Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Molecular Mechanism of Long-range Proton Translocation by Bacteriorhodopsin

The transmembrane electrochemical proton gradient is a key source of cellular energy. Bacteriorhodopsin (bR), the simplest and most studied proton pump, moves protons from low to high concentration by harnessing light energy, creating the transmembrane electrochemical gradient (Lanyi 2006). Despite years of experimental and theoretical studies, the manner by which a protein controls the thermodynamics and kinetics of proton-transfer through the reaction cycle to accomplish proton pumping is still not well understood. Within bR there are several key sites that undergo protonation changes throughout the photocycle. The mechanism that governs the long-range proton translocation between the central (CC-the retinal Schiff base and D85) and exit clusters (EC-E194 and E204) and subsequent release to the low pH side of the membrane remains elusive. To further advance our understanding of the proton pumping mechanism of bR, a systematic study using molecular dynamics (MD) simulations-based approach in conjunction with pKa calculations with MCCE method (Song et al. 2009) were performed for seven bR models. Quantum mechanical (QM) intrinsic reaction coordinate (IRC) calculations were carried out for proton-transfer in guanidinium-water model systems. The goal is to evaluate the connectivity of the hydrogen-bonding network between the CC and EC in different stages of the bR photocycle. The key finding includes:

  1. A correlation was identified between side chain position of R82 and protonation states of E194 and E204 in EC. R82 points toward the EC when its charge is -2 (M2, N' and O states). R82 freely swings between CC and EC when Glu194 hydrogen bonds with Glu204 so the EC charge is -1 (BR and M1 states).

  2. R82 is involved in proton-transfer pathways between the EC and CC. Hydrogen bond analysis and IRC calculations suggest that protons translocate through hydrogen bonds involving polar residues and waters. When R82 is positioned in the middle of CC-EC pathway, proton translocation requires an initial geometry of the R82 side chain that allows it to donate and then accept a proton on the same Arg nitrogen, otherwise the pathway is broken.

  3. The proton exit to the extracellular (low pH, P-) side of the membrane is closed in M2, O and N' states due to a stable hydrogen bond formed by side chains of Ser193 and Glu204.

The equilibrium distribution of key residue positions and correlation of residue motions in combination with hydrogen bond analysis, water occupancy and IRC calculations provide molecular details of the proton-transfer steps in different stages of the reaction cycle. This multi-scale and multi-state study leads to a better understanding of the mechanism by which proton transfer is controlled between the central and exit clusters of bR to achieve the proton release to the low pH side of the membrane.

    Lanyi JK. 2006. Proton transfers in the bacteriorhodopsin photocycle. Biochimica et biophysica acta 1757(8): 1012-1018.

    Song YF, Mao JJ, Gunner MR. 2009. MCCE2: Improving Protein pKa Calculations with extensive side chain rotamer sampling. J Comput Chem 30(14): 2231-2247.

Xiaoxia Ge
Marilyn R. Gunner

Department of Physics
The City College of New York
New York, NY 10031

Phone: 212-650-6872