title: Transform and relax sampling for highly anisotropic systems: application to protein domain motion and folding.
abstract: Transform and relax sampling (TRS) is proposed as a conformational sampling method to enhance "soft" fluctuation in highly anisotropic systems using molecular dynamics simulation. This method consists of three stages; transform, relax, and sampling. In the transform stage, molecular dynamics simulation is performed with randomly assigned force bias to enhance the fluctuations along relatively soft collective movements, as expected from the linear response theory. After relaxing the heated system to equilibrium without force bias in the relax stage, Monte Carlo-type determination is made as to whether the generated state is accepted or not. The sampling stage is then conducted for conformational sampling by conventional molecular dynamics simulation. TRS is first applied for the idealized multidimensional double-well C(α) model to mimic protein open-close transition. Subsequently, it is applied to three different all-atom protein systems in an explicit solvent model; T4 lysozyme, glutamine binding protein, and a mini-protein chignolin. Investigation of structural variations in the hinge angle of T4 lysozyme in crystals is demonstrated by TRS. The liganded close structure of the glutamine binding protein is sampled starting from the unliganded open form. Chignolin is shown to fold into a native structure multiple times starting from highly extended structures within 100 ns. It is concluded that TRS sampled a reasonable conformational space within a relatively short simulation time in these cases. Possible future extensions of TRS are also discussed.
authors.affiliation: Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan. kitao@iam.u-tokyo.ac.jp
authors.forename: Akio
authors.initials: A
authors.lastname: Kitao
mesh_terms: D016880:Anisotropy; D017122:Bacteriophage T4 / Q000201:enzymology; D002352:Carrier Proteins / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry; D009842:Oligopeptides / Q000737:chemistry; D017510:Protein Folding; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry*; D012997:Solvents
chemical_list: D002352:Carrier Proteins; D009842:Oligopeptides; D011506:Proteins; D012997:Solvents; C506175:chignolin; C037853:glutamine transport proteins; D009113:Muramidase