Application of ab initio calculations to collagen and brome mosaic virus

In bio-related research, large proteins are of important interest. We study two such proteins. Collagen contains one such protein, the collagen triple-helix, which forms part of the structural matrix for animals, such as in their bones and teeth. 1JS9 is another protein that is a component of the protein shell of the brome mosaic virus (BMV). And BMV is important for drug delivery and imaging. To better understand the properties of these proteins, quantum mechanically (QM) based results are needed, however computationally feasible methods are also necessary. The Orthogonalized Linear Combination of Atomic Orbitals (OLCAO) method is wellsuited for application to such large proteins. However, a new approach to reduce the computational cost and increase the computational feasibility is required and this extension to the method we call the Amino-Acid Based Method (AAPM) of OLCAO. In brief, the AAPM calculates electronic, self-consistent fi eld (scf) potentials for individual amino-acids with their neighboring amino-acids included as a boundary condition. This allows the costly scf part of the calculation to be skipped out. Additionally, the number of potentials used to describe the 1JS9 protein is also minimized. Results for e ective charge and bond order are obtained and analyzed for Collagen and preliminary eff ective charge results are obtained for 1JS9. The e ffective charge results of the AAPM represent well those already obtained with the scf OLCAO result, but with reduced cost and preserved accuracy. The bond order results for Collagen also represent well the hydrogen bonding based on bond distances observed in experimentally-dervied images between the individual chains of the collagen triple-helix as well as the observed hydrogen bonding network

Name thesis:degree_name

M. S.

Level thesis:degree_level

Masters

Discipline thesis:degree_discipline

Physics (UMKC)

Grantor

University of Missouri--Kansas City

Year dc:date.issued

2014

Author dc:creator

• Eifler, Jay Quinson

Advisor dc:contributor.advisor

• Ching, Wai-Yim

Handle dc:identifier.uri

http://hdl.handle.net/10355/43496

OAI identifier oai:identifier

oai:mospace.umsystem.edu:10355/43496