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  • Structure
  • We are investigating the interactions that (a) dictate the folding of a polypeptide chain in water into the three-dimensional structure of a native protein and (b) determine the reactivity of such a protein molecule (e.g., as an enzyme) with other small and large molecules. (cornell.edu)
  • Structure
  • We are investigating the interactions that (a) dictate the folding of a polypeptide chain in water into the three-dimensional structure of a native protein and (b) determine the reactivity of such a protein molecule (e.g., as an enzyme) with other small and large molecules. (cornell.edu)
  • Mitochondria
  • 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)
  • 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)
  • Changes in sequence that increase flexibility of regions of the enzyme involved in catalytic conformational changes may reduce energy (enthalpy) barriers to these rate-governing shifts in conformation and, thereby, increase kcat. (antibody-antibodies.com)
  • 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)
  • 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)
  • pathways
  • Folding versus aggregation: polypeptide conformations on competing pathways. (springer.com)
  • 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)
  • 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)
  • membrane
  • 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)
  • 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)
  • 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)
  • Fis1p is the first integral membrane protein shown to participate in a eukaryotic membrane fission event. (nih.gov)
  • 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)
  • These proteins form a lattice in the membrane. (wikipedia.org)
  • H. salinarum express the membrane protein bacteriorhodopsin which acts as a light-driven proton pump. (wikipedia.org)
  • Voltage-gated ion channels are a class of transmembrane proteins that form ion channels that are activated by changes in the electrical membrane potential near the channel. (wikipedia.org)
  • The membrane potential alters the conformation of the channel proteins, regulating their opening and closing. (wikipedia.org)
  • Cell membranes are generally impermeable to ions, thus they must diffuse through the membrane through transmembrane protein channels. (wikipedia.org)
  • Oligosaccharyltransferase or OST (EC 2.4.1.119) is a membrane protein complex that transfers a 14-sugar oligosaccharide from dolichol to nascent protein. (wikipedia.org)
  • Yeast OST is composed of eight different membrane-spanning proteins in three subcomplexes (one of them is OST4). (wikipedia.org)
  • The baseplate changes conformation and the tail sheath contracts, causing GP5 at the end of the tail tube to puncture the outer membrane of the cell. (wikipedia.org)
  • residue
  • e.g. a truncation of the receptor protein at residue number 660 leads to domains 3,4 and 5 of the EGF precursor domain being missing. (wikipedia.org)
  • In this closed conformation, the Gly-34 residue of the A domain interacts with UDP-glucose and forces the substrate to adapt a folded structure, facilitating its donation of the hexosyl group. (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)
  • genome
  • Structural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome. (wikipedia.org)
  • The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein. (wikipedia.org)
  • coli
  • 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)
  • affinity
  • For example, many DNA binding proteins that have affinity for specific DNA binding sites bind DNA in only its double-helical form. (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)
  • 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)
  • structural
  • Because protein structure is closely linked with protein function, the structural genomics has the potential to inform knowledge of protein function. (wikipedia.org)
  • As opposed to traditional structural biology, the determination of a protein structure through a structural genomics effort often (but not always) comes before anything is known regarding the protein function. (wikipedia.org)
  • This raises new challenges in structural bioinformatics, i.e. determining protein function from its 3D structure. (wikipedia.org)
  • Thus, the high-throughput structure determination methods of structural genomics have the potential to inform our understanding of protein functions. (wikipedia.org)
  • The Protein Structure Initiative (PSI) is a multifaceted effort funded by the National Institutes of Health with various academic and industrial partners that aims to increase knowledge of protein structure using a structural genomics approach and to improve structure-determination methodology. (wikipedia.org)
  • Structural genomics can also take modeling-based approach that relies on homology between the unknown protein and a solved protein structure. (wikipedia.org)
  • Histone H2B is a structural protein that helps organize eukaryotic DNA. (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)
  • this binding is important for many protein-protein interactions and even for interactions between the domains of a single protein. (wikipedia.org)
  • sequences
  • Noncoding" sequences are not translated into proteins, and nucleic acids with such motifs need not deviate from the typical shape (e.g. the "B-form" DNA double helix). (wikipedia.org)
  • 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)
  • mainly
  • This structure is somewhat similar to that adopted in the fibrous protein collagen, which is composed mainly of proline, hydroxyproline, and glycine. (wikipedia.org)
  • poorly
  • 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)
  • Hydrogen
  • In the open conformation of H. orenii SPS, fructose 6-phosphate forms hydrogen bonds with Gly-33 and Gln-35 residues in the A domain while UDP-glucose interacts with the B-domain. (wikipedia.org)
  • important
  • 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)
  • Arrestins (abbreviated Arr) are a small family of proteins important for regulating signal transduction at G protein-coupled receptors. (wikipedia.org)
  • receptor
  • The receptor also recognizes the apoE protein found in chylomicron remnants and VLDL remnants (IDL). (wikipedia.org)
  • In humans, the LDL receptor protein is encoded by the LDLR gene on chromosome 19. (wikipedia.org)
  • This precludes the movement of the receptor from the ER to the Golgi, and leads to degradation of the receptor protein. (wikipedia.org)
  • The first step is phosphorylation by a class of serine/threonine kinases called G protein coupled receptor kinases (GRKs). (wikipedia.org)
  • First, arrestin binding to the cytoplasmic face of the receptor occludes the binding site for heterotrimeric G-protein, preventing its activation (desensitization). (wikipedia.org)
  • distinct
  • 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)
  • form
  • 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)
  • These octomers do not form higher order oligomers, and three of the eight proteins are glycosylated themselves. (wikipedia.org)
  • Domain
  • A, B and C. A and B are closely linked while C is separated by the YWTD repeat region, which adopts a beta-propeller conformation (LDL-R class B domain). (wikipedia.org)
  • A third domain of the protein is rich in O-linked oligosaccharides but appears to show little function. (wikipedia.org)
  • highly
  • These highly acidic proteins are overwhelmingly negative in charge and are able to remain in solution even at high salt concentrations. (wikipedia.org)
  • These are highly involved in condensing chromatin from the beads-on-a-string conformation to a 30-nm fiber. (wikipedia.org)
  • usually
  • Targeting information is usually present in the cargo proteins themselves. (rupress.org)
  • It usually acts during translation as the nascent protein is entering the ER, but this cotranslational glycosylation is nevertheless called a posttranslational modification. (wikipedia.org)