Structures and spectral signatures of protonated water networks in bacteriorhodopsin.

@article{citeulike:1378374, abstract = {Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed in recent IR spectroscopic measurements on the photodriven proton pump bacteriorhodopsin (BR) suggest such networks may also serve as proton storage and release sites for these reactions. By combining electronic structure calculations with molecular mechanical force fields, we examine the dynamics and the resulting IR spectra of two protonated water networks, H+.(H2O)3 and H+.(H2O)4, in the release pocket of the initial state of BR, which possibly serve as proton donors to the extracellular surface. For both network sizes, topologically similar structures are found, which are anchored at residues E194 and E204 and stabilized by additional hydrogen bonds from neighboring protein side chains. These protonated water networks assume neither the classic Zundel nor Eigen motives but prefer wire-like topologies. Upon gauging calculated IR spectra of finite clusters with experimental gas-phase data, it is possible to link spectral features computed for these chain-like structures in the initial state of the BR photocycle to the measured absorption continua, in particular for the larger H+.(H2O)4 network. Furthermore, the free energy of proton dislocation along these chains is found to be within the range that is easily accessible at room temperature because of fluctuations.}, address = {Lehrstuhl f\"{u}r Theoretische Chemie, Ruhr-Universit\"{a}t Bochum, 44780 Bochum, Germany.}, author = {Mathias, G. and Marx, D. }, citeulike-article-id = {1378374}, doi = {10.1073/pnas.0609229104}, issn = {0027-8424}, journal = {Proc Natl Acad Sci U S A}, keywords = {activation, gpcr, protonation, retinal\_binding\_proteins, rhodopsin, theory, water}, month = {April}, number = {17}, pages = {6980--6985}, posted-at = {2007-06-11 10:25:44}, priority = {3}, title = {Structures and spectral signatures of protonated water networks in bacteriorhodopsin.}, url = {http://dx.doi.org/10.1073/pnas.0609229104}, volume = {104}, year = {2007} }

TY - JOUR ID - citeulike:1378374 L3 - citeulike-article-id:1378374 TI - Structures and spectral signatures of protonated water networks in bacteriorhodopsin. JF - Proc Natl Acad Sci U S A VL - 104 IS - 17 SP - 6980 EP - 6985 AD - Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany. SN - 0027-8424 N2 - Networks of internal water molecules are thought to provide proton transfer pathways in many enzymatic and photosynthetic reactions. Extremely broad absorption continua observed in recent IR spectroscopic measurements on the photodriven proton pump bacteriorhodopsin (BR) suggest such networks may also serve as proton storage and release sites for these reactions. By combining electronic structure calculations with molecular mechanical force fields, we examine the dynamics and the resulting IR spectra of two protonated water networks, H+.(H2O)3 and H+.(H2O)4, in the release pocket of the initial state of BR, which possibly serve as proton donors to the extracellular surface. For both network sizes, topologically similar structures are found, which are anchored at residues E194 and E204 and stabilized by additional hydrogen bonds from neighboring protein side chains. These protonated water networks assume neither the classic Zundel nor Eigen motives but prefer wire-like topologies. Upon gauging calculated IR spectra of finite clusters with experimental gas-phase data, it is possible to link spectral features computed for these chain-like structures in the initial state of the BR photocycle to the measured absorption continua, in particular for the larger H+.(H2O)4 network. Furthermore, the free energy of proton dislocation along these chains is found to be within the range that is easily accessible at room temperature because of fluctuations. KW - activation KW - gpcr KW - protonation KW - retinal_binding_proteins KW - rhodopsin KW - theory KW - water AU - Mathias, G AU - Marx, D PY - 2007/04/24/ UR - http://dx.doi.org/10.1073/pnas.0609229104 ER -