Reference: Levy ED (2010) A simple definition of structural regions in proteins and its use in analyzing interface evolution. J Mol Biol 403(4):660-70

Reference Help

Abstract

Analysis of proteins commonly requires a partition of their structure into regions such as surface, interior, or interface. Despite the frequent use of such categorization, no consensus definition seems to exist. We thus aim at providing a definition that is general, simple to implement, and that yields new biological insights. Our analysis relies on 397, 196 and 701 protein structures from E. coli, S. cerevisiae and H. sapiens respectively, and our conclusions are consistent across all three species. We find that 25% relative accessible surface area best segregates amino acids at the interior and surface. We further use this value to extend the core-rim model of protein-protein interfaces, and introduce a third region that we call support. Interface core, rim and support regions contain similar numbers of residues on average, but core residues contribute over two-thirds of the contact surface. The amino acid composition of each region remains similar across different organisms and interface types. The interface core composition is intermediate between surface and interior, but the compositions of the support and rim are virtually identical to those of the interior and surface respectively. The support and rim could thus "pre-exist" in proteins, and evolving a new interaction could require mutations to form an interface core only. Using the interface regions defined, we show through simulations that only two substitutions are necessary to shift the average composition of a 1000A(2) surface patch involving ~28 residues to that of an equivalent interface. Our analysis and conclusions will help understand the notion of promiscuity in protein-protein interaction networks.CI - Copyright (c) 2010. Published by Elsevier Ltd.

Reference Type
Journal Article
Authors
Levy ED
Primary Lit For
Additional Lit For
Review For

Interaction Annotations

Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.

Interactor Interactor Type Assay Annotation Action Modification Phenotype Source Reference

Gene Ontology Annotations

Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

Gene Gene Ontology Term Qualifier Aspect Method Evidence Source Assigned On Annotation Extension Reference

Phenotype Annotations

Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details.

Gene Phenotype Experiment Type Mutant Information Strain Background Chemical Details Reference

Regulation Annotations

Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, SPELL, or YeastMine.

Regulator Target Experiment Assay Construct Conditions Strain Background Reference