• 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)
  • 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)
  • 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)
  • fold
  • The robust nature of the approach derives from the stability of the fold of the protein under mutational pressures. (springer.com)
  • Taylor, W.R. (1991) Towards protein tertiary fold prediction using distance and motif constraints. (springer.com)
  • Generally scores below 0.20 corresponds to randomly chosen unrelated proteins whereas structures with a score higher than 0.5 assume roughly the same fold. (wikipedia.org)
  • A quantitative study shows that proteins of TM-score = 0.5 have a posterior probability of 37% in the same CATH topology family and of 13% in the same SCOP fold family. (wikipedia.org)
  • There are multiple fold classes of globular proteins, since there are many different architectures that can fold into a roughly spherical shape. (wikipedia.org)
  • The term globin can refer more specifically to proteins including the globin fold. (wikipedia.org)
  • Although it is still unknown how proteins fold up naturally, new evidence has helped advance understanding. (wikipedia.org)
  • Globular proteins seem to have two mechanisms for protein folding, either the diffusion-collision model or nucleation condensation model, although recent findings have shown globular proteins, such as PTP-BL PDZ2, that fold with characteristic features of both models. (wikipedia.org)
  • These new findings have shown that the transition states of proteins may affect the way they fold. (wikipedia.org)
  • Prions are infectious agents composed entirely of a protein material that can fold in multiple, structurally abstract ways, at least one of which is transmissible to other prion proteins, leading to disease in a manner that is epidemiologically comparable to the spread of viral infection. (wikipedia.org)
  • All known prions induce the formation of an amyloid fold, in which the protein polymerises into an aggregate consisting of tightly packed beta sheets. (wikipedia.org)
  • The millisecond regime for all-atom simulations was not reached until 2010, and it is still not possible to fold all real proteins on a computer. (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)
  • hydrophobic
  • This is due to the exposure of hydrophilic, acidic ad basic amino acids to the outside and hiding of the hydrophobic amino acids such as aromatic amino acids and the amino acids with alkyl groups in the core of the protein structure. (pediaa.com)
  • Instead of a simple methyl group, the myristoyl group has a tail of 14 hydrophobic carbons, which make it ideal for anchoring proteins to cellular membranes. (wikipedia.org)
  • glycosyl phosphatidylinositol (GPI) attachment Glycosyl phosphatidylinositol is a large, hydrophobic phospholipid prosthetic group that achors proteins to cellular membranes. (wikipedia.org)
  • apoptosis
  • Inhibition of apoptosis and NF-κB activation by vaccinia protein N1 occur via distinct binding surfaces and make different contributions to virulence. (biomedsearch.com)
  • Vaccinia virus (VACV) protein N1 is an intracellular virulence factor and belongs to a family of VACV B-cell lymphoma (Bcl)-2-like proteins whose members inhibit apoptosis or activation of pro-inflammatory transcription factors, such as interferon (IFN) regulatory factor-3 (IRF-3) and nuclear factor-κB (NF-κB). (biomedsearch.com)
  • Binding
  • TatC captures substrate proteins by binding their signal peptides. (biomedsearch.com)
  • Transthyretin (prealbumin) = complexes with retinal binding protein to transport retinol (Vit. (brainscape.com)
  • This gene encodes a transcription factor that belongs to the family of zinc-finger DNA-binding proteins associated with chromatin remodeling. (cancerindex.org)
  • The structures of the BT4663 sensor domain reveal a significant conformational change in the homodimer on ligand binding, which results in a scissor-like closing of the C-termini of each protomer. (biomedsearch.com)
  • A methyl group (CH3) binds to an arginine on the histone protein, altering DNA binding to the histone and allowing transcription to take place. (wikipedia.org)
  • Skolnick is most known for demonstrating that the number of ligand binding pockets in proteins is quite small, thereby justifying the likelihood that large scale drug repurposing will work. (wikipedia.org)
  • He also pioneered the field of ligand homology modeling with his threading based, FINDSITE approach for protein function inference, binding site prediction and virtual ligand screening. (wikipedia.org)
