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CRK: An evolutionary approach for distinguishing biologically relevant interfaces from crystal contacts by Martin A. Schärer; Markus G. Grütter; Guido Capitani is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

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## Abstract Protein crystals contain two different types of interfaces: biologically relevant ones, observed in protein–protein complexes and oligomeric proteins, and nonspecific ones, corresponding to crystal lattice contacts. Because of the increasing complexity of the objects being tackled in structural biology, distinguishing biological contacts from crystal contacts is not always a trivial task and can lead to wrong interpretation of macromolecular structures. We devised an approach (CRK, core‐rim __K__~a~/__K__~s~ ratio) for distinguishing biologically relevant interfaces from nonspecific ones. Given a protein–protein interface, CRK finds a set of homologs to the sequences of the proteins involved in the interface, retrieves and aligns the corresponding coding sequences, on which it carries out a residue‐by‐residue __K__~a~/__K__~s~ ratio (ω) calculation. It divides interface residues into a “rim” and a “core” set and analyzes the selection pressure on the residues belonging to the two sets. We developed and tested CRK on different datasets and test cases, consisting of biologically relevant contacts, nonspecific ones or of both types. The method proves very effective in dist

Who reads CRK: An evolutionary approach for distinguishing biologically relevant interfaces from crystal contacts?

Author

Martin A. Schärer; Markus G. Grütter; Guido Capitani

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

2010

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)