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 ...

... a common piece in the structural patchwork of signalling proteins". Trends in Biochemical Sciences. 18 (9): 343-8. doi:10.1016/ ... ARAP proteins contain five PH domains. Serine/threonine-specific protein kinases such as the Akt/Rac family, protein kinase D1 ... and proteins such as the βγ-subunits of heterotrimeric G proteins, and protein kinase C. Through these interactions, PH domains ... Pleckstrin homology domain (PH domain) or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide ...

Hazai E, Bikádi Z (April 2008). "Homology modeling of breast cancer resistance protein (ABCG2)". Journal of Structural Biology ... April 2018). "Structural basis of small-molecule inhibition of human multidrug transporter ABCG2". Nature Structural & ... Alternatively referred to as the breast cancer resistance protein (BCRP), this protein functions as a xenobiotic transporter ... The protein also carries the Jr(a) antigen, which defines the Junior blood group system. It is inhibited by some calcium ...

"Phyre2: Protein Homology/analogY Recognition Engine V 2.0". Structural Bioinformatics Group, Imperial College, London. ... "Phyre: Protein Homology/analogY Recognition Engine". Structural Bioinformatics Group, Imperial College, London. Retrieved 22 ... Phyre and Phyre2 (Protein Homology/AnalogY Recognition Engine; pronounced as 'fire') are free web-based services for protein ... Like other remote homology recognition techniques (see protein threading), it is able to regularly generate reliable protein ...

"Structural modeling of ataxin-3 reveals distant homology to adaptins". Proteins. 50 (2): 355-70. doi:10.1002/prot.10280. PMID ... The protein encoded by the ATXN3 gene contains CAG repeats in the coding region, and the expansion of these repeats from the ... Ataxin-3 is a protein that in humans is encoded by the ATXN3 gene. Machado-Joseph disease, also known as spinocerebellar ataxia ... Wang Q, Li L, Ye Y (Mar 2008). "Inhibition of p97-dependent protein degradation by Eeyarestatin I". The Journal of Biological ...

Chung SY, Subbiah S (October 1996). "A structural explanation for the twilight zone of protein sequence homology". Structure. 4 ... Protein tandem repeats, Protein folds, Protein superfamilies, Protein domains). ... a de novo protein designed to adopt the alpha/beta-barrel packing)". Protein Engineering. 4 (7): 745-9. doi:10.1093/protein/4.7 ... Structural inserts ranging from extended loops to independent protein domains may be inserted in place of these loops or at the ...

This region shares homology with cholesterol-dependent cytolysins from Gram-positive bacteria. Perforin has structural and ... This protein is one of the main cytolytic proteins of cytolytic granules, and it is known to be a key effector molecule for T- ... Tschopp J; Masson D; Stanley KK (1986). "Structural/functional similarity between proteins involved in complement- and ... Perforin-1 is a protein that in humans is encoded by the PRF1 gene and the Prf1 gene in mice. Perforin is a pore forming ...

Andrade MA, Ponting CP, Gibson TJ, Bork P (May 2000). "Homology-based method for identification of protein repeats using ... Kajava AV (September 2012). "Tandem repeats in proteins: from sequence to structure". Journal of Structural Biology. 179 (3): ... Tandem repeat proteins frequently function as protein-protein interaction modules. The WD40 repeat is a prime example of this ... Specialized methods were built for the identification of repeat proteins. Sequence-based strategies, based on homology search ...

However, many proteins have retained very similar structures, and structural alignment can be used to demonstrate their ... As with anatomical structures, sequence homology between protein or DNA sequences is defined in terms of shared ancestry. Two ... "Homology: From jaws to ears - an unusual example of a homology". UC Berkeley. Retrieved 15 December 2016. Hyde, Janet Shibley; ... Sattler, R. (1994). "Homology, homeosis, and process morphology in plants". In Hall, Brian Keith (ed.). Homology: the ...

HSSP (Homology-derived Secondary Structure of Proteins) is a database that combines structural and sequence information about ... HSSP is also a database of homology-based implied protein structures. Protein Data Bank (PDB) STING Schneider, R.; de Daruvar, ... This database has the information of the alignment of all available homologs of proteins from the PDB database As a result of ... A. & Sander, C. (1997). "The HSSP database of protein structure-sequence alignments". Nucleic Acids Research. 25 (1): 226-230. ...

Mobarec JC, Sanchez R, Filizola M (2009). "Modern homology modeling of G-protein coupled receptors: which structural template ... "G Protein-Coupled Receptors - Modeling and Simulation" and "G Protein-Coupled Receptors in Drug Discovery". She is also an ... "Structural Aspects of Oligomerization in the Function of GPCRs - Marta Filizola". Grantome.com. Retrieved 2016-01-31. "Marta ... She is best known for her work aimed at providing mechanistic insight into the structure, dynamics, and function of G protein- ...

