Application of Ab Initio Calculations and Molecular Dynamics to Collagen and Brome Mosaic Virus
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Molecular Dynamics (MD) simulations are no more accurate than the underlying force field which represents the molecular interactions. In this thesis, we have calculated ab initio atomic partial charges for proteins of collagen and the brome mosaic virus (BMV) capsid. These proteins contain from 1000-3000 atoms and efficient and accurate ab initio quantum modeling methods have only become more recently available for systems of this size. We have used our own in-house quantum modeling package: the Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) for calculating ab initio atomic partial charges and Nanoscale Molecular Dynamics (NAMD) as a MD engine. We first examine the charge and bonding for proteins of collagen and BMV using a simplified method based on amino acids as a structural unit of proteins and secondly using fully self-consistent field (scf) calculations. We find that the charge and bonding properties of amino acids are significantly altered by their environment within the protein and by surrounding solvent but can be modeled accurately with an amino acid method or fully scf calculation. Both amino acid method and scf partial charges are used as input into NAMD for MD simulation with the purpose of comparing the default NAMD partial charges and the protein-specific partial charges of OLCAO. We find that both NAMD and OLCAO partial charges produce MD simulations that can equilibrate to similar structures as measured by root-mean-square-deviation (RMSD) of coordinates relative to the starting structure and radius of gyration (Rg) of coordinates but that differences still exist in the trajectories and details of the structures. We conclude that more system specific charge parameters are necessary for larger proteins to accurately model the MD trajectory than can be provided for by charge parameters derived from model peptides as used in the NAMD charge parameters.
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Introduction -- Theoretical background -- Methods -- Models -- Results using amino acid methods -- Charge and bonding of a Collagen a2-chain and BMV protein subunits -- Molecular dynamics using OLCAO charges for collagen and BMV -- Future work
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Ph.D.