The advance in structural studies of biological electron transfer (ET) presents the exciting opportunity of progressing towards a more molecular level in correlaring structure and function of electron transport proteins. The overall aim of this project is to advance the understanding of ET processes in biological and chemical systems to a more niicroscopie level using the available structural information and computer simulation approaches. During the past grant periods we developed, refined and examined a wide range of strategies for studies of ET processes. These approaches were used in studies of the energetics and dynamics of the primary event in bacterial RC, in evaluating redox potentials of proteins, and in studies of other aspects of ET in proteins. Although our studies were very useful they did not resolve all of the fundamental problems in the field and actually in some cases they presented new and exciting questions. In order to fiirther progress in this important field we propose the following projects: (i) We will conduct a systematic evaluation of the redox potential of proteins, focusing on iron sulfiir proteins. We will concentrate on all-atom models trying to understand the role of water penetration and the effect of averaging over differet configurations with different degrees of penetation. We will use our understanding in refining computationally efficient models with simplified solvent representation. (ii) We will attack the nalin open questions about the primary ET in bacterial RC using microscopic simulations. This will include (a) exaznination of the time dependence of the dielectric screening, (b)analyzing the local dielectric constant in the sites of the electron- transporting chromophores and relating it to a recent interpretation of Stark effects, (c) determining the energetics of the charge transfer-states of the special pair, (d) studying the energetics of mutatin~charged residues and (e) exploring the origin of the oscillations in the time dependent spectra of P*. (iii) We will study the reorganization energies of biological donor-acceptor complexes. (iv) We will simulate ET reactions in solution focusing on the following: (a) evaluating reorganization energies of covalently linked donor-acceptor pairs, (b) studying the effect of solvent dynamics while representing the solute by consistent quantum mechanical approaches, (c) developing density matrix methods, and (d) pushing the frontiers of calculations of electronic coupling matrix element by treating the solvent quantum mechanically.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM040283-10
Application #
2022231
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Project Start
1988-07-01
Project End
2001-06-30
Budget Start
1997-07-01
Budget End
1998-06-30
Support Year
10
Fiscal Year
1997
Total Cost
Indirect Cost
Name
University of Southern California
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
041544081
City
Los Angeles
State
CA
Country
United States
Zip Code
90089
Mukherjee, Shayantani; Warshel, Arieh (2017) The FOF1 ATP synthase: from atomistic three-dimensional structure to the rotary-chemical function. Photosynth Res 134:1-15
Yoon, Hanwool; Kolev, Vesselin; Warshel, Arieh (2017) Validating the Water Flooding Approach by Comparing It to Grand Canonical Monte Carlo Simulations. J Phys Chem B 121:9358-9365
Astumian, R Dean; Mukherjee, Shayantani; Warshel, Arieh (2016) The Physics and Physical Chemistry of Molecular Machines. Chemphyschem 17:1719-41
Kim, Ilsoo; Warshel, Arieh (2016) Analyzing the electrogenicity of cytochrome c oxidase. Proc Natl Acad Sci U S A 113:7810-5
Matute, Ricardo A; Yoon, Hanwool; Warshel, Arieh (2016) Exploring the mechanism of DNA polymerases by analyzing the effect of mutations of active site acidic groups in Polymerase ?. Proteins 84:1644-1657
Alhadeff, Raphael; Warshel, Arieh (2016) Simulating the Function of the MjNhaP1 Transporter. J Phys Chem B :
Yoon, Hanwool; Warshel, Arieh (2016) The control of the discrimination between dNTP and rNTP in DNA and RNA polymerase. Proteins 84:1616-1624
Kim, Ilsoo; Warshel, Arieh (2016) A Microscopic Capacitor Model of Voltage Coupling in Membrane Proteins: Gating Charge Fluctuations in Ci-VSD. J Phys Chem B 120:418-32
Vorobyov, Igor; Kim, Ilsoo; Chu, Zhen T et al. (2016) Refining the treatment of membrane proteins by coarse-grained models. Proteins 84:92-117
Kim, Ilsoo; Warshel, Arieh (2015) Equilibrium fluctuation relations for voltage coupling in membrane proteins. Biochim Biophys Acta 1848:2985-97

Showing the most recent 10 out of 65 publications