Mechanism of a proton pump analyzed with computer simulations

Journal Article · Wed Apr 01 00:00:00 EDT 2009 · Theoretical Chemistry Accounts: Theory, Computation, and Modeling / Theoretica Chimica Acta

OSTI ID:1017372

Bondar, A N ^[1]; Smith, Jeremy C ^[2]; Elstner, Marcus ^[3]

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1. University of California, Irvine
2. ORNL
3. Technical University of Braunschweig

Understanding the mechanism of proton pumping requires a detailed description of the energetics and sequence of events associated with the proton transfers, and of how proton transfer couples to conformational rearrangements of the protein. Here, we discuss our recent advances in using computer simulations to understand how bacteriorhodopsin pumps protons. We emphasize the importance of accurately describing the retinal geometry and the location of water molecules

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Laboratory Directed Research and Development (LDRD) Program
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 1017372
• Journal Information: Theoretical Chemistry Accounts: Theory, Computation, and Modeling / Theoretica Chimica Acta, Vol. 125
• Country of Publication: United States
• Language: English

Related Subjects

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS
COMPUTERIZED SIMULATION
GEOMETRY
PROTONS
PUMPING
WATER
Proton transfer - QM/MM - Reaction path - Bacteriorhodopsin - Opsin shift - Water molecules