Analysis of regulatory mechanism of protein functions with advanced computations
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Abstract
Understanding the regulatory mechanisms of protein function is of major significance from both fundamental and biomedical points of view. Due to potential contributions from a multitude of physicochemical factors, analysis of regulatory mechanisms poses significant challenges to both experiments and computations. In this dissertation, a range of computational techniques have been developed and applied to better understand several representative regulatory mechanisms of protein function. One important regulatory mechanism of protein function emerged in recent studies concerns the hydration level of internal cavities. For example, water penetration was proposed to stabilize buried charges/dipoles, which play key roles in enzymes and bioenergetics systems. However, much uncertainty remains regarding the methodologies for describing the time scale and energetic driving forces for water penetration. Using extensive free energy simulations with polarizable force fields, we demonstrated that to properly describe the stability, hydration, dynamics, and therefore function of buried charges/dipoles, it is essential to explicitly include electronic polarization. Motivated by this observation, we have revised and implemented a grand canonical nonequilibrium candidate Monte Carlo approach to enable efficient sampling of cavity hydration level using a polarizable force field. These insights and method- ologies were essential to the analysis of the gating mechanism of the big potassium channel, in which the hydration level of the central hydrophobic cavity was proposed to regulate ion transport. Combined with nuclear magnetic resonance (NMR) spectroscopy, our enhanced sampling simulations also illustrated the roles and timescales of conformational change and internal hydration dynamics in determining the higher temperature-sensitivity of an engineered potassium channel. Another hallmark for biomolecules is that distal residues make significant cumulative contributions. However, their individual and specific roles remain difficult to predict and understand. We analyzed the contributions of second-shell residues in a metalloenzyme. By adopting a multifaceted approach that included both quantum mechanical and classical models, we probed the rate-limiting chemical step and structural properties of all relevant enzyme states. In combination with available experimental kinetics data, our results showed that mutations of those second-shell residues impact catalytic efficiency mainly by perturbation of the apo state and there- fore substrate binding, while they do not affect the ground state or transition state significantly. In another study, by examining a range of structural and dynamical properties in a transcription factor at both local and global scales in extensive molecular dynamics simulations, we showed that experimentally identified hotspot residues modulate allostery in distinct ways. The results motivated a thermodynamic model that qualitatively explained the broad distribution of hotspot residues observed in the experiment. We further demonstrated that the mutation effects of hotspot residues can be evaluated and ranked with functional free energy simulations. Collectively, these studies highlighted the power of integrating multiple computational approaches to better define the complex contributions of distal residues to function regulation.
Description
2024
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Attribution-NonCommercial-NoDerivatives 4.0 International