Water-mediated Proton Transfer Research Articles

Effect of Xenon Binding to a Hydrophobic Cavity on the Proton Pumping Cycle in Bacteriorhodopsin

To understand the functional role of apolar cavities in bacteriorhodopsin, a light-driven proton pump found in Halobacterium salinarum, we investigated the crystal structure in pressurized xenon or krypton. Diffraction data from the P622 crystal showed that one Xe or Kr atom binds to a preexisting hydrophobic cavity buried between helices C and D, located at the same depth from the membrane surface as Asp96, a key residue in the proton uptake pathway. The occupation fraction of Xe or Kr was calculated as approximately 0.32 at a pressure of 1 MPa. In the unphotolyzed state, the binding of Xe or Kr caused no large deformation of the cavity. However, the proton pumping cycle was greatly perturbed when an aqueous suspension of purple membrane was pressurized with xenon gas; that is, the decay of the M state was accelerated significantly (~5 times at full occupancy), while the decay of an equilibrium state of N and O was slightly decelerated. A similar but much smaller perturbation in the reaction kinetics was observed upon pressurization with krypton gas. In a glycerol/water mixture, xenon-induced acceleration of M decay became less significant in proportion to the water activity. Together with the structure of the xenon-bound protein, these observations suggest that xenon binding helps water molecules permeate into apolar cavities in the proton uptake pathway, thereby accelerating the water-mediated proton transfer from Asp96 to the Schiff base.

Minimum Energy Pathways for Proton Transfer between Adjacent Sites Exposed to Water

The capacity to transfer protons between surface groups is an innate property of many proteins. The transfer of a proton between donor and acceptor, located as far as 6-7 A apart, necessitates the participation of water molecules in the process. In a previous study we investigated the mechanism of proton transfer (PT) between bulk exposed sites, a few ångströms apart, using as a model the proton exchange between the proton-binding sites of the fluorescein molecule in dilute aqueous solution.1 The present study expands the understanding of PT reactions between adjacent sites exposed to water through the calculation the minimum energy pathways (MEPs) by the conjugate peak refinement algorithm2 and a quantum-mechanical potential. The PT reaction trajectories were calculated for the fluorescein system with an increasing number of water molecules. The MEP calculations reveal that the transition state is highly strained and involves a supramolecular structure in which fluorescein and the interconnecting water molecules are covalently bonded together and the protons are shared between neighboring oxygens. These findings are in accord with the high activation energy, as measured for the reaction, and indicate that PT reactions on the surface proceed by a semi- or fully concerted rather than stepwise mechanism. A similar mechanism is assumed to be operative on the surface of proteins and renders water-mediated PT reactions as highly efficient as they are.

Ultrafast Proton Transfer Dynamics of Hydroxystilbene Photoacids

The effects of 4-cyano and 3-cyano substituents on the spectroscopic properties and photoacidity of 3- and 4-hydroxystilbene have been investigated. In nonpolar solvents, the 3-hydroxycyanostilbenes have much longer singlet lifetimes and larger fluorescence quantum yields than do the 4-hydroxycyanostilbenes. The longer lifetimes of 3-hydroxystilbene and its cyano derivatives are attributed to a "meta effect" on the stilbene torsional barrier, similar to that previously observed for the aminostilbenes. The cyano substituent causes a marked increase in both ground state and excited-state acidity of the hydroxystilbenes in aqueous solution. The dynamics of excited-state proton transfer in methanol-water solution have been investigated by means of femtosecond time-resolved transient absorption spectroscopy. Assignment of the transient absorption spectra is facilitated by comparison to the spectra of the corresponding potassium salts of the conjugate bases and the methyl ethers, which do not undergo excited-state proton transfer. The 4-cyanohydroxystilbenes undergo excited-state proton transfer with rate constants of 5 x 10(11) s(-1). These rate constants are comparable to the fastest that have been reported to date for a hydroxyaromatic photoacid and approach the theoretical limit for water-mediated proton transfer. The isotope effect for proton transfer in deuterated methanol-water is 1.3 +/- 0.2, similar to the isotope effect for the dielectric response of water. The barrier for excited state double bond torsion of the conjugate bases is small for 4-cyano-4-hydroxystilbene but large for 4-cyano-3-hydroxystilbene. Thus the "meta effect" is observed for the singlet states of both the neutral and conjugate base.

Molecular modeling of transmembrane helices 6 and 7 of the heptahelical lutropin receptor.

