The objective for this proposal is the development of theoretical models for chromophores in biologically important metalloproteins. The methods to be employed include analysis of optical experiments of various types (e.g., absorption, resonance Raman, circular dichroism, and photochemical holeburning) and a novel method for carrying out accurate ab initio electronic structure calculations for large chromophores in a realistically parametrized protein environment which is expected to be two orders of magnitude faster than conventional techniques. The combination of these approaches will allow determination of the important electronic (exchange matrix elements, excitation energies, oxidation and spin states, redox potential) and nuclear (ground and excited state equilibrium geometry, vibrational force fields) parameters which characterize the in vivo chromophore at a level superior to previous efforts. The key factors leading to enhanced results include substantially improved numerical algorithms, extensive collaboration with experimental groups, and development of efficient, automated computer codes. The metalloproteins to be studied include the blue copper proteins, iron-sulfur proteins, heme proteins, and the photosynthetic reaction center. A particular focus will be on electron transport processes; for photosynthetic primary charge separation, a detailed dynamical model will be developed and compared with experimental results. For the remaining proteins, systematic studies of both model compounds and a series of related proteins will be carried out in order to establish correlations of chromophore properties with spectroscopic observables. The importance of metalloproteins in the respiratory electron transport chain and in oxygen transport is self-evident. The ability to reliably interpret in vivo spectroscopic experiments on these systems and to construct significantly improved theoretical models of the chromophore and its interaction with the protein is fundamental to the goal of developing predictive capabilities for biological systems at the molecular level. The long term, health- related benefits of such a research program are the application of the improved theoretical models to the design of drugs targeted towards, e.g., metabolic disorders. Determination of the factors which control electron transport efficiency and ligand binding and the capacity to predict the effects of chemical modifications on these properties should greatly facilitate the drug design process.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM040526-02
Application #
3298152
Study Section
Metallobiochemistry Study Section (BMT)
Project Start
1988-07-01
Project End
1991-06-30
Budget Start
1989-07-01
Budget End
1990-06-30
Support Year
2
Fiscal Year
1989
Total Cost
Indirect Cost
Name
University of Texas Austin
Department
Type
Schools of Arts and Sciences
DUNS #
City
Austin
State
TX
Country
United States
Zip Code
78713
Friesner, Richard A; Abel, Robert; Goldfeld, Dahlia A et al. (2013) Computational methods for high resolution prediction and refinement of protein structures. Curr Opin Struct Biol 23:177-84
Zeiske, Tim; Stafford, Kate A; Friesner, Richard A et al. (2013) Starting-structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD-derived order parameters. Proteins 81:499-509
Miller, Edward B; Murrett, Colleen S; Zhu, Kai et al. (2013) Prediction of Long Loops with Embedded Secondary Structure using the Protein Local Optimization Program. J Chem Theory Comput 9:1846-4864
Li, Jianing; Abel, Robert; Zhu, Kai et al. (2011) The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling. Proteins 79:2794-812
Li, Jianing; Schneebeli, Severin T; Bylund, Joseph et al. (2011) IDSite: An accurate approach to predict P450-mediated drug metabolism. J Chem Theory Comput 7:3829-3845
Bochevarov, Arteum D; Li, Jianing; Song, Woon Ju et al. (2011) Insights into the different dioxygen activation pathways of methane and toluene monooxygenase hydroxylases. J Am Chem Soc 133:7384-97
Wang, Lingle; Friesner, Richard A; Berne, B J (2011) Replica exchange with solute scaling: a more efficient version of replica exchange with solute tempering (REST2). J Phys Chem B 115:9431-8
Bochevarov, Arteum D; Friesner, Richard A; Lippard, Stephen J (2010) The prediction of Fe Mössbauer parameters by the density functional theory: a benchmark study. J Chem Theory Comput 6:3735-3749
Schneebeli, Severin T; Hall, Michelle Lynn; Breslow, Ronald et al. (2009) Quantitative DFT modeling of the enantiomeric excess for dioxirane-catalyzed epoxidations. J Am Chem Soc 131:3965-73
Tian, Li; Friesner, Richard A (2009) QM/MM Simulation on P450 BM3 Enzyme Catalysis Mechanism. J Chem Theory Comput 5:1421-1431

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