• Two heat-stable globulins constitute 90% of the pulp-derived proteins: beta-conglycinin, which has a molecular weight (MW) of 180,000, and glycinin, which has an MW of 320,000. (medscape.com)
  • Insight II is a sophisticated molecular modeling environment that provides a graphical interface to best-of-breed algorithms for molecular dynamics, homology modeling, de novo design, and electrostatic. (file-extensions.org)
  • In the present study, we explored through computational molecular modeling the dynamic and flexibility properties of NS1 from three important influenza virus A strains belonging to three distinct subtypes (H1N1, H6N6, H5N1), for which at least one conformation is available in the Protein Data Bank. (fao.org)
  • Therefore, characterization and homology modeling of histamine receptors is of great importance. (scialert.net)
  • Histamine receptors are members of family G protein-coupled rhodopsin-like receptor. (scialert.net)
  • These receptors were seven pass transmembrane protein and found the gap between transmembrane helix number 5th and 6th of each histamine receptor except histamine H2 receptor which can be potential drug target candidate. (scialert.net)
  • Finally, 3D models of these receptors were developed through homology modeling and best models were selected by applying different model validation tools. (scialert.net)
  • Like all other histamine receptors, H3 is also a G protein coupled receptor but it inhibits cAMP synthesis. (scialert.net)
  • Its activity is directed by intracellular signals mediated by various types of receptors such as G protein-coupled receptors. (embl.de)
  • Our results suggest that life may have been constrained in its sampling of protein sequence space to catalyze one of the most energetically challenging biochemical reactions in nature. (elifesciences.org)
  • Proteomic and biochemical studies establish this plasma protein to be a liver-derived alkaloid-binding globulin (ABG) that is a member of the serine-protease inhibitor (serpin) family. (stanford.edu)
  • Due to the structural and biochemical homology between IGF-2 and insulin, elevated levels of IGF-2 can result in hypoglycemia. (medscape.com)
  • even the quaternary structure of a protein may be difficult to predict from homology models of its subunit(s). (wikipedia.org)
  • Nakamuta M, Chang BH, Hoogeveen R, Li WH, Chan L. Mouse microsomal triglyceride transfer protein large subunit: cDNA cloning, tissue-specific expression and chromosomal localization. (bdbiosciences.com)
  • 1 Department of Human Biological Chemistry and Genetics and Sealy Center for Structural Biology, University of Texas Medical Branch at Galveston, Galveston, Texas 77555-1055, USA. (nih.gov)
  • Unexpectedly, ABG is not related to saxiphilin, albumin, or other known vitamin carriers, but instead exhibits sequence and structural homology to mammalian hormone carriers and amphibian biliverdin-binding proteins. (stanford.edu)
  • In mammalian cells, adenylylation of small GTPases through Fic proteins injected by pathogenic bacteria can cause collapse of the actin cytoskeleton and cell death. (unibas.ch)
  • Because protein structures are more conserved than DNA sequences, and detectable levels of sequence similarity usually imply significant structural similarity. (wikipedia.org)
  • Thus, even proteins that have diverged appreciably in sequence but still share detectable similarity will also share common structural properties, particularly the overall fold. (wikipedia.org)
  • The degree of 3-dimensional shape similarity between proteins. (bvsalud.org)
  • Specifically, techniques such as domain identification, homology modeling, in silico drug screening, and pharmacophore identification allow us to develop a greater understanding of the potential roles of these proteins in signal transduction and gene expression. (mdpi.com)
  • The transcription of COX-1 yields a 2.7-kilobase (kb) messenger ribonucleic acid (mRNA) that encodes a 576-residue, 65-kd protein. (medscape.com)
  • Conversely, the transcription of COX-2 yields a 4.5-kb mRNA that encodes a 70-kd protein with roughly 70-75% homology to the COX-1 protein. (medscape.com)
  • BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. (nih.gov)
  • BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions. (nih.gov)
  • There are 39736 RhoGEF domains in 38458 proteins in SMART's nrdb database. (embl.de)
  • The flexibility of NS1 is a key property that allows its effector domains and its RNA binding domain to interact with several protein partners or RNAs. (fao.org)
  • It is unknown how this potentially deleterious adenylylation activity is regulated in the widespread Fic proteins that are found in all domains of life and that are thought to have critical roles in intrinsic signalling processes. (unibas.ch)
  • Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. (wikipedia.org)
  • Nevertheless, homology models can be useful in reaching qualitative conclusions about the biochemistry of the query sequence, especially in formulating hypotheses about why certain residues are conserved, which may in turn lead to experiments to test those hypotheses. (wikipedia.org)
