Unit

UNIT 5.3 Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions

  1. Uzi Kochva1,
  2. Hadas Leonov1,
  3. Isaiah T. Arkin1,
  4. Paul D. Adams2

Published Online: 1 FEB 2004

DOI: 10.1002/0471250953.bi0503s04

Lab Protocol Title

Current Protocols in Bioinformatics

Current Protocols in Bioinformatics

Additional Information

How to Cite

Kochva, U., Leonov, H., Arkin, I. T. and Adams, P. D. 2004. Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions. Current Protocols in Bioinformatics. 4:5.3:5.3.1–5.3.15.

Author Information

  1. 1

    The Hebrew University, Jerusalem, Israel

  2. 2

    Lawrence Berkeley Laboratory, Berkeley, California

Publication History

  1. Published Online: 1 FEB 2004
  2. Published Print: DEC 2003
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Abstract

This unit describes predicting the structure of simple transmembrane α-helical bundles. The protocol is based on a global molecular dynamics search (GMDS) of the configuration space of the helical bundle, yielding several candidates structures. The correct structure amongst these candidates is selected using information from silent amino acid substitutions, employing the following premise: Only the correct structure must (by definition) accept all of the silent amino acid substitutions. Thus, the correct structure is found by repeating the GMDS for several close homologues and selecting the structure that persists in all of the trials.

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