Structural homology indicated it may have some similarity to the enzyme family, hydrolase. At the cellular level, the YjeF-N ... In molecular biology, the YjeF N terminal is a protein domain found in the N-terminal of the protein, EDC3. The YjeF N-terminal ... Examples of such include: pyridoxal phosphate biosynthetic protein PdxJ; phosphopanteine-protein transferase; ATP/GTP hydrolase ... YjeF N-terminal domains are often fused to a YjeF C-terminal domain with high structural homology to the members of a ...

The degree of similarity with the latter proteins is insufficient to establish homology. As of early 2016, no crystal ... structural data is available for members of the BenE family. The generalized transport reaction catalyzed by BenE of A. ... These proteins are about 400 residues in length and probably span the membrane 12 times. Some members of the BenE family can ... Portal: Biology v t e (Articles with short description, Short description matches Wikidata, Protein families, Solute carrier ...

The virus particles contain two major structural proteins, surface antigens (sAg) and core antigens (cAg). Both proteins were ... GSHV has greater nucleotide and amino acid homology with WHV than HBV, with 82% nucleotide and 78% amino acid homology between ... Two are for the genes encoding the structural proteins (surface antigens and core antigens), and the other two are unassigned. ... A protein is covalently bound to the 5' end of the minus strand which may be used as a primer for DNA synthesis. There are four ...

"Refinement of protein structure homology models via long, all-atom molecular dynamics simulations". Proteins. 80 (8): 2071-2079 ... In biophysics and structural biology, the method is frequently applied to study the motions of macromolecules such as proteins ... These experiments can be used to reveal structural changes in a protein at the atomic level. SMD is often used to simulate ... Koehl P, Levitt M (February 1999). "A brighter future for protein structure prediction". Nature Structural Biology. 6 (2): 108- ...

... exhibits conserved structural homology with another transcriptional coregulator, yes-associated protein 1 (YAP). Both YAP ... WWTR1 (TAZ) has a similar structural sequence and binding motifs to yes-associated protein 1 (YAP). YAP and TAZ are often ... However, WWTR1 (TAZ) is not to be confused with the protein tafazzin, which originally held the official gene symbol TAZ, and ... This recruits the binding of the regulatory protein, 14-3-3, which prevents YAP/TAZ from localizing to the nucleus and marks it ...

Endomembrane system Integral membrane protein Protein topology Structural biology Transmembrane domain von Heijne, Gunnar ( ... Another feature used to increase the accuracy of the prediction is the homology (PolyPhobius)." It is also possible to predict ... "Topology Prediction of Helical Transmembrane Proteins: How Far Have We Reached?" (PDF). Current Protein & Peptide Science. 11 ( ... Topology of a transmembrane protein refers to locations of N- and C-termini of membrane-spanning polypeptide chain with respect ...

The C-terminal domain has an 'open fold' with no structural homology to other proteins. The dimer structure reveals the C- ... Qian D, Jiang L, Lu L, Wei C, Li Y (March 2011). "Biochemical and structural properties of cyanases from Arabidopsis thaliana ... Positively charged amino acids that make up the protein help form this site between subunits. This adjacent anion binding site ... Schlachter CR, Klapper V, Wybouw N, Radford T, Van Leeuwen T, Grbic M, Chruszcz M (July 2017). "Structural Characterization of ...

LC3 shares structural homology with ubiquitin, and therefore has been termed a ubiquitin-like protein. LC3 has a LDS (LIR ... Microtubule-associated proteins 1A/1B light chain 3B (hereafter referred to as LC3) is a protein that in humans is encoded by ... Overview of all the structural information available in the PDB for UniProt: Q9GZQ8 (Microtubule-associated proteins 1A/1B ... MAP1LC3B is a member of the highly conserved ATG8 protein family. ATG8 proteins are present in all known eukaryotic organisms. ...

... several integrin-like proteins were proposed based on structural homology with the metazoan receptors. Plants contain integrin- ... PIP3 and other phosphoinositides do the same thing to the Pleckstrin homology domains of proteins such as the kinase protein ... Most commonly, protein phosphorylation is catalyzed by protein kinases, ultimately resulting in a cellular response. Proteins ... Other activated proteins interact with adaptor proteins that facilitate signaling protein interactions and coordination of ...

... of proteins for which common ancestry can be inferred (see homology). Usually this common ancestry is inferred from structural ... Structural alignment programs, such as DALI, use the 3D structure of a protein of interest to find proteins with similar folds ... Consequently, protein tertiary structure can be used to detect homology between proteins even when no evidence of relatedness ... however secondary structural elements and tertiary structural motifs are highly conserved. Some protein dynamics and ...

"Structural homology between rbs repressor and ribose binding protein implies functional similarity". Protein Science. 1 (7): ... The Ribose repressor (RbsR) is a bacterial DNA-binding transcription repressor protein and a member of the LacI/GalR protein ... an allosteric effector of the related LacI/GalR protein Catabolite Control Protein A (CcpA). RbsR in EcoGene RbsR in EColiWiki ... v t e (Orphaned articles from February 2016, All orphaned articles, Bacterial proteins, Gene expression, All stub articles, ...

