Uses of the structural models include protein-protein interaction prediction, protein-protein docking, molecular docking, and ... Chung SY, Subbiah S. (1996.) A structural explanation for the twilight zone of protein sequence homology. Structure 4: 1123-27 ... Protein structure prediction Protein structure prediction software Protein threading Molecular replacement Chothia, C; Lesk, AM ... Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein ...

In this work, homology models of both proteins were constructed and analyzed for a number of structural properties. The ... Homology modeling reveals the structural background of the striking difference in thermal stability between two related [NiFe] ... the homology models reliably predict that HydSL contains at least five more inter-subunit ion pairs than HupSL. The subunit ... the role of electrostatic interactions in protein stability increases. Electronic supplementary material to this paper can be ...

... is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling ... Protein Structure, Tertiary * Proteome / chemistry * Scattering, Small Angle * Structural Homology, Protein* * X-Ray ... Structural Bioinformatics Unit, Structural Biology and Chemistry department, Institut Pasteur, 25 rue du Docteur Roux, 75015 ... ModBase, a database of annotated comparative protein structure models and associated resources Nucleic Acids Res. 2014 Jan;42( ...

Three Dimensional Structural Modelling of Lipase Encoding Gene from Soil Bacterium Alcaligenes sp. JG3 Using Automated Protein ... JG3 Using Automated Protein Homology Analysis. https://doi.org/10.22146/ijc.34152 Dilin Rahayu Nataningtyas(1), Tri Joko ... 14] Kelley, L.A., Mezulis, S., Yates, C.M., Wass, M.N., and Sternberg, M.J., 2015, The Phyre2 web portal for protein modeling, ... 34] Muneyuki, E., Noji, H., Amano, T., Masaike, T., and Yoshida, M., 2000, F0F1-ATP synthase: General structural features of ...

... family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic ... Complexes containing a pair of structural maintenance of chromosomes (SMC) ... SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Res. 46, W296-W303 (2018). ... Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three- ...

The isoflavones have structural homology to steroidal estrogens; therefore, they are considered to be phytoestrogens, but ... However, other soy proteins can act as allergens in humans. At least 9 proteins with MW ranging from 14,875-54,500 were found ... According to some animal study findings, soy proteins appear to be less sensitizing than cows milk proteins; however, infants ... Among children with cows milk protein intolerance, infants younger than 3 months are at higher risk for developing soy protein ...

SCOPe: Structural Classification of Proteins - extended. Release 2.08 (updated 2023-01-06, stable release September 2021) ... Lineage for Superfamily a.40.1: Calponin-homology domain, CH-domain. *Root: SCOPe 2.08 *. Class a: All alpha proteins [46456] ( ... Timeline for Superfamily a.40.1: Calponin-homology domain, CH-domain: *Superfamily a.40.1: Calponin-homology domain, CH-domain ... a.40.1.1: Calponin-homology domain, CH-domain [47577] (10 proteins). Pfam PF00307. ...

SCOPe: Structural Classification of Proteins - extended. Release 2.08 (updated 2023-01-06, stable release September 2021) ... e.40.1.1: Cullin homology domain [75633] (2 proteins). More info for Superfamily e.40.1: Cullin homology domain. Timeline for ... Lineage for Superfamily e.40.1: Cullin homology domain. *Root: SCOPe 2.08 *. Class e: Multi-domain proteins (alpha and beta) [ ... Superfamily e.40.1: Cullin homology domain first appeared in SCOP 1.61, called Superfamily e.40.1: Culin homology domain. * ...

Protein structure homology models SwissDock Docking of small ligands into protein active sites ...

Proteins in high-quality scientific databases and software tools using Expasy, the Swiss Bioinformatics Resource Portal. ... You can also query Proteins into a selection of SIB databases in parallel ...

In this work, we generated and optimized a new synthetic fusion protein using an evolutionary approach. The optimization was ... Computational design of novel proteins with well-defined functions is an ongoing topic in computational biology. ... However, analogous proteins may have structural homology although this is not a prerequisite. Prominent examples are the ... Protein Z and MyoD. Protein Z is derived from staphylococcal protein A and holds an IgG Fc-binding domain. It consists of a ...

