have a reasonable probability of predicting the folds of small, single-domain proteins within 1.5 angstroms over the entire structure. (wikipedia.org)
  • Skolnick was first to demonstrate that the library of single domain protein structures is likely complete and that the observed folds in nature arise from the confinement of dense polymer chains. (wikipedia.org)
  • stable
  • Globular proteins are only marginally stable because the free energy released when the protein folded into its native conformation is relatively small. (wikipedia.org)
  • As the free energy difference in a globular protein that results from folding into its native conformation is small, it is marginally stable, thus providing a rapid turnover rate and effective control of protein degradation and synthesis. (wikipedia.org)
  • molecules
  • To obtain PDB coordinates for a protein of your interest, go to the Protein Data Bank or Molecules to Go or NCBI . (molbiol-tools.ca)
  • Like many other types of molecules, proteins can be prompted to form crystals when the solution in which they are dissolved becomes supersaturated. (wikipedia.org)
  • Crystallization of protein molecules has been known for over 150 years. (wikipedia.org)
  • The solubility of protein molecules is subject to many factors, especially the interaction with other compounds in solution. (wikipedia.org)
  • Because proteins are such large molecules, there are severe computational limits on the simulated timescales of their behaviour when modeled in all-atom detail. (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)
  • biological
  • As a result, inferring the tertiary structure of a protein from its primary structure poses a research problem of the first order for a wide range of biological applications, and one that is still far from fully understood. (rosalind.info)
  • 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)
  • side chains
  • Finally, the peptide side chains can also be modified covalently, e.g., phosphorylation Aside from cleavage, phosphorylation is perhaps the most important chemical modification of proteins. (wikipedia.org)
  • conformations
  • Knowledge-based functions are formed with statistical models capturing aspects of the properties of native protein conformations. (wikipedia.org)
  • The alternative structures of the same protein are referred to as different conformational isomers, or simply, conformations, and transitions between them are called conformational changes. (wikipedia.org)
  • gene
  • p>Describes annotations that are concluded from looking at variations or changes in a gene product such as mutations or abnormal levels and includes techniques such as knockouts, overexpression, anti-sense experiments and use of specific protein inhibitors. (uniprot.org)
  • 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)
  • Proteasome subunit beta type-3, also known as 20S proteasome subunit beta-3, is a protein that in humans is encoded by the PSMB3 gene. (wikipedia.org)
  • 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)
  • sequence
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (uniprot.org)
  • The IbpB protein, whose expression is regulated by the IbpB thermometer, is 48% identical to IbpA (at the level of amino acid sequence) yet fulfils a different role in heat shock. (wikipedia.org)
  • Cruciform DNA is a form of non-B DNA that requires at least a 6 nucleotide sequence of inverted repeats to form a structure consisting of a stem, branch point and loop in the shape of a cruciform, stabilized by negative DNA supercoiling. (wikipedia.org)
  • 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)
  • amino acid
  • In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. (wikipedia.org)
  • cleavage
  • A typical TAP tag consists of the calmodulin-binding protein (CBP), a tobacco etch virus (TEV) protease cleavage site, and the immunoglobulin G-binding (IgG) units of protein A (ProtA) of Staphylococcus aureus (Fig. 2B). (pharmacologicalsciences.us)
  • POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. (wikipedia.org)
  • form
  • Linear combinations of _______ form proteins. (cram.com)
  • 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)
  • genes
  • 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)
  • 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)
  • 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)
  • indicates
  • p>This indicates the type of evidence that supports the existence of the protein. (uniprot.org)
  • The crystal structure of Sav1866 indicates that ABC transporters may use an alternating access and release mechanism where ATP binding and hydrolysis control the conversion of one state into the other, and that domain swapping and subunit twisting takes place in the transport. (pharmacologicalsciences.us)
  • 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)
  • beta
  • In describing amino acids, what structure is described as an alpha helix or a beta pleated sheet? (cram.com)
  • Amyloids are ordered protein assemblies, typically rich in beta sheet, that underlie multiple disorders such as Alzheimer's disease (AD). (elifesciences.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)
  • 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)
  • 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)
  • 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)
  • primary
  • 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)
  • specific
  • Like all proteins, tau is built from a string of amino acids that folds into a specific shape. (elifesciences.org)
  • 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)
  • 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)