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  • novel
  • Thus the foundations are set for a novel encoding based on L-systems for evolutionary approaches to both the Protein Structure Prediction and Inverse Folding Problems. (springer.com)
  • New partner proteins containing novel internal recognition motif for human glutaminase interacting protein (hGIP) , BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS 432: (1) pp. 10-15. (doktori.hu)
  • He was a NIH Director's Pioneer Award finalist in 2006 (25/465 applicants were selected as finalists) for a novel idea to determine the structures of all proteins in a solution that he then presented at the seventh community wide assessment of protein structure prediction methods (CASP7). (wikipedia.org)
  • In 2010, he again became a finalist and went on to receive the Pioneer Award for his Computational Analysis of Novel Drug Opportunities (CANDO) drug discovery platform to screen every known drug against every known target structure in a shotgun manner to discover new repurposeable therapeutics, particularly for underserved diseases. (wikipedia.org)
  • He discovered novel blood group and tumor antigen specific lectins and made original contribution towards elucidation of the energetics and mechanism of protein-sugar recognition. (wikipedia.org)
  • He discovered the unusual quaternary structure of peanut agglutinin and a novel lectin fold in Jacalin as well as the structural basis of inactivation of ribosomes by gelonin. (wikipedia.org)
  • Codon-tRNA combinations not found in nature can also be used to "expand" the genetic code and form novel proteins known as alloproteins incorporating non-proteinogenic amino acids. (wikipedia.org)
  • reversible
  • ii) PfRds cold-denaturation behavior during cooling after thermo-chemical perturbation is incompletely reversible, unlike PfuTIMs, which was clearly reversible (from each different conformation generated). (duhnnae.com)
  • The binding of lapatinib to the ATP-binding site in the EGFR and human epidermal growth factor receptor 2 (HER2) protein kinase domains inhibits signal mechanism activation (through reversible, competitive inhibition). (wikipedia.org)
  • computational
  • In computational biology, de novo protein structure prediction refers to an algorithmic process by which protein tertiary structure is predicted from its amino acid primary sequence. (wikipedia.org)
  • De novo methods tend to require vast computational resources, and have thus only been carried out for relatively small proteins. (wikipedia.org)
  • 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)
  • Macromolecular docking is the computational modelling of the quaternary structure of complexes formed by two or more interacting biological macromolecules. (wikipedia.org)
  • In the early 1990s, more structures of complexes were determined, and available computational power had increased substantially. (wikipedia.org)
  • Atoms
  • 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)
  • HER2
  • Lapatinib inhibits receptor signal processes by binding to the ATP-binding pocket of the EGFR/HER2 protein kinase domain, preventing self-phosphorylation and subsequent activation of the signal mechanism (see Receptor tyrosine kinase#Signal transduction). (wikipedia.org)
  • kinase
  • The specific systems studied by him include RecA, RuvA, uracil DNA glycosylase, single stranded DNA binding protein, ribosome recycling factor, peptidyl tRNA hydrolase, pantothenate kinase and DNA binding protein in stationary phase cells. (wikipedia.org)
  • Like sorafenib, lapatinib is a protein kinase inhibitor shown to decrease tumor-causing breast cancer stem cells. (wikipedia.org)
  • The drug, produced by AstraZeneca, is an inhibitor of the protein kinase of epidermal growth factor receptor (EGFR). (wikipedia.org)
  • roles
  • We focus on elucidating the roles and interrelation of non pathogenic prion-family proteins that is necessary for a successful development of a cure to transmissible spongiform enchephalopaties. (doktori.hu)
  • The biological roles of most proteins, as characterized by which other macromolecules they interact with, are known at best incompletely. (wikipedia.org)
  • chains
  • Here we investigate a recently discovered Fe 4 O 5 that adopts an orthorhombic CaFe 3 O 5 -type crystal structure that features linear chains of Fe ions. (esrf.eu)
  • function
  • In this field, the main interest is on proteins, because discovering their three-dimensional conformation allows us to get clues about the function they are able to perform. (wikipedia.org)
  • Samudrala's work has thus focussed on proteins, which is the fundamental unit of biological function within the structeome. (wikipedia.org)
  • The methyl side-chain of alanine is non-reactive and is therefore hardly ever directly involved in protein function. (wikipedia.org)
  • The sequence of a protein is unique to that protein, and defines the structure and function of the protein. (wikipedia.org)
