Modeling protonated water networks in bacteriorhodopsin

Rousseau, Roger; Kleinschmidt, Volker; Schmitt, Udo W.; Marx, Dominik

doi:10.1039/b313220j

Cited by 49 publications

(55 citation statements)

References 42 publications

(54 reference statements)

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…These two mostprobable possibilities are investigated separately, which yield H ϩ ⅐(H 2 O) 3 and H ϩ ⅐(H 2 O) 4 WLANs together with the excess proton. However, at variance with the well known Zundel and Eigen structures considered earlier (33,39), the generated hydrogen-bonding topologies turn out to be much less symmetric, as observed for some H ϩ ⅐(H 2 O) n clusters in the gas phase (23), and lead to quasilinear protonated water wires in both cases.…”

mentioning

confidence: 63%

“…The general approach, system setups, and simulation protocols follow previous work (33,39) on the L-intermediate of BR.…”

Section: Methodsmentioning

confidence: 99%

“…These hybrid Car-Parrinello molecular dynamics simulations have demonstrated that (i) the spectral features of protonated WLANs are mainly determined by the local protonation pattern and thus by their hydrogen-bonding topology, and (ii) the solvated Zundel and Eigen IR spectra are complementary in the regions below and above Ϸ2,000 cm Ϫ1. However, Zundel-like topologies were found to desymmetrize spontaneously, such that the solvated Zundel complex had to be artificially stabilized by imposing external constraints on the four solvating water molecules to establish the proton-sharing Zundel symmetry (39).…”

mentioning

confidence: 99%

“…However, it is possible to include very approximately the resulting effects by increasing the temperature, thus enhancing fluctuation effects, and applying suitable quantum corrections to spectra obtained from classical autocorrelations (37,38). As a first step, Rousseau et al (33,39) computed IR spectra of protonated WLANs in the release pocket of the L state of BR embedded in a fully hydrated 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) membrane. At this later stage in the photocycle, the release pocket is large enough to accommodate additional water molecules such that solvated Zundel and Eigen complexes, i.e., H 5 O 2 ϩ ⅐4(H 2 O) and H 3 O ϩ ⅐3(H 2 O), respectively, were investigated as sensible qualitative models in terms of an Ansatz.…”

mentioning

confidence: 99%

See 3 more Smart Citations

Structures and spectral signatures of protonated water networks in bacteriorhodopsin

Mathias

Marx

2007

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

137

144

View full text Add to dashboard Cite

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 ؉ ⅐(H2O)3 and H ؉ ⅐(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 ؉ ⅐(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.hydrogen-bonded networks ͉ hybrid molecular dynamics ͉ proton transport ͉ IR spectroscopy T he light-driven proton pump bacteriorhodopsin (BR) converts light energy to chemical energy by a vectorial proton transport against a membrane potential (1). In addition to belonging to the best-studied proton-permeable ion channels (2) as such and being a natural host for studying proton conducting water wires (3), BR is an important representative of the G protein-coupled seven-␣-helix receptor family (4). Thus, it comes as no surprise that this protein serves as a paradigmatic workhorse for both experiment and simulation. During its photocycle, protons are translocated to different positions within the transport channel, and a detailed dynamical picture is currently emerging for BR from the level of conformational changes to side-chain motion to individual atom displacements (5-9). In addition, biomolecular simulation strongly suggests the presence of locally mobile internal water molecules inside BR, which could easily serve as proton hosts and relays and thus establish a pathway from intracellular to extracellular space (10-12). A crucial step in this vectorial proton transfer is the actual release of a proton to the extracellular surface involving the so-called proton release group (XH). However, the very nature of XH is still a puzzling and disputed question.Whereas other initial as well as transient proton positions in BR have been quite well characterized (9), the terminal release group has withdrawn itself from identification for a long time. Recent IR spectroscopic meas...

show abstract

mentioning

confidence: 63%

“…The general approach, system setups, and simulation protocols follow previous work (33,39) on the L-intermediate of BR.…”

Section: Methodsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

See 2 more Smart Citations

Structures and spectral signatures of protonated water networks in bacteriorhodopsin

Mathias

Marx

2007

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

137

144

View full text Add to dashboard Cite

show abstract

“…In almost all isomers propene prefers to bind at a corner. This follows the pattern seen for the adsorption of H, 57 CO, 50 O 2 , 23-25,58 methanol, 59 and pyridine 60 on the Au clusters.…”

Section: A the Adsorption Of Propene On Au N "Nä1 -5 8…: Structuresmentioning

confidence: 75%

Binding of propene on small gold clusters and on Au(111): Simple rules for binding sites and relative binding energies

