Quantitative Study of Protein Folding and Conformational Switch with Molecular Dynamics Simulation and Multi-Dimensional Spectroscopy

This dissertation presents the quantitative approaches towards the study of dynamics and nonlinear spectroscopy of protein folding and conformational switches. Molecular dynamics (MD) simulations and two-dimensional spectroscopy computations were employed in the investigation of two protein systems: Glutamine-binding protein (GlnBP) and the Trp-cage. GlnBP is one of the periplasmic binding proteins that carry small ligands from the periplasmic space into the cytoplasmic space. In the process of the conformational transition, GlnBP exhibits two stable states, that is, the ligand-free open state and the ligand-bound closed state. Traditionally, the potential energy shape in the molecular dynamics simulation is one basin. In this work we applied a structure-based two-well potential energy model to study the properties of the kinetics and statistical distributions for the conformational transition of GlnBP. The analysis shows that below the melting temperature, the open and closed basin of attractions emerge and the kinetic analysis through the mean and distribution of the first passage time as well as the auto-correlation function implies the complexity and the hierarchical structure of the underlying energy landscape. The multi-dimensional diffusion dynamics of GlnBP conformational change were also investigated in this work. We found that the diffusion is anisotropic and in- homogeneous. The directional and positional dependence of diffusion have signicant impacts on the protein conformational kinetics: the dominant kinetic path of conformational change is shifted from the naively expected steepest descent gradient paths. The kinetic transition barrier with considering coordinate-dependent diffusion coefficient is shifted away from the transition barrier without considering the coodinate-dependent effect.;This work also proposes the use two-dimensional infrared spectroscopy(2DIR) and two-dimensional ultraviolet spectroscopy(2DUV) to characterize the folding mechanism of the mini-protein Trp-cage. In this study the Trp-cage was folded by atomistic MD simulation and intermediate conformational ensembles were clustered along the dominant folding pathway of energy landscape. The nonchiral and chiral two-dimensional coherent spectra were calculated for the intermediate and folded states of the mini-protein. A direct structure-spectra relationship was determined by the analysis of conformational properties. The structural origins of diagonal and off-diagonal peaks in the 2DIR spectrum were identified for the folded and intermediate conformational ensembles in the folding mechanism and isotope-labeling was used to reveal residue-spectrum information. Besides, the complexity of 2DUV signals decreases as the conformational entropy decreases during the folding process, implying that the approximate entropy of the signals provides a quantitative marker of the protein folding status. These works support the implementation of computational techniques in conjunction with experimental two-dimensional spectroscopy to study the folding mechanism of proteins.