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Self-consistent QM/MM methodologies for structural refinement of photosystem II and other macromolecules of biological interest [electronic resource].

Published
Washington, D.C. : United States. Dept. of Energy, 2008.
Oak Ridge, Tenn. : Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy.
Additional Creators
Los Alamos National Laboratory, United States. Department of Energy, and United States. Department of Energy. Office of Scientific and Technical Information
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Summary
The combination of quantum mechanics and molecular mechanics (QM/MM) is one of the most promising approaches to study the structure, function, and properties of proteins and nucleic acids. However, there some instances in which the limitations of either the MM (lack of a proper electronic description) or QM (limited to a few number of atoms) methods prevent a proper description of the system. To address this issue, we review here our approach to fine-tune the structure of biological systems using post-QM/MM refinements. These protocols are based on spectroscopy data, and/or partitioning of the system to extend the QM description to a larger region of a protein. We illustrate these methodologies through applications to several biomolecules, which were pre-optimized at the QM/MM level and then further refined using postQM/MM refinement methodologies: mod(QM/MM), which refines the atomic charges of the residues included in the MM region accounting for polarization effects; mod(QM/MM)-opt that partition the MM region in smaller parts and optimizes each part in an iterative. self-consistent way, and the Polarized-Extended X-Ray Absorption Fine Structure (P-EXAFS) fitting procedure, which fine-tune the atomic coordinates to reproduce experimental polarized EXAFS spectra. The first two techniques were applied to the guanine quadruplex. while the P-EXAFS refinement was applied to the oxygen evolving complex of photosystem II.
Report Numbers
E 1.99:la-ur-08-07679
E 1.99: la-ur-08-7679
la-ur-08-7679
la-ur-08-07679
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Note
Published through SciTech Connect.
01/01/2008.
"la-ur-08-07679"
" la-ur-08-7679"
Photosynthesis Research ISSN 0166-8595; PHRSDI FT
Batista, Victor S; Batista, Enrique R; Gascon, Jose A; Sproviero, Eduardo M; Newcomer, Michael.
Funding Information
AC52-06NA25396
View MARC record | catkey: 13805207