In response to ligand binding and activating mutations, the lutropin receptor undergoes a conformational change to trigger a cellular response. D556 is the most common locus for naturally occurring activating mutations of the lutropin receptor, and a D556A mutant is shown to be constitutively active. A water-mediated proton transfer is postulated as part of the transmembrane signaling mechanism. Using energy minimization and ab initio calculations, a hydrogen bonding network involving a highly constrained water molecule(s) and D556 (helix 6) and N593/N597/Y601 (helix 7) is presented.

Water-Mediated Proton Transfer: A Mechanistic Investigation on the Example of the Hydration of Sulfur Oxides

We outline general mechanistic features of “water-mediated proton transfer” in the example of the isomerization reaction in hydrogen-bonded sulfur oxide−water supermolecules containing up to three water molecules. The nucleophilic attack of a water oxygen on the sulfur atom occurs concertedly with the (multiple) proton-transfer event(s). The protons are transferred according to the well-known hydrogen-bond compression mechanism. However, contrary to “pure” multiple proton-transfer reactions, the protons are transferred asynchronously. These mechanistic features force the reaction to be classical rather than quantum-tunneling-dominated down to rather low temperatures. In the quantum-dominated temperature region, tunneling takes place only if all protons tunnel through the barrier. Straight line corner cutting (large curvature tunneling) does not dominate at any temperature, as the reduced mass corresponding to reaction coordinate motion does not drop to values low enough in the reaction barrier region. The...

The reaction rate constant of chlorine nitrate hydrolysis.

The first-order rate constant for the decomposition of chlorine nitrate (ClONO2) by water in a cyclic 1:3 complex at stratospheric temperatures is shown to be close to the values for the hydrolysis rate coefficient of chlorine nitrate on an ice surface determined in the laboratory. On the other hand the rate constants calculated for the cyclic 1:1 and 1:2 complexes are much lower than the experimental results. From the mechanistic point of view the reaction is found to be similar to a SN2 mechanism and coupled with water-mediated proton transfer in accordance with the intriguing findings of Bianco and Hynes [R. Bianco, J. T. Hynes. J. Phys. Chem. A 1998, 102, 309-314]. The function of additional water molecules is to act as a catalyst, that is, to accelerate the hydrolysis process. Quantum-mechanical tunneling is negligible above 125 K in the 1:3 complex and above 175 K in the 1:2 complex. At temperatures below these limits all involved protons tunnel through the barrier at energies at least 5 kcalmol(-1) below the barrier-top in a concerted, but asynchronous manner.

Toward elimination of discrepancies between theory and experiment: the rate constant of the atmospheric conversion of SO3 to H2SO4.

The hydration rate constant of sulfur trioxide to sulfuric acid is shown to depend sensitively on water vapor pressure. In the 1:1 SO3-H2O complex, the rate is predicted to be slower by about 25 orders of magnitude compared with laboratory results [Lovejoy, E. R., Hanson, D. R. & Huey, L. G. (1996) J. Phys. Chem. 100, 19911-19916; Jayne, J. T., Poschl, U., Chen, Y.-m., Dai, D., Molina, L. T., Worsnop, D. R., Kolb, C. E. & Molina, M. J. (1997) J. Phys. Chem. A 101, 10000-10011]. This discrepancy is removed mostly by allowing a second and third water molecule to participate. An asynchronous water-mediated double proton transfer concerted with the nucleophilic attack and a double proton transfer accompanied by a transient H3O+ rotation are predicted to be the fastest reaction mechanisms. Comparison of the predicted negative apparent "activation" energies with the experimental finding indicates that in our atmosphere, different reaction paths involving two and three water molecules are taken in the process of forming sulfate aerosols and consequently acid rain.

Water-Mediated Proton Transfer in Proteins: An FTIR Study of Bacteriorhodopsin

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTWater-Mediated Proton Transfer in Proteins: An FTIR Study of BacteriorhodopsinHideki Kandori, Yoichi Yamazaki, Jun Sasaki, Richard Needleman, Janos K. Lanyi, and Akio MaedaCite this: J. Am. Chem. Soc. 1995, 117, 7, 2118–2119Publication Date (Print):February 1, 1995Publication History Published online1 May 2002Published inissue 1 February 1995https://doi.org/10.1021/ja00112a036RIGHTS & PERMISSIONSArticle Views172Altmetric-Citations58LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (290 KB) Get e-Alerts Get e-Alerts