Force Field Development in Protein Design

Citation

Zollars, Eric Stafford (2006) Force Field Development in Protein Design. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/55br-9a21. https://resolver.caltech.edu/CaltechETD:etd-06052006-155305

Abstract

Protein design requires the rapid evaluation of very large numbers of equations during the course of a calculation. These equations must represent the important contributors to protein stability in simple and accurate terms. Some physical phenomena are relatively easy to model such as van der Waals forces. Electrostatics and solvation in a protein environment are forces that are more difficult to adequately capture. Additionally, the balance of the terms used must be determined in order to design sequences that fold to stable, specific folds.

The electrostatic interactions within the protein and between the protein and solvent are important in both the stability and function of the protein. The effects of the protein-solvent interactions are evaluated using implicit models that consider the solvent as a bulk. These interactions are quantified using the Poisson-Boltzmann equation that must be solved using discrete numerical methods. We sought to avoid this performance hit by scaling a simpler model of electrostatics, Coulomb's law, to reproduce one aspect of the protein-solvent interaction: solvent screening. By dividing the Coulombic dielectric into two parts and scaling to correlate with the Poisson-Boltzmann results we significantly increased the strength of electrostatics in our force field that led to the design of a more stable engrailed homeodomain.

The second part of this work describes attempts to reparameterize our protein design force field. Many protein mutants have been expressed and biophysically characterized in the literature. We sought to use the measured stabilities of protein mutants in the literature to balance the terms in the force field. While we were able to produce a force field that could reproduce experimental energies, this force field led to unsatisfactory designed sequences. To more fully satisfy the unique conditions of a protein design force field we explored other optimization techniques and found that the balance of the terms in the existing force field is nearly optimal.

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