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Bioinformatics 2007 23(2):e212-e218; doi:10.1093/bioinformatics/btl325
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Structural Bioinformatics

Prediction and simulation of motion in pairs of transmembrane {alpha}-helices

Angela Enosh 1,*, Sarel J. Fleishman 2, Nir Ben-Tal 2 and Dan Halperin 1

1 School of Computer Science Ramat Aviv 69978, Israel
2 Department of Biochemistry Tel Aviv University Ramat Aviv 69978, Israel

*To whom correspondence should be addressed.


  Abstract

Motivation: Motion in transmembrane (TM) proteins plays an essential role in a variety of biological phenomena. Thus, developing an automated method for predicting and simulating motion in this class of proteins should result in an increased level of understanding of crucial physiological mechanisms. We have developed an algorithm for predicting and simulating motion in TM proteins of the {alpha}-helix bundle type. Our method employs probabilistic motion-planning techniques to suggest possible collision-free motion paths. The resulting paths are ranked according to the quality of the van der Waals interactions between the TM helices. Our algorithm considers a wide range of degrees of freedom (dofs) involved in the motion, including external and internal moves. However, in order to handle the vast dimensionality of the problem, we employ some constraints on these dofs in a way that is unlikely to rule out the native motion of the protein. Our algorithm simulates the motion, including all the dofs, and automatically produces a movie that demonstrates it.

Results: Overexpression of the RTK ErbB2 was implicated in causing a variety of human cancers. Recently, a molecular mechanism for rotation-coupled activation of the receptor was suggested. We applied our algorithm to investigate the TM domain of this protein, and compared our results with this mechanism. A motion pathway that was similar to the proposed mechanism ranked first, and motions with partial overlap to this pathway followed in rank order. In addition, we conducted a negative-control computational-experiment using Glycophorin A. Our results confirmed the immobility of this TM protein, resulting in degenerate paths comprising native-like conformations.

Supplementary information: Supplementary data are available at http://www.cs.tau.ac.il/~angela/EGFR.html

Contact: angela{at}post.tau.ac.il


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