Multi-Scale Hierarchical Structure Prediction of Helical Transmembrane Proteins

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. Nativelike 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.

• Type: Conference
• Year: 2005
• Where: CSB
• Authors: Zhong Chen, Ying Xu
• Keywords: Atomistic Levels, Bioinformatics, CSB 2005, Hierarchical Computational Approach, Structure Prediction