  • 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)
  • Acta
  • The protein-lipid interface: perspectives from magnetic resonance and crystal structures , BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 1666: pp. 118-141. (doktori.hu)
  • Methods
  • 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)
  • Research into de novo structure prediction has been primarily focused into three areas: alternate lower-resolution representations of proteins, accurate energy functions, and efficient sampling methods. (wikipedia.org)
  • These candidates must be ranked using methods such as scoring functions to identify structures that are most likely to occur in nature. (wikipedia.org)
  • mechanism
  • However, the mechanism underpinning their photovoltaic effect is still far from understood, which is impeded by a lack of clarity on their structures. (esrf.eu)
  • A crucial feature of the tetragonal structure is that the methylammonium ions do not sit centrally in the A-site cavity, but disordered around two off-centre orientations that facilitate the interstitial ion migration via a gate opening mechanism. (esrf.eu)
  • pathways
  • CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures. (nih.gov)
  • Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. (nih.gov)
  • CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. (nih.gov)
  • Arrestin binding to the receptor blocks further G protein-mediated signaling and targets receptors for internalization, and redirects signaling to alternative G protein-independent pathways, such as β-arrestin signaling. (wikipedia.org)
  • sequence
  • Sequence-specific recognition of the internalization motif of the Alzheimer's amyloid precursor protein by the X11 PTB domain. (cam.ac.uk)
  • Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed. (uniprot.org)
  • In E. coli, the direction for orisome assembly are built into a short stretch of nucleotide sequence called as origin of replication (oriC) which contains multiple binding sites for the initiator protein DnaA (a highly homologous protein amongst bacterial kingdom). (wikipedia.org)
  • Meanwhile, several other proteins interact directly with the oriC sequence to regulate initiation, usually by inhibition. (wikipedia.org)
  • The main functional part of the voltage-sensitive protein domain of these channels generally contains a region composed of S3b and S4 helices, known as the "paddle" due to its shape, which appears to be a conserved sequence, interchangeable across a wide variety of cells and species. (wikipedia.org)
  • The high sequence similarity between the prokaryotic and the eukaryotic STT3 suggests that their structures are similar. (wikipedia.org)
  • Structural genomics involves taking a large number of approaches to structure determination, including experimental methods using genomic sequences or modeling-based approaches based on sequence or structural homology to a protein of known structure or based on chemical and physical principles for a protein with no homology to any known structure. (wikipedia.org)
  • The gene sequence of the target protein can also be compared to a known sequence and structural information can then be inferred from the known protein's structure. (wikipedia.org)
  • variants
  • The majority of these are located in the intergenic or intragenic regions suggesting that the implicated variants may alter chromatin conformation. (technologynetworks.com)
  • By decreasing the probe radius from 0.9 Å to 0.8 Å, more than ten potential tunnels were identified in each crystal structure, including the p1 variants (p1a, p1a′ and p1b), p2ab and p3 tunnels (Table S3). (nih.gov)
  • Histone H2B helps regulate chromatin structure and function through post-translational modifications and specialized histone variants. (wikipedia.org)
  • mammals
  • In the cells of extant organisms, the vast majority of the proteins present in the mitochondria (numbering approximately 1500 different types in mammals) are coded for by nuclear DNA, but the genes for some, if not most, of them are thought to have originally been of bacterial origin, having since been transferred to the eukaryotic nucleus during evolution. (wikipedia.org)
  • isoforms
  • Histone H2B isoforms interact differently with other proteins, are found in specific regions of chromatin, have different types and numbers of post-translational modifications, and are more or less stable than regular histone H2B. (wikipedia.org)
  • genomes
  • With full-genome sequences available, structure prediction can be done more quickly through a combination of experimental and modeling approaches, especially because the availability of large number of sequenced genomes and previously solved protein structures allows scientists to model protein structure on the structures of previously solved homologs. (wikipedia.org)
  • specificity
  • These results indicate that SNARE proteins contribute to the overall specificity of membrane trafficking in vivo, and that the polarity of syntaxin 3 is essential for epithelial cell polarization. (rupress.org)
