UNIT 5.3 Modeling Membrane Proteins Utilizing Information from Silent Amino Acid Substitutions
Published Online: 1 FEB 2004
Copyright © 2003 by John Wiley and Sons, Inc.
Lab Protocol Title
Current Protocols in Bioinformatics
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. 4:5.3.1–5.3.15.
- Published Online: 1 FEB 2004
- Published Print: DEC 2003
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.