A) Three-dimensional structural homology model for the hemagglutinin protein of EG-CA285 created by using... ... A) Three-dimensional structural homology model for the hemagglutinin protein of EG-CA285 created... ... Structural and phylogenetic modeling of highly pathogenic avian influenza virus (H5N8), EG-CA285, from migratory birds, Egypt, ... Structural and phylogenetic modeling of highly pathogenic avian influenza virus (H5N8), EG-CA285, from migratory birds, Egypt, ...

Rab isoforms are thought to be functionally related on the basis of structural homology. However, there is very little direct ... VPS21 encodes a rab5-like GTP binding protein that is required for the sorting of yeast vacuolar proteins. EMBO J 1994. 15:1297 ... The protein concentration of all lysates and fractions was determined using Coomassie Plus Protein Assay Reagent (Perbio ... no protein could be detected in homozygous ashen (ash/ash) mutants, presumably because the truncated mutant protein is unstable ...

... of PI3KC2α at membranes that involves large-scale repositioning of its Ras-binding and lipid-binding distal Phox-homology and C ... 1c), suggesting that it exhibits a structural role as a protein interaction scaffold, as corroborated below (Fig. 6). The HBD ... 26). Consistently, we found that the HBD of PI3KC2α with its four antiparallel α-helices displays strong structural homology to ... 4,7,8,27) that are understood in structural detail, little is known about the structural and functional architecture, and ...

show a high degree of structural homology with myoglobin. a1b1 act as a pair as well as a2b2. each subunits contain a molecule ... Intrinsically Unstructured Proteins (IUP)/Natively Unfolded Proteins. Definition. Low molecular weight proteins that are fully ... Three Major Classes of Proteins based upon their final folded shape. Definition. Fibrous Proteins, Globular Proteins, and ... The energy formed from the formation of ADP is used to (re)fold the protein, release GroES (again), and release the protein. It ...

Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is ... Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is ... Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and ... Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and ...

Oezguen is interested in the structural aspects of protein function, protein-protein and protein-ligand interactions. His ... expertise includes sequence analysis, homology modeling, molecular dynamic simulations and docking. He is also interested in ... are keenly focused on the development of bioanalytical methods to measure endogenous and exogenous small-molecules and proteins ... interactions in the gastrointestinal tract using a range of techniques that include computational and structural biology, ...

Structural similarity, serological and sequence homology; the principal aim of this is to determine whether and to what level ... The use of the protein database offers the possibility of determining the similarity of the novel protein of interest with ... This means that there is a need for improving the methods that are used in plant profiling of their proteins as well as ... This is through the determination of the overall structure of the protein of interest and its similarity to allergens that are ...

Every tenth protein had no known homolog in current databases, and 30%-40% of the proteins fell into structural families with , ... the regions with structural homology covered 20%-30% of all residues. These numbers may or may not suggest that there are 1200- ... We could not find a correlation between the content of membrane proteins and the complexity of the organism. In particular, we ... We found twice as many coiled-coil proteins in eukaryotes (10%) as in prokaryotes and archaes (4%-5%), and we predicted ...

Analysis of the protein sequences of the three CpHsps indicated the presence of 83 amino acids with homology to the a- ... consistent with the conserved structural features of sHsps. Real-time PCR, used to determine the expression patterns of each of ... Title: Characterization of three transcripts encoding small heat shock proteins expressed in the codling moth, Cydia pomonella ... The small heat shock proteins (sHsps) play a major role in cellular responses to environmental stressors. A degenerate ...

The Solution Structure of the Adhesion Protein Bd37 from Babesia divergens Reveals Structural Homology with Eukaryotic Proteins ... Structural and Functional Characterization of Bc28.1, Major Erythrocyte-binding Protein from Babesia canis Merozoite Surface ... Protein sequence database searches suggested that the 41-kDa protein belongs to the phosphofructokinase B type family (PFK-B). ... Protein sequence database searches suggested that the 41-kDa protein belongs to the phosphofructokinase B type family (PFK-B). ...