  • For example, the spatial arrangement of conserved residues may suggest whether a particular residue is conserved to stabilize the folding, to participate in binding some small molecule, or to foster association with another protein or nucleic acid. (wikipedia.org)
  • In the past, several methods for predicting protein solvent accessible surface area have been implemented mostly in a discrete fashion as the two-state or three-state classification of the exposure rate of residues. (biomedcentral.com)
  • The proteins encoded by members of the Dbl family share a common domain, presented in this entry, of about 200 residues (designated the Dbl homology or DH domain) that has been shown to encode a GEF activity specific for a number of Rho family members. (embl.de)
  • The current view of protein folding and stability is largely based on SAXS and DLS data13-16 and the extensive exposure of hydropho- a generic structural classification into native (N), compact dena- bic residues suggested by the finding that the heat capacity of the tured or molten globule (MG), and unfolded or denatured (D) MG state is midway between that of the N and D states7 have been conformational states1-10. (lu.se)
  • The approach can be complicated by the presence of alignment gaps (commonly called indels) that indicate a structural region present in the target but not in the template, and by structure gaps in the template that arise from poor resolution in the experimental procedure (usually X-ray crystallography) used to solve the structure. (wikipedia.org)
  • Because it is difficult and time-consuming to obtain experimental structures from methods such as X-ray crystallography and protein NMR for every protein of interest, homology modeling can provide useful structural models for generating hypotheses about a protein's function and directing further experimental work. (wikipedia.org)
  • We obtain 0.70 three-state accuracy for solvent accessibility, 0.33 15-state accuracy and 0.74 Pearson Correlation Coefficient (PCC) for the contact number on the 5729 monomeric soluble globular protein dataset. (biomedcentral.com)
  • Inferences about hydration have usually been indirect (where the ous structural and dynamic information about the internal peptide chain is not, there is solvent) or have relied on uncertain (buried) and external (surface) hydration of globular proteins in premises. (lu.se)
  • Specific and non-specific diffusion channels, together with biogenesis/secretion proteins have a crucial role in the bacterial life. (frontiersin.org)
  • Our observations support an active role of the ER in mitochondrial protein biogenesis. (biorxiv.org)
  • After mutation of the inhibitory motif in various Fic proteins, including the human homologue FICD (also known as HYPE), adenylylation activity is considerably boosted, consistent with the anticipated relief of inhibition. (unibas.ch)
  • In this study, we present DeepSacon, a computational method that can effectively predict protein solvent accessibility and contact number by using a deep neural network, which is built based on stacked autoencoder and a dropout method. (biomedcentral.com)
  • During the past few years, there are numerous studies focused on developing computational methods to predict contact number in the protein sequence. (biomedcentral.com)
  • It making it the perfect solution for protein modelers, computational chemists, and structural biologists. (file-extensions.org)
  • Thus, MTP is a microsomal protein that is required for transport of lipids between membranes in liver and small intestines. (bdbiosciences.com)
  • Both methods yield antibody in solution that is free of most other soluble proteins, lipids, etc. (bdbiosciences.com)
  • ApoB100 is required for increased VLDL-triglyceride secretion by microsomal triglyceride transfer protein in ob/ob mice. (bdbiosciences.com)
  • ABG represents a new small molecule binding functionality in serpin proteins, a novel mechanism of plasma alkaloid transport in poison frogs, and more broadly points toward serpins acting as tunable scaffolds for small molecule binding and transport across different organisms. (stanford.edu)
  • Like all members of the Ras superfamily, the Rho proteins cycle between active GTP-bound and inactive GDP-bound conformational states. (embl.de)
  • Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. (wikipedia.org)
  • It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence conservation alone. (wikipedia.org)
  • It does not share significant sequence homology with other subtypes of small G-protein GEF motifs such as the Cdc25 domain and the Sec7 domain, which specifically interact with Ras and ARF family small GTPases, respectively, nor with other Rho protein interactive motifs, indicating that the Dbl family proteins are evolutionarily unique. (embl.de)
  • The structural elements preserved in two viral strains, were identified using the comparative analysis of simulated structure with that of homologous site for the HIV-Thailand gp120 V3 loop. (msk.ru)
  • In order to verify whether NS1 is stable in three forms for the three strains, we constructed homology models if the corresponding forms were not available in the Protein Data Bank. (fao.org)
  • SNX9, also known as SH3PX1, is a cytosolic protein that interacts with proteins associated with clathrin-coated pits such as Cdc-42-associated tyrosine kinase 2 (ACK2). (nih.gov)
