• disulfide bond
  • 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)
  • 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)
  • 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)
  • found in proteins
  • 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)
  • 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)
  • 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)
  • hydrophobic
  • 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)
  • nucleic acids
  • A protein as a stand-alone infectious agent stands in contrast to all other known infectious agents such as viruses, bacteria, fungi, and parasites, all of which contain nucleic acids (DNA, RNA, or both). (wikipedia.org)
  • polymers
  • It also investigates the characterization of atomic arrangements in crystalline and amorphous solids: metals, ceramics, semiconductors, and polymers (including proteins). (verycd.com)
  • large molecules
  • 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)
  • membrane
  • 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)
  • The defining, and highly unusual, property of the Tat pathway is that it transports folded proteins, a task that must be achieved without allowing appreciable ion leakage across the membrane. (biomedsearch.com)
  • The integral membrane TatC protein is the central component of the Tat pathway. (biomedsearch.com)
  • For example, whereas X-ray crystallography has been successful in crystallizing approximately 80,000 cytosolic proteins, it has been far less successful in crystallizing membrane proteins - approximately 280. (wikipedia.org)
  • Globular proteins or spheroproteins are spherical ("globe-like") proteins and are one of the common protein types (the others being fibrous, disordered and membrane proteins). (wikipedia.org)
  • Globular proteins are somewhat water-soluble (forming colloids in water), unlike the fibrous or membrane 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)
  • 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)
  • prediction of protein
  • Prediction of protein structure de novo for larger proteins will require better algorithms and larger computational resources such as those afforded by either powerful supercomputers (such as Blue Gene or MDGRAPE-3) or distributed computing projects (such as Folding@home, Rosetta@home, the Human Proteome Folding Project, or Nutritious Rice for the World). (wikipedia.org)
  • Binding
  • TatC captures substrate proteins by binding their signal peptides. (biomedsearch.com)
  • This gene encodes a transcription factor that belongs to the family of zinc-finger DNA-binding proteins associated with chromatin remodeling. (cancerindex.org)
  • 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)
  • conformational
  • The phosphorylated tyrosines are often used as "handles" by which proteins can bind to one another, whereas phosphorylation of Ser/Thr often induces conformational changes, presumably because of the introduced negative charge. (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)
  • Chemical
  • It deals with the relationship between electronic structure, chemical bonding, and atomic order. (verycd.com)
  • DNA is wrapped around histones, and the histone proteins can control DNA expression when chemical groups are added and removed. (wikipedia.org)
  • 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)
  • biological function
  • 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)
  • Function
  • 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)
  • Based on these findings, we propose a model for merlin folding critical to its ability to function as a tumor suppressor protein. (biomedsearch.com)
  • Second, several different human diseases, such as Duchenne muscular dystrophy, can be linked to loss of protein function resulting from a change in just a single amino acid in the primary sequence. (wikipedia.org)
  • Bowie JU, Eisenberg D (1994) An evolutionary approach to folding small alpha-helical proteins that uses sequence information and an empirical guiding fitness function. (springer.com)
  • 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)
  • For any sequence in any particular structure, an energy can be rapidly calculated from the energy function. (wikipedia.org)
  • By varying the energy function and the bead sequence of the chain (the primary structure), effects on the native state structure and the kinetics of folding can be explored, and this may provide insights into the folding of real proteins. (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)
  • The sequence of a protein is unique to that protein, and defines the structure and function of the protein. (wikipedia.org)
  • cytochrome
  • Several common protein domains were less abundant in A. apis compared with related ascomycete genomes, particularly cytochrome p450 and protein kinase domains. (biomedsearch.com)
  • 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)
  • functionally important
  • Neurofibromatosis 2 tumor suppressor protein, merlin, forms two functionally important intramolecular associations. (biomedsearch.com)
  • The detection of positive selection can also help identify functionally important protein regions and thus guide protein engineering. (genetics.org)
  • Its identification may point to functionally important regions of a gene and is thus of potential interest to protein engineers who alter proteins to produce new functions. (genetics.org)
  • topological
  • Definition of general topological equivalence in protein structures: a procedure involving comparison of properties and relationship through simulated annealing and dynamic programming. (springer.com)
  • escherichia
  • Abstract Tricodon regions on messenger RNAs corresponding to a set of proteins from Escherichia coli were scrutinized for their translation speed. (bio.net)
  • whereas
  • Enzymes called arginine deiminases (ADIs) catalyze the deimination of free arginine, while protein arginine deiminases or peptidylarginine deiminases (PADs) replace the primary ketimine group (=NH) by a ketone group (=O). Arginine is positively charged at a neutral pH, whereas citrulline has no net charge. (wikipedia.org)