title: Enhanced conformational sampling method for proteins based on the TaBoo SeArch algorithm: application to the folding of a mini-protein, chignolin.
abstract: The conformational samplings are indispensible for obtaining reliable canonical ensembles, which provide statistical averages of physical quantities such as free energies. However, the samplings of vast conformational space of biomacromolecules by conventional molecular dynamics (MD) simulations might be insufficient, due to their inadequate accessible time-scales for investigating biological functions. Therefore, the development of methodologies for enhancing the conformational sampling of biomacromolecules still remains as a challenging issue in computational biology. To tackle this problem, we newly propose an efficient conformational search method, which is referred as TaBoo SeArch (TBSA) algorithm. In TBSA, an inverse energy histogram is used to select seeds for the conformational resampling so that states with high frequencies are inhibited, while states with low frequencies are efficiently sampled to explore the unvisited conformational space. As a demonstration, TBSA was applied to the folding of a mini-protein, chignolin, and automatically sampled the native structure (Cα root mean square deviation < 1.0 Å) with nanosecond order computational costs started from a completely extended structure, although a long-time 1-µs normal MD simulation failed to sample the native structure. Furthermore, a multiscale free energy landscape method based on the conformational sampling of TBSA were quantitatively evaluated through free energy calculations with both implicit and explicit solvent models, which enable us to find several metastable states on the folding landscape.
authors.affiliation: Devision of Life Science, Center for Computational Sciences, University of Tsukuba, 1-1-1, Tennodai, Ibaraki, 305-8577, Japan; Japan Science and Technology, CREST, 4-1-8, Honcho, Kawaguchi, Saitama, 332-0012, Japan.
authors.forename: Ryuhei
authors.initials: R
authors.lastname: Harada
authors.forename: Yu
authors.initials: Y
authors.lastname: Takano
authors.forename: Yasuteru
authors.initials: Y
authors.lastname: Shigeta
mesh_terms: D000465:Algorithms; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009842:Oligopeptides / Q000737:chemistry*; D011487:Protein Conformation; D017510:Protein Folding; D013816:Thermodynamics
chemical_list: D009842:Oligopeptides; C506175:chignolin
keywords: conformational sampling; conformational transitions; extractions of biologically rare events; massively parallel computing; structural predictions