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001-es BibID:	BIBFORM055472
Első szerző:	Owen, Michael C.
Cím:	The Effect of Newly Developed OPLS-AA Alanyl Radical Parameters on Peptide Secondary Structure / Michael C. Owen, László Tóth, Balázs Jojárt, István Komáromi, Imre G. Csizmadia, Bela Viskolcz
Dátum:	2012
ISSN:	1549-9618
Megjegyzések:	Recent studies using ab initio calculations have-shown that C-alpha-centered radical formation by H-abstraction from the backbone of peptide residues has dramatic effects on peptide structure and have suggested that this reaction may contribute to the protein misfolding observed in Alzheimer's and Parkinson's diseases. To enable the effects of C-alpha-centered radicals to be studied in longer peptides and proteins over longer time intervals, force-field parameters for the C-alpha-centered Ala radical were developed for use with the OPLS force field by minimizing the sum of squares deviation between the quantum chemical and OPLS-AA energy hypersurfaces. These parameters were used to determine the effect of the C-alpha-centered Ala radical on the structure of a hepta-alanyl peptide in molecular dynamics (MD) simulations. A negligible sum-of-squares energy deviation was observed in the stretching parameters, and the newly developed OPLS-AA torsional parameters showed a good agreement with the LMP2/cc-pVTZ(-f) hypersurface. The parametrization also demonstrated that derived force-field bond length and bond angle parameters can deviate from the quantum chemical equilibrium values, and that the improper torsional parameters should be developed explicitly with respect to the coupled torsional parameters. The MD simulations showed planar conformations of the C-alpha-containing residue (Alr) are preferred and these conformations increase the formation of gamma-, alpha-, and pi-turn structures depending on the position in the turn occupied by the Alr residue. Higher-ordered structures are destabilized by Alr except when this residue occupies position "i + 1" of the 3(10)-helix. These results offer new insight into the protein-misfolding mechanisms initiated by H-abstraction from the C-alpha of peptide and protein residues.
Tárgyszavak:	Természettudományok Kémiai tudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:	Journal of Chemical Theory and Computation. - 8 : 8 (2012), p. 2569-2580. -
További szerzők:	Tóth László (1983-) (vegyész) Jójárt Balázs Komáromi István (1957-) (vegyész, molekuláris biológus, biokémikus) Csizmadia, Imre G. Viskolcz Béla
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001-es BibID:	BIBFORM040365
Első szerző:	Vreven, Thom
Cím:	Combining quantum mechanics methods with molecular mechanics methods in ONIOM / Vreven, T., Byun, K. S., Komaromi, I., Dapprich, S., Montgomery, J. A. Jr., Morokuma, K., Frisch, M. J.
Dátum:	2006
Megjegyzések:	The purpose of this paper is 2-fold. First, we present several extensions to the ONIOM(QM:MM) scheme. In its original formulation, the electrostatic interaction between the regions is included at the classical level. Here we present the extension to electronic embedding. We show how the behavior of ONIOM with electronic embedding can be more stable than QM/MM with electronic embedding. We also investigate the link atom correction, which is implicit in ONIOM but not in QM/MM. Second, we demonstrate some of the practical aspects of ONIOM(QM:MM) calculations. Specifically, we show that the potential surface can be discontinuous when there is bond breaking and forming closer than three bonds from the MM region.
Tárgyszavak:	Orvostudományok Elméleti orvostudományok idegen nyelvű folyóiratközlemény külföldi lapban
Megjelenés:	Journal of Chemical Theory and Computation. - 2 : 3 (2006), p. 815-826. -
További szerzők:	Byun, K. Suzie Komáromi István (1957-) (vegyész, molekuláris biológus, biokémikus) Dapprich, Stefan Montgomery, John A. Jr. Morokuma, Keiji Frisch, Michael J.
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