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. 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.
Chen
Zhong
Z
Dept. of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA. zc@csbl.bmb.uga.edu
Xu
Ying
Y
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008565:Membrane Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D011487:Protein Conformation; D020539:Sequence Analysis, Protein / Q000379:methods*
D008565:Membrane Proteins