  • The research showed that remotely related proteins identified by threading often share a common ligand binding site occupied by chemically similar ligands that contain strongly conserved anchor functional groups as well as a variable region that accounts for their binding specificity. (wikipedia.org)
  • These insights enable low-resolution predicted structures to be used for ligand screening/binding pose prediction, with comparable accuracy as with high-resolution experimental structures. (wikipedia.org)
  • translocation
  • The twin-arginine translocation (Tat) pathway is one of two general protein transport systems found in the prokaryotic cytoplasmic membrane and is conserved in the thylakoid membrane of plant chloroplasts. (biomedsearch.com)
  • TatC then recruits TatA family proteins to form the active translocation complex. (biomedsearch.com)
  • degradation
  • Here, we identify the activating ligand of the hybrid two-component system, BT4663, which controls heparin and heparan sulfate acquisition and degradation in this prominent gut microbe, and report the crystal structure of the extracellular sensor domain in both apo and ligand-bound forms. (biomedsearch.com)
  • Mutation
  • Mutagenesis of the surface groove abolished only the N1 anti-apoptotic activity and protein crystallography showed these mutants differed from wild-type N1 only at the site of mutation. (biomedsearch.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)
  • kinase
  • Several common protein domains were less abundant in A. apis compared with related ascomycete genomes, particularly cytochrome p450 and protein kinase domains. (biomedsearch.com)
  • cytochrome
  • Examples include zinc in zinc fingers and alcohol dehydrogenase, copper in the blue copper proteins, iron in cytochrome P450 and nickel in the [NiFe]-hydrogenases. (wikipedia.org)
  • surfaces
  • Collectively, these data show that N1 inhibits pro-inflammatory and pro-apoptotic signalling using independent surfaces of the protein. (biomedsearch.com)
  • Proteins have irregularly shaped surfaces, which results in the formation of large channels within any protein crystal. (wikipedia.org)
  • side chains
  • Also, ionic bonds called salt bridges form between positively- and negatively-charged side-chains of amino acids, further stabilizing the tertiary structure. (pediaa.com)
  • 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)
  • crystallography
  • While some protein crystals have been observed in nature, protein crystallization is predominantly used for scientific or industrial purposes, most notably for study by X-ray crystallography. (wikipedia.org)
  • Prior to Bernal and Hodgkin, protein crystallography had only been performed in dry conditions with inconsistent and unreliable results. (wikipedia.org)
  • In 1958, the structure of myoglobin, determined by X-ray crystallography, was first reported by John Kendrew. (wikipedia.org)
  • Cysteine
  • Latisemin is a cysteine-rich secretory protein that can be isolated from the venom of the Black-banded sea krait, a sea snake indigenous to the warmer waters of the western Pacific Ocean. (wikipedia.org)
  • The thiol group also has a high affinity for heavy metals, so that proteins containing cysteine, such as metallothionein, will bind metals such as mercury, lead and cadmium tightly. (wikipedia.org)
  • function
  • There is a specific function of the protein. (biochemden.com)
  • Also, this gene is down-regulated during transformation of normal myoblasts to rhabdomyosarcoma cells and the encoded protein may function as a link between presenilin-2 and an intracellular signaling pathway. (cancerindex.org)
  • These studies have shown that the folding of globular proteins affects its function. (wikipedia.org)
  • This increases the hydrophobicity of the protein, which can lead to changes in protein folding, affecting the structure and function. (wikipedia.org)
  • Lattice proteins are made to resemble real proteins by introducing an energy function, a set of conditions which specify the interaction energy between neighbouring beads, usually those occupying adjacent lattice sites. (wikipedia.org)
  • Typically
  • Typically, protein samples above 97% purity are considered suitable for crystallization[citation needed], although high purity is neither necessary nor sufficient for crystallization. (wikipedia.org)
  • Different versions of lattice proteins may adopt different types of lattice (typically square and triangular ones), in two or three dimensions, but it has been shown that generic lattices can be used and handled via a uniform approach. (wikipedia.org)
  • Chemical
  • DNA is wrapped around histones, and the histone proteins can control DNA expression when chemical groups are added and removed. (wikipedia.org)