Publication: Molecular mechanics and all-electron fragment molecular orbital calculations on mutated polyglutamine peptides

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Title	Molecular mechanics and all-electron fragment molecular orbital calculations on mutated polyglutamine peptides
Authors/Editors*	B.M.B. Van Schouwen, M. Nakano, H. Watanabe, S. Tanaka, H.L. Gordon, and S.M. Rothstein
Where published*	Journal of Molecular Structure: THEOCHEM
How published*	Journal
Year*	2010
Volume	944
Number
Pages	12-20
Publisher	Elsevier
Keywords	simulated annealing, proline mutation, molecular mechanics, fragment molecular orbitals, polyglutamine
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Abstract	We perform potential energy calculations on mutant polyglutamine peptides that were studied experimentally, and found to aggregate with varying efficiencies. Low-energy structures were generated for each peptide by simulated annealing molecular dynamics, and were analyzed by molecular mechanics and by all-electron fragment molecular orbital energy calculations. In order to make a comparison between the two sets of potential energies, we devised a means of computing molecular-mechanical analogues of the quantum-mechanical energies. Our results suggest that in accordance with a previous paper the experimentally-observed inhibition of aggregation is due to localized, geometry-based effects on peptide structure, with little appreciable perturbation from longer-range non-bonded effects.