A computational study of protein dynamics, structure ensembles, and functional mechanisms
نویسندگان
چکیده
. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . xiii CHAPTER 1. OVERVIEW AND OBJECTIVES . . . . . . . . . . . . . . . . 1 Aim # 1: Establish new computational methods for protein dynamics . . . . . . . . 1 Subgoal # 1.1: Represent protein dynamics using weighted structure ensembles 1 Subgoal # 1.2: Improve existing coarse-grained models with multi-body potentials using generalized spring tensors . . . . . . . . . . . . . . . . . . . . 2 Aim # 2: Determine the functional mechanisms of ligand migration and allostery communication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Subgoal # 2.1: Chart the ligand migration channels in heme proteins using different structure ensembles . . . . . . . . . . . . . . . . . . . . . . . . 3 Subgoal # 2.2: Determine the allosteric communication pathways using dynamic motion correlation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 Thesis Organization . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 CHAPTER 2. DETERMINE THE POPULATIONS OF PROTEIN CONFORMATION STATES USING EXPERIMENTAL RESIDUAL DIPOLAR COUPLING DATA . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
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