  • Most mitochondrial proteins are synthesized on cytosolic ribosomes and imported into mitochondria in a post-translational reaction. (biorxiv.org)
  • Except for a handful of mitochondrially encoded proteins, all these proteins are encoded by nuclear genes and synthesized on cytosolic ribosomes. (biorxiv.org)
  • Putative characterizations of hypothetical proteins open doors to novel insights expanding our knowledge of the pathophysiology of both acute and chronic diseases. (mdpi.com)
  • Here, we present the upgrade of OMPdb, which from now on aims to become a global repository for all transmembrane β-barrel proteins, both eukaryotic and bacterial. (frontiersin.org)
  • However, the β-barrel membrane proteins participate in crucial biological activities in prokaryotic organisms, as well as in the eukaryotic organelles. (frontiersin.org)
  • Despite the universality of this process, eukaryotic ribosomes are significantly larger in size than their bacterial counterparts due in part to the presence of 80 r proteins rather than 54 in bacteria. (cipsm.de)
  • These findings shed new light on hydrophobic stabilization of proteins. (lu.se)
  • Whereas the N state has been character- taken to imply that hundreds of water molecules penetrate the MG ized at high resolution, many aspects of the D and MG states are protein (except for a relatively small hydrophobic core)5,7,8,17-19. (lu.se)
  • However, the errors are significantly higher in the loop regions, where the amino acid sequences of the target and template proteins may be completely different. (wikipedia.org)
  • However, it is exceedingly difficult to directly predict proteins 3D structures from amino acid sequences [ 4 ]. (biomedcentral.com)
  • Histamine H1 receptor is G protein coupled receptor, which up regulates NF-κB activity there by, elicits inflammation. (scialert.net)
  • Protein phosphorylation is the most common post-translation modification of proteins and regulates many biological processes. (lu.se)
  • We use chemical approaches to show that a ~50 kDa plasma protein is the principal alkaloid-binding molecule in blood of poison frogs. (stanford.edu)
  • Homology modeling can produce high-quality structural models when the target and template are closely related, which has inspired the formation of a structural genomics consortium dedicated to the production of representative experimental structures for all classes of protein folds. (wikipedia.org)
  • The field of structural genomics has been expanding rapidly for several years. (mdpi.com)
  • Mitochondrial precursor proteins which use the ER-SURF pathway employ the surface of the endoplasmic reticulum (ER) as an important sorting platform. (biorxiv.org)
  • Here we show that mitochondrial contact sites play a crucial role in the ER-to-mitochondria transfer of precursor proteins. (biorxiv.org)
  • When ER-to-mitochondria transfer is prevented, many mitochondrial precursor proteins associate with ER membranes, resulting in mitochondrial dysfunction. (biorxiv.org)
  • Owing to a very powerful in vitro import system based on isolated yeast mitochondria and radiolabeled precursor proteins, the different steps of the mitochondrial import reaction were elucidated in great detail. (biorxiv.org)
  • Self-assembly of a membrane protein governed by the fluctuation of the anchor peptide and the self-organization. (nii.ac.jp)
  • Binding energy were calculated for the protein-ligand poses of lowest -Cdocker Energy and -Cdocker Interaction. (bvsalud.org)
  • It has been seen that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure. (wikipedia.org)
  • The sequence alignment and template structure are then used to produce a structural model of the target. (wikipedia.org)
  • The quality of the homology model is dependent on the quality of the sequence alignment and template structure. (wikipedia.org)
  • Like other methods of structure prediction, current practice in homology modeling is assessed in a biennial large-scale experiment known as the Critical Assessment of Techniques for Protein Structure Prediction, or CASP. (wikipedia.org)
  • The method of homology modeling is based on the observation that protein tertiary structure is better conserved than amino acid sequence. (wikipedia.org)
  • We determined the crystal structure of NL63-CoV spike protein receptor-binding domain (RBD) complexed with human ACE2. (proteopedia.org)
  • Significant structural characteristics such as solvent accessibility and contact number are essential for deriving restrains in modeling protein folding and protein 3D structure. (biomedcentral.com)
  • Accurate prediction of structural characteristics from the primary sequence is a crucial intermediate step in protein 3D structure prediction [ 8 , 9 ]. (biomedcentral.com)
  • The contact number is also essential for protein structure prediction since the number of possible protein conformations is very limited [ 34 ] within a certain number of contacts along the protein chain. (biomedcentral.com)
  • Although the high-resolution structure of a protein may provide significant insight into which regions are important for function, it is well-known that proteins undergo significant conformational fluctuations, even under native conditions. (nih.gov)
