title: A method for predicting protein conformational pathways by using molecular dynamics simulations guided by difference distance matrices.
abstract: Here, an efficient method that predicts natural transition pathways between two endpoint states of an allosteric protein has been proposed. This method helps create structures that bridge these endpoints through multiple iterative and unbiased molecular dynamics simulations with explicit water. Difference distance matrices provide an approach for identifying states involving concerted slow motion. A series of structures are readily generated along the transition pathways of adenylate kinase. Predicted structures may be useful for an initial pathway to evaluate free energy landscapes via umbrella sampling and chain-of-states methods. © 2016 Wiley Periodicals, Inc.
authors.affiliation: High Pressure Protein Research Center, Institute of Advanced Technology, Kinki University, 930 Nishimitani, Kinokawa, Wakayama, 649-6493, Japan.
authors.forename: Yasushige
authors.initials: Y
authors.lastname: Yonezawa
keywords: conformational transition; molecular dynamics simulation; protein conformational change; protein dynamics; secondary structure