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Multi-scale hierarchical structure prediction of helical transmembrane proteins

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2 Author(s)
Z. Chen ; Dept. of Biochem. & Molecular Biol., Georgia Univ., Athens, GA, USA ; Y. Xu

As the first step toward a multi-scale, hierarchical computational approach for membrane protein structure prediction, the packing of transmembrane helices was modeled at the residual and atomistic levels, respectively. For predictions at the residual level, the helix-helix and helix-lipid interactions were described by a set of knowledge-based energy functions. For predictions at the atomistic level, CHARMM19 force field was employed. To facilitate the system to overcome energy barriers, Wang-Landau sampling was carried out by performing a random walk in the energy and conformational spaces. Native-like structures were predicted at both levels for 2- and 7-helix systems. Interestingly, consistent results were obtained from simulations at residual and atomistic levels for the same system, strongly suggesting the feasibility of a hierarchical approach for membrane structure prediction.

Published in:

2005 IEEE Computational Systems Bioinformatics Conference (CSB'05)

Date of Conference:

8-11 Aug. 2005