  • A medicinal enzyme inhibitor is often judged by its specificity (its lack of binding to other proteins) and its potency (its dissociation constant, which indicates the concentration needed to inhibit the enzyme). (wikipedia.org)
  • bind
  • However, at a common temperature of measurement, the higher configurational entropy of a cold-adapted enzyme may foster conformations that bind ligands poorly, leading to high Km values relative to warm-adapted orthologs. (antibody-antibodies.com)
  • For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. (wikipedia.org)
  • Scan the nascent protein in order to recognize and bind sequons. (wikipedia.org)
  • In addition to GPCRs, arrestins bind to other classes of cell surface receptors and a variety of other signaling proteins. (wikipedia.org)
  • Other cellular enzyme inhibitors are proteins that specifically bind to and inhibit an enzyme target. (wikipedia.org)
  • Targeting
  • Targeting information is usually present in the cargo proteins themselves. (rupress.org)
  • These targeting signals are thought to be recognized in the TGN or endosomes, which leads to the sorting of cargo proteins into transport vesicles destined for the apical or basolateral plasma membrane. (rupress.org)
  • 7. The fusion protein according to claim 1, wherein the Targeting Moiety is an opioid. (patentsencyclopedia.com)
  • 13. The fusion protein according to claim 10, wherein the Targeting Moiety has at least 70% homology to SEQ ID No. 38 or a fragment thereof. (patentsencyclopedia.com)
  • enzyme
  • First, antibodies with high specificities for plant SPS also target the bacterial SPS, indicating the structure is conserved enough for the antibody to recognize the enzyme as an antigen. (wikipedia.org)
  • Annotation
  • 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)
  • The Bioinformatics core of the Joint center for structural genomics (JCSG) has recently developed a wiki-based approach namely Open protein structure annotation network (TOPSAN) for annotating protein structures emerging from high-throughput structural genomics centers. (wikipedia.org)
  • occur
  • 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)
  • At extremely high salt concentrations protein precipitation will occur. (wikipedia.org)
  • Current opinion is that post-translational activity may occur if the protein is poorly folded or folds slowly. (wikipedia.org)
  • 1993) "Left-handed Polyproline II Helices Commonly Occur in Globular Proteins", J. Mol. (wikipedia.org)
  • coli
  • A few other mechanisms in E. coli that variously regulate initiation are DDAH (datA-Dependent DnaA Hydrolysis, which is also regulated by IHF), inhibition of the dnaA gene (by the SeqA protein), and reactivation of DnaA by the lipid membrane. (wikipedia.org)
  • The T4 phage initiates an Escherichia coli infection by binding OmpC porin proteins and Lipopolysaccharide (LPS) on the surface of E. coli cells with its long tail fibers (LTF). (wikipedia.org)
  • folds
  • In addition to elucidating protein functions, structural genomics can be used to identify novel protein folds and potential targets for drug discovery. (wikipedia.org)
  • One goal of structural genomics is to identify novel protein folds. (wikipedia.org)
  • Experimental methods of protein structure determination require proteins that express and/or crystallize well, which may inherently bias the kinds of proteins folds that this experimental data elucidate. (wikipedia.org)
  • A genomic, modeling-based approach such as ab initio modeling may be better able to identify novel protein folds than the experimental approaches because they are not limited by experimental constraints. (wikipedia.org)
  • Structural genomics can be used to predict novel protein folds based on other structural data. (wikipedia.org)
  • Hydrogen
  • The dotted orange lines indicate bottleneck radii of the p1 tunnel in DhaA crystal structures with added hydrogen atoms: PDB-IDs 1BN6 and 1BN7 (bottleneck radius 1.2 Å) and 1CQW (1.3 Å). (nih.gov)
  • B) The p1 tunnel identified in DhaA crystal structures with added hydrogen atoms (PDB-IDs 1CQW, 1BN6, 1BN7). (nih.gov)
  • The PPII helix is relatively open and has no internal hydrogen bonding, as opposed to the more common helical secondary structures, the alpha helix and its relatives the 310 helix and the pi helix, as well as the β-helix. (wikipedia.org)
  • Several different crystalline structures of cellulose are known, corresponding to the location of hydrogen bonds between and within strands. (wikipedia.org)
  • biological
  • Stefani M, Dobson CM. Protein aggregation and aggregate toxicity: new insights into protein folding, misfolding diseases and biological evolution. (springer.com)
  • p>This section provides any useful information about the protein, mostly biological knowledge. (uniprot.org)
  • binds