... whereas about one third possessed a novel protein fold. Some DUF families share remote sequence homology with domains that has ... Structural genomics programmes have attempted to understand the function of DUFs through structure determination. The ... identified 238 DUFs in 355 essential proteins (in 16 model bacterial species), most of which represent single-domain proteins, ... As a result, these proteins and the DUF only become relevant when the cells starve. It is thus believed that many DUFs (or ...

... is a structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Homology ... SWISS-MODEL Homology modelling Protein structure prediction Protein structure prediction software CASP (Critical Assessment of ... Homology (or comparative) modelling methods make use of experimental protein structures ("templates") to build models for ... SWISS-MODEL pipeline comprises the four main steps that are involved in building a homology model of a given protein structure ...

This protein maintains structural similarity and sequence homology to the α-subunits of human leukocyte integrins. The αInt1p ... A plant protein with structural similarity to integrins contains the amino acid sequence Asn-Gly-Asp (NGD). ILRs play a role in ... This protein shares functional homology with mammalian integrins in that it connects the ECM to the intracellular matrix to ... Most commonly, ILRs resembles the β1 subunit found in integrin proteins. This structural similarity between ILRs and integrins ...

Although RpiA and RpiB catalyze the same reaction, they show no sequence or overall structural homology. According to Jung et ... This αβα motif is not uncommon in other proteins, suggesting possible homology with other enzymes. The separate molecules of ... The protein encoded by RPIA gene is an enzyme, which catalyzes the reversible conversion between ribose-5-phosphate and ... Rossmann MG, Moras D, Olsen KW (July 1974). "Chemical and biological evolution of nucleotide-binding protein". Nature. 250 (463 ...

These methods are based upon the fact that proteins can exhibit similar structural identity while lacking sequence homology. ... Without structural information about a protein, sequence analysis is often useful in elucidating information about the protein ... homology modeling, and protein threading.[page needed] These methods involve free modeling without using any structural ... This knowledge of existing protein structure assists with the prediction of new protein structures. Methods for protein ...

Proteins may be classified according to both structural and sequence similarity. For structural classification, the sizes and ... A great number of software tools for protein structure prediction exist. Approaches include homology modeling, protein ... Biology portal Protein design Protein function prediction Protein-protein interaction prediction Gene prediction Protein ... January 2022). "AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space ...

FK506 binding protein 6, also known as FKBP6, is a human gene. The encoded protein shows structural homology to FKBP ... PDB: 3B7X​; "RCSB Protein Data Bank - Structure Summary for 3B7X - Crystal structure of human FK506-Binding Protein 6". ... FKBP6 contains 3 α-helices and 11 β-sheet strands, and as a FK506-family protein, has been shown to be a potent ... Siekierka JJ, Hung SH, Poe M, Lin CS, Sigal NH (October 1989). "A cytosolic binding protein for the immunosuppressant FK506 has ...

The highly conserved Pleckstrin homology domain (PH) is a structural domain approximately 120 amino acids in length. It binds ... α-synuclein is the primary structural component of Lewy bodies, protein aggregates that are the hallmarks of Parkinson's ... it must first be activated by proteins such as Arf, Rho, Rac, and protein kinase C. The activity of phospholipase D is ... The protein may also undergo a conformational change upon PIP2 binding, but this has not been shown experimentally and would ...

Many proteins are composed of several protein domains, i.e. segments of a protein that fold into distinct structural units. ... Xiang Z (June 2006). "Advances in homology protein structure modeling". Current Protein & Peptide Science. 7 (3): 217-27. doi: ... This may use either whole proteins or protein domains, especially in multi-domain proteins. Protein domains allow protein ... and membrane proteins. Almost all globular proteins are soluble and many are enzymes. Fibrous proteins are often structural, ...

In structural biology, a heterologous association is a binding mode between the protomers of a protein structure. In a ... Autologous Homologous Homology (biology) Heterogeneous Mus-Veteau I (2002). "Heterologous expression and purification systems ... Typically the protein itself is not transferred, but instead the 'correctly edited' genetic material coding for the protein ( ... In cell biology and protein biochemistry, heterologous expression means that a protein is experimentally put into a cell that ...

Collagen XXIII shows structural homology with collagen XIII and collagen XXV . Apart from having the characteristic structure ... Collagen Protein domain Transmembrane protein Non-small-cell lung carcinoma Prostate cancer Homotrimer Lipid raft Integrin, ... Both proteins co-localize on basal keratinocytes surface. Collagen XXIII plays a role as a biomarker for detection and ... Proteins which are included in this group present an amino-terminal cytoplasmic domain followed by a membrane-spanning ...

A common usage is that superfamilies' (structural homology) contain families (sequence homology), which contain subfamilies. ... A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family ... The term "protein family" should not be confused with family as it is used in taxonomy. Proteins in a family descend from a ... Since that time, many proteins were found to comprise multiple independent structural and functional units or domains. Due to ...