Application of molecular dynamics simulation in the study of protein structure and function

Abstract

Molecular dynamic (MD) simulation is a powerful theoretical tool which equips users with the ability to study the structures and functions of proteins by monitoring the intricate dynamics of proteins at the atomic level. With the utilization of MD simulation, dynamic processes occurring in the biological system such as protein folding and unfolding can be examined in great detail. In this thesis, the use of MD simulation in the dynamical study of protein folding and changes in protein conformations will be discussed. In addition, the predictive power of MD simulation will also be highlighted through two studies involving the determination of the stability of apomyoglobin variants and the reduction potential of rubredoxin. Besides its application, this thesis will also bring attention to a limitation of MD simulation which is the lack of polarization energy terms in classical force fields that effectively describe the inhomogeneous electrostatic properties of proteins. The important role of polarization effect in effectively modeling protein folding will be demonstrated through a study concerning the folding of a helical peptide, 2KHK. The folding of 2KHK close to its NMR structure was observed when polarization effects of hydrogen bonds were considered through an on-the-fly charge scheme termed adaptive hydrogen bond-specific charge (AHBC) scheme while a non-native structure was attained when non-polarized force field was used. The AHBC scheme periodically updates the charges of amino acids involve in hydrogen bonding hence incorporating into the force field the variation in charge distribution between hydrogen bond pairs upon formation/disruption of hydrogen bonds. This effectively represents the changes in the protein environment arising from the rapid configurational changes of proteins during folding. The significance of electrostatic environment in accurately determining the reduction potential of rubredoxin will also be illustrated in this thesis through the use of two charge derivation schemes which differ in terms of the number of amino acid residues included during quantum mechanical calculations. From this study, a greater consideration of the electrostatic environment surrounding the iron atom of rubredoxin led to predictions which approached the experimentally determined reduction potentials. Also, the ability of the basic force field to model proteins will be portrayed through simple simulations that have been conducted to examine the conformational change of a protein from α/4β-fold to 3α-fold and to determine the stability of apomyoglobin upon mutation. Combined with appropriate tools for data analysis, MD simulations conducted were able to provide insights on the dynamics involved during the conformational change from α/4β-fold to 3α-fold and predict the stability of apomyoglobin variants relative to a wild type protein with reasonable agreement to experiment.