  • Lipid-binding protein that is able to promote the tubulation of the phosphatidic acid-containing membranes it preferentially binds. (uniprot.org)
  • The systematic arrestin name (1-4) plus the most widely used aliases for each arrestin subtype are listed in bold below: Arrestin-1 was originally identified as the S-antigen (SAG) causing uveitis (autoimmune eye disease), then independently described as a 48 kDa protein that binds light-activated phosphorylated rhodopsin before it became clear that both are one and the same. (wikipedia.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)
  • Interactions
  • Similar to other histone proteins, histone H2B has a distinct histone fold that is optimized for histone-histone as well as histone-DNA interactions. (wikipedia.org)
  • Hyperacetylation of histone tails helps DNA-binding proteins access chromatin by weakening histone-DNA and nucleosome-nucleosome interactions. (wikipedia.org)
  • this binding is important for many protein-protein interactions and even for interactions between the domains of a single protein. (wikipedia.org)
  • sequences
  • Promoters contain specific DNA sequences such as response elements that provide a secure initial binding site for RNA polymerase and for proteins called transcription factors that recruit RNA polymerase. (wikipedia.org)
  • Structural genomics takes advantage of completed genome sequences in several ways in order to determine protein structures. (wikipedia.org)
  • molecules
  • Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. (nih.gov)
  • Domains
  • This protein belongs to the LDLR family and is made up of a number of functionally distinct domains, including 3 EGF-like domains, 7 LDL-R class A domains, and 6 LDL-R class B repeats. (wikipedia.org)
  • Like other GT-B proteins, SPS contains two Rossman fold domains that are named the A domain and the B domain. (wikipedia.org)
  • Generally, the structure of these domains are somewhat similar, as both contain central beta sheets that are surrounded by alpha helices. (wikipedia.org)
  • kinases
  • In facultative aerobes the bacterial members of this family encode a single domain as a stand-alone protein, and genes that encode for either putative histidine kinases or diguanylate cyclases are found in the same predicted operon. (alusdomundo.com)
  • aggregation
  • Non-polyQ host protein regions modulate the misfolding pathway, suggesting an importance of protein context in aggregation. (springer.com)
  • This chapter describes the current research regarding polyQ misfolding, with emphasis on the species populated during aggregation, suggesting an important role of protein context in modulating the aggregation pathway. (springer.com)
  • Ferrone F. Analysis of protein aggregation kinetics. (springer.com)
  • aggregate
  • 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)
  • Modeling
  • This genome-based approach allows for a high-throughput method of structure determination by a combination of experimental and modeling approaches. (wikipedia.org)
  • mechanism
  • Arrestins were first discovered as a part of a conserved two-step mechanism for regulating the activity of G protein-coupled receptors (GPCRs) in the visual rhodopsin system by Hermann Kühn, Scott Hall, and Ursula Wilden and in the β-adrenergic system by Martin J. Lohse and co-workers. (wikipedia.org)
  • Images of an aerolysin oligomer derived from electron microscopy and molecular dynamics simulations have helped to construct a model of the protein in its heptameric conformation, and to outline a mechanism by which this assembly might insert into lipid bilayers to form ion channels. (wikipedia.org)
  • cell
  • The S-layer is made of a cell-surface glycoprotein, which accounts for approximately 50% of the cell surface proteins. (wikipedia.org)
  • Cell membranes are generally impermeable to ions, thus they must diffuse through the membrane through transmembrane protein channels. (wikipedia.org)
  • indicate
  • Although H. orenii is a non-photosynthetic bacterium, various studies indicate that the structure of its SPS is similar to plant SPS. (wikipedia.org)
  • form
  • Expression of mislocalized mutant syntaxin 3 in Madin-Darby canine kidney cells leads to basolateral mistargeting of apical membrane proteins, disturbance of tight junction formation, and loss of ability to form an organized polarized epithelium. (rupress.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)
  • These proteins form a lattice in the membrane. (wikipedia.org)
  • These octomers do not form higher order oligomers, and three of the eight proteins are glycosylated themselves. (wikipedia.org)
  • Two copies of histone H2B come together with two copies each of histone H2A, histone H3, and histone H4 to form the octamer core of the nucleosome to give structure to DNA. (wikipedia.org)
  • bacterial
  • Bacterial origins regulate orisome assembly, a nuclei-protein complex assembled on the origin responsible for unwinding the origin and loading all the replication machinery. (wikipedia.org)