| This dissertation focuses on two aspects of the molecular dynamics simulation method: accuracy of molecular mechanics force fields and application of molecular dynamics simulation in the NMR study of protein dynamics. In the first half of the study, combined quantum mechanics/molecular mechanics force field has been used to simulate the conformational distribution of alanine and glycine dipeptides in solution, with comparison to the results of different molecular mechanics force fields. The results indicate that, due to the lacking of explicit polarization interaction, current molecular mechanics force fields poorly reproduce the conformational distribution sampled by high-resolution PDB structural database, and their results show evident diversities between each other; while the combined quantum mechanics/molecular mechanics force field remarkably resembles the PDB statistics. This raises a question to the accuracy of currently commonly used molecular mechanics force fields, and also a challenge to their improvement and how they should be used in the simulation of unfolded states of protein molecule. In the second half of the study, molecular dynamics simulation has been combined with NMR experiments to study the protein dynamics, specifically, the dynamics change of eglin c upon acidification. The two methods have produced consistent results, revealing a destabilized but rigidified protein at lower pH, against naive expectation. The results make a clear distinction between the stability and rigidity of protein molecules, as a molecular mechanism has been rationalized for the rigidification process, in terms of both structural and energetic analysis from the simulations at atomic level, complementary to experimental measurements at ensemble-averaged level. Furthermore, for the significance in NMR studies, the motions of the side-chain methyl group have been investigated in depth. We propose a molecular model for the side-chain methyl motions, which leads to a semi-quantitative relationship between the order parameters and population of rotamer states and will be useful in the quantitative energetics study by NMR methods. The study carried out in this dissertation shows the great productivity and efficiency of combined molecular dynamics simulation and NMR spin relaxation experiments in the study of protein dynamics. |
