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Computational identification of novel peripheral protein-membrane interactions

¹ Molecular Biology, The Scripps Research Institute, La Jolla, CA
² CR-UK Institute of Cancer Studies, University of Birmingham, Birmingham, United Kingdom

ABSTRACT

Soluble proteins are recruited to membranes in many cellular processes. The information about the ability of a protein to transiently interact with the bilayer often helps understanding its function. However, obtaining such information experimentally is costly and complicated.

In this study, we present a fast computational method for detecting potential peripheral membrane proteins and their individual membrane-inserting residues. The method relies on 3D structure alone and does not refer to homology with known membrane-targeting modules. It is based on the analysis of protein surface curvature and statistical membrane propensities of the chemical groups.

Using the method, we screened a set of 521 medium-size protein domains with known X-ray structures and residue chemical shift assignments. We identified four novel transient membrane binders: plant acetyltransferase AT1G, bacterial methionine sulfoxide reductase, human ARF-1, and human von Willebrand factor. Bilayer interaction of these proteins was assessed by monitoring chemical shift changes in their ¹H,¹⁵N HSQC spectra upon micelle addition. Based on the obtained per-residue data, membrane docking position of each domain was determined by rigid-body Monte Carlo optimization in a membrane/solvent boundary map. Analysis of the obtained positions proved the validity of our prediction.

This work was supported by NIH grant 5-R01-GM071872-02.

This Article Alert me when this article is cited Alert me if a correction is posted Services Email this article to a friend Similar articles in this journal Alert me to new issues of the journal Download to citation manager Google Scholar Articles by Kufareva, I. Articles by Abagyan, R. PubMed Articles by Kufareva, I. Articles by Abagyan, R.