X-ray crystallography of OIF and NGF-beta confirmed their structural and sequence homology. ... This led Adams and collaborator Marcelo Ratto at Universidad Austral de Chile to hypothesize that OIF was a single protein ... In order to identify the chemical structure of OIF, Addams and Ratto collaborated with protein chemist Louis Delbaere at the ... a neurotrophic protein involved in nerve development, which has the same chemical structure as OIF. The research may help shed ...

2006) Bruchpilot, a protein with homology to ELKS/CAST, is required for structural integrity and function of synaptic active ... 2000) The RIM/NIM family of neuronal C2 domain proteins. Interactions with Rab3 and a new class of Src homology 3 domain ... Studies of RIM in rodents and C. elegans indicate that RIM proteins localize to presynaptic release sites and bind to proteins ... 2003) Genomic definition of RIM proteins: evolutionary amplification of a family of synaptic regulatory proteins (small star, ...

A selection of influential publications from the Principal Investigators of the Structural Cell Biology Section ... Structural Insights into the Mechanism of Dynamin Superfamily Proteins.. Jimah JR, Hinshaw JE.. Trends Cell Biol (2019 Mar) 29: ... A possible effector role for the pleckstrin homology (PH) domain of dynamin.. Bethoney KA, King MC, Hinshaw JE, Ostap EM, ... Membrane-bending proteins.. Prinz WA, Hinshaw JE.. Crit Rev Biochem Mol Biol (2009 Sep-Oct) 44:278-91. Abstract/Full Text. ...

It belongs to the CD34/Podocalyxin family of sialomucins that share structural similarity and sequence homology. It is ... Identification of the SHREK family of proteins as broad-spectrum host antiviral factors Authors: D Dabbagh, S He, B Hetrick, L ... Endoglycan, also named Podocalyxin-like 2 protein, is a type I transmembrane glycoprotein. ...

... and refined by homology with the yeast subunit a (Vph1p).9 The putative structural consequences of mutations were estimated in ... completely disrupt the protein function.12 For example, the two siblings (cases 25 and 26) who were homozygotes for c.1371delC ... 6 Prediction of the protein domains was based on the potential topological domains reported in UniProt database (Q13488; www. ...

The table covers roughly 92 percent of known protein complex structures while also enabling predictions of new structures ... "So you could combine it with [for instance] crosslinking mass spec and homology modeling for trying to predict the actual ... They also analyzed large collections of protein complex structural data taken from resources including the Protein Data Bank. ... Researchers Use Mass Spec, Structural Data to Devise Periodic Table of Protein Complexes Dec 23, 2015 , Adam Bonislawski ...

Structural data may reveal homologies not detectable at the sequence level, helping to reveal the functions of individual ... Protein-protein interactions and proximity interactions. Numerous candidate ALMS1-interacting proteins have been reported. ... It is not hard to imagine ALMS1 performing a structural role such as tethering other proteins to the base of centrioles. ... The ALMS1 protein. ALMS1 is a large (, 4000 residue) protein that lacks known catalytic domains [11, 12]. It has several ...

Wheat germ cell-free expression system as a pathway to improve protein yield and solubility for the SSGCID pipeline ... Protein selection. Proteins in this analysis are a subset of protein targets entered into the Seattle Structural Genomics ... Proteins within target organisms were selected bioinformatically for homology to current drug targets or nominated for ... Keywords: cell-free expression; protein expression; protein solubility; Seattle Structural Genomics Center for Infectious ...

We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the ... We also constructed, by homology modeling, a theoretical structure of the pUL105 N-terminal domain which indicates that the ... The homology model for both proteins was built through CPHmodels-3.2 server that used as template the coordinates of the ... To assess this potential similarity of function at the structural level, we also built a first homology model of the HSV-1 ...