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J Comput Aided Mol Des. 2006 Feb;20(2):97-107. Epub 2006 May 10.

TRAJELIX: a computational tool for the geometric characterization of protein helices during molecular dynamics simulations.

Author information

1
Department of Physiology and Biophysics, Mount Sinai School of Medicine, NYU, One Gustave L. Levy Place, Box 1218, New York, NY 10029, USA. mezei@inka.mssm.edu

Abstract

We have developed a computer program with the necessary mathematical formalism for the geometric characterization of distorted conformations of alpha-helices proteins, such as those that can potentially be sampled during typical molecular dynamics simulations. This formalism has been incorporated into TRAJELIX, a new module within the SIMULAID framework (http://inka.mssm.edu/~mezei/simulaid/) that is capable of monitoring distortions of alpha-helices in terms of their displacement, global and local tilting, rotation around their axes, compression/extension, winding/unwinding, and bending. Accurate evaluation of these global and local structural properties of the helix can help study possible intramolecular and intermolecular changes in the helix packing of alpha-helical membrane proteins, as shown here in an application to the interacting helical domains of rhodopsin dimers. Quantification of the dynamic structural behavior of alpha-helical membrane proteins is critical for our understanding of signal transduction, and may enable structure-based design of more specific and efficient drugs.

PMID:
16783601
DOI:
10.1007/s10822-006-9039-1
[Indexed for MEDLINE]

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