Dynamics of proteins: elements and function.

INTRODUCTION ........................................................................................................ 263 OVERVIEW .................................................................................................................. 265 DYNAMICS METHODOLOGY ................................................................................ 268 Molecular Dynamics ................................................................................................ 270 Stochastic Dynamics .................................................................................................. 270 Harmonic Dynamics ................. . ................................................................................ 272 Activated Dynamics .................................................................................................. 272 Simplified Model Dynamics ...................................................................................... 273 ATOMIC FLUCTUATIONS ........................................................................................ 273 Mean-Square Fluctuations and Temperature Factors .............................................. 273 Time-Dependence: Local and Collective Effects ...................................................... 277 Biological Function .................................................................................................... 278 SIDECHAIN MOTIONS .............................................................................................. 279 Tyrosines in PT1 ........................................................................................................ 279 Ligand-Protein Interaction i Myoglobin ................................................................ 283 Exterior Sidechain d Loop Motions ...................................................................... 287 RIGID BODY MOTIONS ............................................................................................ 288 Hinge Bending .......................................................................................................... 288 Quaternary Structural Change ................................................................................ 290 a-HELIX MOTION: HARMONIC AND SIMPLIFIED MODEL DYNAMICS ........................................................................................ 291 PERSPECTIVE .............................................................................................................. 292