Probing the protein folding mechanism by simulation of dynamics and nonlinear infrared spectroscopy

This dissertation presents simulation based approaches towards the study of the dynamics and nonlinear spectroscopy of protein folding. The folding mechanisms of two model protein systems, the N-terminal domain of ribosomal protein L9 (NTL9) and the synthetic Beta3s mini-protein were investigated. All-atom molecular dynamics (MD) simulations and two-dimensional infrared spectroscopy (2DIR) computations were employed in the investigation of the folding mechanisms of these model systems. In this work, the folding mechanism and transition state ensemble (TSE) of the 56-residue N-terminal domain of L9 (NTL9) was probed. The TSE was identified from high temperature unfolding all-atom MD simulations in conjunction with experimentally determined phi-values. The TSE ensemble of NTL9 was found to be largely native in composition, with a well defined secondary structure. In the progression to folding after crossing the TSE our data suggests that much of the drive towards the native state of NTL9 is spent optimizing electrostatic interactions between stable secondary structure elements. This work also proposes the use two-dimensional infrared spectroscopy (2DIR) to characterize the folding mechanism of the mini-protein Beta3s. In this study Beta3s was folded by MD simulation and intermediate conformational ensembles were identified. The two-dimensional infrared spectrum was calculated for the intermediate and native states of the mini-protein. A direct structure-spectra relationship was determined by analysis of conformational properties and specific residue contributions. The structural origins of diagonal and off-diagonal peaks in the 2DIR spectrum were identified for the native and intermediate conformational ensembles in the folding mechanism. This work supports the implementation of computational techniques in conjunction with experimental 2DIR to study the folding mechanism of proteins. In addition to exploring the folding mechanism the work presented here may also be applied in combination with experiment to refine and validate current molecular dynamics force fields.