The relationship between sequence and interaction divergence in proteins.

By Patrick Aloy, Hugo Ceulemans, Alexander Stark, Robert B. Russell. 2003

321 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Materials Chemistry

In Molecular Biology

Citations in the corpus

Protein–protein interaction and quaternary structure (2008, background): “An earlier report by Aloy et al. (2003) finds that the interaction between domains is almost invariably conserved above 30% sequence identity.”
Interactome3D: adding structural details to protein networks (2013, background): “We have previously shown that homologous pairs of inter-acting proteins (that is, interologues 15 ) tend to interact using the same binding interfaces 16 , which has opened the door for homology modeling of protein-protein interactions 17 .”
HawkDock: a web server to predict and analyze the protein–protein complex based on computational docking and MM/GBSA (2019, background): “Template-based modeling is based on the observation that protein–protein complexes usually interact in the same way if their interacting pairs share > 30% sequence identity (4).”
Templates are available to model nearly all complexes of structurally characterized proteins (2012, methodology): “Two complexes with sequence identities > 40% adopt similar binding modes in a majority of cases (18, 19).”
Template-based structure modeling of protein-protein interactions (2013, background): “It has been shown that there is a ‘twilight zone’ of sequence similarity ( 25% sequence identity) below which it is almost impossible to tell whether domains will interact similarly [40].”
A de novo protein binding pair by computational design and directed evolution (2011, background): “In certain cases, complexes between pairs of related proteins have been found to interact via different sets of contacts (Aloy et al., 2003).”
Flexible backbone assembly and refinement of symmetrical homomeric complexes (2018, background): “Unfortunately, >90% sequence identity is required to guarantee symmetry type conservation (Levy et al., 2008); at <30% identity, interactions may differ completely (Aloy et al., 2003).”
Prediction‐based fingerprints of protein–protein interactions (2006, background): “5,6 Progress in structural genomics provides an opportunity to further advance the field.”
Protein interface conservation across structure space (2010, background): “Using a measure of geometric conservation that depends on translations/rotations, Aloy et al. (13) found that below 30% pairwise sequence identity, little geometric conservation is expected.”
3D Complex: A Structural Classification of Protein Complexes (2006, background): “30% to 40%, recent work suggests that differences in interface geometry will be rare [35].”
Structural systems biology: modelling protein interactions (2006, background): “There are now many thousands of interactions for which structural data are availabl”
Exploiting sequence and structure homologs to identify protein–protein binding sites (2005, unknown): “15,20 Several additional computational methods can also predict protein-binding sites without any knowledge of binding partners.”
Deciphering Protein–Protein Interactions. Part I. Experimental Techniques and Databases (2007, background): “InterPreTS is a Web-based service associated with 3did that predicts domain interactions based on sequence homology of query proteins to a database of interacting domains (DBID) [21].”