  • In addition to determining the first solution structure of the unliganded protein, we have performed (15)N relaxation and native state hydrogen-deuterium exchange. (nih.gov)
  • Higher-order multi-protein complexes such as RNA polymerase II (Pol II) complexes with transcription initiation factors are often not amenable to X-ray structure determination. (cipsm.de)
  • Structural Maintenance of Chromosomes (SMC) proteins are essential for a wide range of processes including chromosome structure and dynamics, gene regulation, and DNA repair. (cipsm.de)
  • For -lactalbu- min, only water molecules conserved in the human and baboon structures are shown (the structure of the bovine protein has not been reported). (lu.se)
  • Direct prediction of the three-dimensional (3D) structures of proteins from one-dimensional (1D) sequences is a challenging problem. (biomedcentral.com)
  • Nitrogenase ancestors are active and robust to variable incorporation of one or more ancestral protein subunits. (elifesciences.org)
  • Association of the proto-oncogene product dbl with G protein betagamma subunits. (embl.de)
  • Their non-structural protein NS1, a homodimer of two 230-residue chains, is the main viral factor in counteracting the antiviral defenses of the host cell. (fao.org)
  • While bacteria and archaea have one SMC protein that forms a homodimer, eukaryotes possess three distinct SMC complexes, consisting of heterodimeric pairs of six different SMC proteins. (cipsm.de)
  • The chief inaccuracies in homology modeling, which worsen with lower sequence identity, derive from errors in the initial sequence alignment and from improper template selection. (wikipedia.org)
  • The results show that nonnative proteins are more structured and less solvent exposed than commonly believed. (lu.se)
  • Considering the widely acknowledged Accordingly, theoretical models of the MG state invariably invoke importance of protein-solvent interactions for stability and fold- a substantial internal hydration20-22. (lu.se)
  • The microsomal triglyceride transfer protein (MTP) catalyzes the transport of triglyceride, cholesteryl ester, and phospholipid between membranes within the lumen of microsomes in hepatocytes and enterocytes. (bdbiosciences.com)
  • The origin of this structural polymorphism is currently being investigated and several hypotheses are proposed, among which one posits that it is a strain-specific property. (fao.org)
  • There are exceptions to the general rule that proteins sharing significant sequence identity will share a fold. (wikipedia.org)
  • However, the general agreement is that a significant number of children with cow's milk protein intolerance develop soy protein intolerance when soy milk is used in dietary management. (medscape.com)
  • All soybean proteins and foods currently available for human consumption contain significant amounts of the isoflavones daidzein and genistein, either in the unconjugate form or as different types of glycoside conjugates. (medscape.com)
  • Despite the proposed roles of plasma proteins as mediators of alkaloid trafficking and bioavailability, the responsible proteins have not been identified. (stanford.edu)
  • p27 is a protein that binds to and prevents the activation of different G1. (lu.se)
  • Protein and Peptide Sci. (msk.ru)
  • The elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer RNAs to the aminoacyl-tRNA-binding site (A site) of the ribosome, followed by peptide-bond formation and translocation of the tRNAs through the ribosome to reopen the A site1, 2. (cipsm.de)
  • the c-terminal membrane-binding portion contributes to the Golgi disassembly and, therefore, functionally similar to the picornavirus 2B protein" /protein_id="NP_786945.1" mat_peptide 1199. (cdc.gov)
  • the calicivirus NTPase was found in membranous replication complexes" /protein_id="NP_786946.1" mat_peptide 2288. (cdc.gov)
  • The gene expression of DNA damage inducible protein and DNA damage in response to head DNA % and tail DNA % was protected by Mn-NPs diets. (bvsalud.org)
  • Activation of Rho proteins through release of bound GDP and subsequent binding of GTP, is catalysed by guanine nucleotide exchange factors (GEFs) in the Dbl family. (embl.de)
  • PDI catalyzes the isomerization of intramolecular disulfide bridges, thereby allowing them to generate their most thermodynamically stable configuration within proteins. (bdbiosciences.com)
  • Our results favor the co-existence of three stable structural forms, regardless of the strain, but also suggest that the length of the linker, along with the presence of specific amino acids, modulate the dynamic properties and the flexibility of NS1. (fao.org)
  • The need for high-quality analyses of protein structures is valuable to drug design efforts and chemotherapeutic applications. (mdpi.com)
  • For many years after the first description by Duke in 1934, soy was considered a weak sensitizing protein based on animal study findings. (medscape.com)
  • Findings suggest that fibrodysplasia ossificans progressiva maps to band 4q27-31, a region that contains at least 1 gene involved in the bone morphogenic protein (BMP) signaling pathway. (medscape.com)