Chrétien

Gordon

Metiu

2004

The Journal of Chemical Physics

View full text Add to dashboard Cite

We use density functional theory(DFT) to investigate the bonding of propene to small gas-phase gold clusters and to a Au(111) surface. The desorption energy trends and the geometry of the binding sites are consistent with the following set of rules.(1) The bond of propene to gold is formed by donation of electron density from the highest occupied molecular orbital (HOMO) of propene to one of the low-lying empty orbitals [denoted by LUMO1, LUMO2, … (LUMO-lowest unoccupied molecular orbital)] of the gold cluster. (2) Propene binds to a site on the Au cluster where one of the low-lying LUMOs protrudes in the vacuum. Different isomers (same cluster, but different binding sites for propene) correspond to sites where different low-lying LUMOs protrude in space. (3) The desorption energy of the lowest energy isomer correlates with the energy of the lowest empty orbital of the cluster; the lower the energy of that LUMO, the higher the desorption energy. (4) If the lowest-lying LUMO protrudes into space at two nonequivalent sites at the edge of a cluster, propene binds more strongly to the site with the lowest coordination. These rules are consistent with the calculated bond energies and geometries for [Aun(C3H6)]q, for n=1−5 and n=8 and q=−1, 0, +1. Based on them we have made a number of predictions that have been confirmed by DFT calculations. The bond of propene to gold is strengthened as the net charge of the cluster varies from −1, to zero, to +1. Compared to a gas-phase cluster, a cluster on a support binds propene more strongly if the support takes electron density from the cluster (e.g., a Au cluster on a goldsurface) and more weakly if the support donates electron density to the cluster (e.g., a Au cluster on an oxygen vacancy on an oxide surface). KeywordsGold, Binding sites, Density functional theory, Desorption, Oxide surfaces Disciplines Chemistry CommentsThe following article appeared in Journal of Chemical Physics 121 (2004) We use density functional theory ͑DFT͒ to investigate the bonding of propene to small gas-phase gold clusters and to a Au͑111͒ surface. The desorption energy trends and the geometry of the binding sites are consistent with the following set of rules. ͑1͒ The bond of propene to gold is formed by donation of electron density from the highest occupied molecular orbital ͑HOMO͒ of propene to one of the low-lying empty orbitals ͓denoted by LUMO1, LUMO2, ... ͑LUMO-lowest unoccupied molecular orbital͔͒ of the gold cluster. ͑2͒ Propene binds to a site on the Au cluster where one of the low-lying LUMOs protrudes in the vacuum. Different isomers ͑same cluster, but different binding sites for propene͒ correspond to sites where different low-lying LUMOs protrude in space. ͑3͒ The desorption energy of the lowest energy isomer correlates with the energy of the lowest empty orbital of the cluster; the lower the energy of that LUMO, the higher the desorption energy. ͑4͒ If the lowest-lying LUMO protrudes into space at two nonequivalent sites at the edge of a cluster, propene binds more strong...

show abstract

Gas Phase Vibrational Spectroscopy of Strong Hydrogen Bonds

Asmis

Neumark

Bowman

2006

Hydrogen‐Transfer Reactions

View full text Add to dashboard Cite

The hydrogen bond interaction is key to understanding the structure and properties of water, biomolecules, self-assembled nanostructures and molecular crystals. However, much confusion remains about its electronic nature, a combination of van der Waals, electrostatic and covalent contributions, leading to a wide variety of hydrogen bonds with bond strengths ranging from 2 to 40 kcal mol -1 . In particular, our understanding of strong, low-barrier hydrogen bonds and their central role in enzyme catalysis [1], biomolecular recognition [2], proton transfer across biomembranes [3] and proton transport in aqueous media [4] remains incomplete. The central aim of this chapter is to outline some recent advances in the research on strongly hydrogen bonded model systems in the gas phase with emphasis on the work from our research groups.Strong hydrogen bonds (A_H_B) are often classified based on their hydrogen bond energy; a typically cited lower limit is >15 kcal mol -1 [5]. Their most prominent physical properties are large NMR downfield chemical shifts and considerably red-shifted hydrogen stretch frequencies. Moreover, the H-atom transfer barrier, a characteristic feature of weak hydrogen bonds A-H_B, is either absent or very small in these systems (at their minimum energy geometry). Consequently, the H-atom in homoconjugated (A = B) strong hydrogen bonds is equally shared by the two heavy atoms forming two identical strong hydrogen bonds. This symmetry is lost in heteroconjugated (A " B) systems, but the H-atom remains in a more centered position, i.e., the distance between the heavy atoms is smaller than in weaker hydrogen bonded systems. Strong hydrogen bonds can either be lowbarrier, as in (HO_H_OH) -, or single-well, as in (Br_H_I) -, depending on the form of the potential curve along the H-atom exchange coordinate (see Fig. 3.1 and below).Hydrogen bonds are very sensitive to perturbation, due to an intimate interdependence between the heavy atom separation, the H-atom exchange barrier and the position of the light H-atom leading to unusually high proton polarizabilities. Therefore it can prove advantageous to study strong hydrogen bonds in the gas Hydrogen-Transfer Reactions. Edited by

show abstract

Modeling protonated water networks in bacteriorhodopsin

Cited by 49 publications

References 42 publications

Structures and spectral signatures of protonated water networks in bacteriorhodopsin

Structures and spectral signatures of protonated water networks in bacteriorhodopsin

Binding of propene on small gold clusters and on Au(111): Simple rules for binding sites and relative binding energies

Gas Phase Vibrational Spectroscopy of Strong Hydrogen Bonds

Contact Info

Product

Resources

About