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- Title
TRAJELIX: A Computational Tool for the Geometric Characterization of Protein Helices During Molecular Dynamics Simulations.
- Authors
Mezei, Mihaly; Filizola, Marta
- 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.
- Subjects
COMPUTER software; HELICES (Algebraic topology); PROTEINS; MOLECULAR dynamics; GEOMETRY
- Publication
Journal of Computer-Aided Molecular Design, 2006, Vol 20, Issue 2, p97
- ISSN
0920-654X
- Publication type
Article
- DOI
10.1007/s10822-006-9039-1