title: Comparative molecular dynamics simulation study of crystal environment effect on protein structure.
abstract: Crystal structures of proteins are under the influence from the crystal environment. In this study, we used molecular dynamics (MD) simulations to explore the possibility of eliminating the effect of the crystal packing and recovering the structure in solution. Ten representative proteins were chosen from the Protein Structural Change Database as the target systems, and 50 ns MD stimulations starting from two crystal structures having different domain arrangements were performed for each. The MD trajectories of the relaxation processes upon the release from the crystal environment revealed that the behaviors of the proteins were classified into three groups: "single domain linker", "harmonic motion", and "large barrier". We discuss the structural features common to the proteins in each group.
authors.affiliation: Molecular Scale Team, Computational Science Research Program, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan. tterada@iu.a.u-tokyo.ac.jp
authors.forename: Tohru
authors.initials: T
authors.lastname: Terada
authors.forename: Akinori
authors.initials: A
authors.lastname: Kidera
mesh_terms: D030562:Databases, Protein; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins