Bacteriorhodopsin (bR) is a transmembrane protein that functions as a light-driven proton pump in the cell membrane of Halobacterium salinarium. The function is achieved through a cyclic process initiated by the absorption of a photon [34]. The pump cycle is characterized by a series of intermediates that differ both spectroscopically and structurally. Water molecules near the chromophore of bR are experimentally known to play an important role in the function of the protein. Recently, a better resolved structure of bR has been reported [47], yet the position of the water molecules is still not well-defined. Our work* aims at placing the water molecules in the new structure according to thermodynamic criteria [74]. The free energy of solvation is calculated, and the probability of occupation of cavities in the proton channel by one (or more) water molecule(s) is calculated. Our simulations indicate that in the new structure, a water molecule located near the Schiff Base, on the extracellular side is very stable, while a water molecule on the cytoplasmic side is less stable. These results differ from the ones obtained using the previous structure [74]. We plan to continue this work and explore other possible hydration sites. The resulting model will be used for quantum mechanical simulations of the primary photo-event.

National Institute of Health (NIH)
National Center for Research Resources (NCRR)
Biotechnology Resource Grants (P41)
Project #
Application #
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of Illinois Urbana-Champaign
United States
Zip Code
Wolfe, Aaron J; Si, Wei; Zhang, Zhengqi et al. (2017) Quantification of Membrane Protein-Detergent Complex Interactions. J Phys Chem B 121:10228-10241
Decker, Karl; Page, Martin; Aksimentiev, Aleksei (2017) Nanoscale Ion Pump Derived from a Biological Water Channel. J Phys Chem B 121:7899-7906
Radak, Brian K; Chipot, Christophe; Suh, Donghyuk et al. (2017) Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. J Chem Theory Comput 13:5933-5944
Shim, Jiwook; Banerjee, Shouvik; Qiu, Hu et al. (2017) Detection of methylation on dsDNA using nanopores in a MoS2 membrane. Nanoscale 9:14836-14845
Sun, Chang; Taguchi, Alexander T; Vermaas, Josh V et al. (2016) Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli. Biochemistry 55:5714-5725
Belkin, Maxim; Aksimentiev, Aleksei (2016) Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores. ACS Appl Mater Interfaces 8:12599-608
Poudel, Kumud R; Dong, Yongming; Yu, Hang et al. (2016) A time course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes. Mol Biol Cell 27:2119-32
Vermaas, Josh V; Taguchi, Alexander T; Dikanov, Sergei A et al. (2015) Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides. Biochemistry 54:2104-16
Belkin, Maxim; Chao, Shu-Han; Jonsson, Magnus P et al. (2015) Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA. ACS Nano 9:10598-611
Shen, Rong; Han, Wei; Fiorin, Giacomo et al. (2015) Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLoS Comput Biol 11:e1004368

Showing the most recent 10 out of 371 publications