301
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Matsuoka D, Nakasako M. Prediction of Hydration Structures around Hydrophilic Surfaces of Proteins by Using the Empirical Hydration Distribution Functions from a Database Analysis. J Phys Chem B 2010; 114:4652-63. [DOI: 10.1021/jp9100224] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Daisuke Matsuoka
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
| | - Masayoshi Nakasako
- Department of Physics, Faculty of Science and Technology, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan, and RIKEN Harima Institute, 1-1-1 Kouto, Mikaduki, Sayo, Hyogo, Japan
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302
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Excitation of the M intermediates of wild-type bacteriorhodopsin and mutant D96N: temperature dependence of absorbance, electric responses and proton movements. Theor Chem Acc 2010. [DOI: 10.1007/s00214-009-0632-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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303
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del Rosario RCH, Oppawsky C, Tittor J, Oesterhelt D. Modeling the membrane potential generation of bacteriorhodopsin. Math Biosci 2010; 225:68-80. [PMID: 20188746 DOI: 10.1016/j.mbs.2010.02.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 02/10/2010] [Accepted: 02/13/2010] [Indexed: 10/19/2022]
Abstract
The archaeon Halobacterium salinarum can grow phototrophically with only light as its energy source. It uses the retinal containing and light-driven proton pump bacteriorhodopsin to enhance the membrane potential which drives the ATP synthase. Therefore, a model of the membrane potential generation of bacteriorhodopsin is of central importance to the development of a mathematical model of the bioenergetics of H. salinarum. To measure the current produced by bacteriorhodopsin at different light intensities and clamped voltages, we expressed the gene in Xenopus laevis oocytes. We present current-voltage measurements and a mathematical model of the current-voltage relationship of bacteriorhodopsin and its generation of the membrane potential. The model consists of three intermediate states, the BR, L, and M states, and comparisons between model predictions and experimental data show that the L to M reaction must be inhibited by the membrane potential. The model is not able to fit the current-voltage measurements when only the M to BR phase is membrane potential dependent, while it is able to do so when either only the L to M reaction or both reactions (L to M and M to BR) are membrane potential dependent. We also show that a decay term is necessary for modeling the rate of change of the membrane potential.
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Affiliation(s)
- Ricardo C H del Rosario
- Max Planck Institute of Biochemistry, Department of Membrane Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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304
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Antoranz Contera S, Voïtchovsky K, Ryan JF. Controlled ionic condensation at the surface of a native extremophile membrane. NANOSCALE 2010; 2:222-229. [PMID: 20644798 DOI: 10.1039/b9nr00248k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
At the nanoscale level biological membranes present a complex interface with the solvent. The functional dynamics and relative flexibility of membrane components together with the presence of specific ionic effects can combine to create exciting new phenomena that challenge traditional theories such as the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory or models interpreting the role of ions in terms of their ability to structure water (structure making/breaking). Here we investigate ionic effects at the surface of a highly charged extremophile membrane composed of a proton pump (bacteriorhodopsin) and archaeal lipids naturally assembled into a 2D crystal. Using amplitude-modulation atomic force microscopy (AM-AFM) in solution, we obtained sub-molecular resolution images of ion-induced surface restructuring of the membrane. We demonstrate the presence of a stiff cationic layer condensed at its extracellular surface. This layer cannot be explained by traditional continuum theories. Dynamic force spectroscopy experiments suggest that it is produced by electrostatic correlation mediated by a Manning-type condensation of ions. In contrast, the cytoplasmic surface is dominated by short-range repulsive hydration forces. These findings are relevant to archaeal bioenergetics and halophilic adaptation. Importantly, they present experimental evidence of a natural system that locally controls its interactions with the surrounding medium and challenges our current understanding of biological interfaces.
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Affiliation(s)
- Sonia Antoranz Contera
- University of Oxford, Bionanotechnology IRC, Clarendon Laboratory, Physics Department, Parks Road, OX1 3PU, Oxford, UK.
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305
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Hielscher R, Hellwig P. The Temperature-Dependent Hydrogen-Bonding Signature of Lipids Monitored in the Far-Infrared Domain. Chemphyschem 2010; 11:435-41. [DOI: 10.1002/cphc.200900430] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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306
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Sterpone F, Stirnemann G, Hynes JT, Laage D. Water Hydrogen-Bond Dynamics around Amino Acids: The Key Role of Hydrophilic Hydrogen-Bond Acceptor Groups. J Phys Chem B 2010; 114:2083-9. [DOI: 10.1021/jp9119793] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fabio Sterpone
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond 75005 Paris, France, Fondation Pierre Gilles de Gennes pour la Recherche, Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - Guillaume Stirnemann
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond 75005 Paris, France, Fondation Pierre Gilles de Gennes pour la Recherche, Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - James T. Hynes
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond 75005 Paris, France, Fondation Pierre Gilles de Gennes pour la Recherche, Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
| | - Damien Laage
- Department of Chemistry, Ecole Normale Supérieure, 24 rue Lhomond 75005 Paris, France, UMR ENS-CNRS-UPMC 8640, 24 rue Lhomond 75005 Paris, France, Fondation Pierre Gilles de Gennes pour la Recherche, Paris, France, and Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215
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307
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Ranaghan KE, Mulholland AJ. Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. INT REV PHYS CHEM 2010. [DOI: 10.1080/01442350903495417] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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308
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Lu SY, Jiang YJ, Zhou P, Zou JW, Wu TX. Geometric characteristics and energy landscapes of halogen–water–hydrogen bridges at protein–ligand interfaces. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2009.12.077] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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309
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Shekhter T, Metanis N, Dawson PE, Keinan E. A residue outside the active site CXXC motif regulates the catalytic efficiency of Glutaredoxin 3. MOLECULAR BIOSYSTEMS 2010; 6:241-8. [PMID: 20024086 PMCID: PMC3820274 DOI: 10.1039/b912753d] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The glutaredoxin (Grx) family of oxidoreductases has a conserved residue at position 8 that varies between Arginine in Grx1 and Lysine in Grx3. It has been proposed that this Arg/Lys change is the main cause for the 35 mV difference in redox potential between the two enzymes. To gain insights into the catalytic machinery of Grx3 and directly evaluate the role of residue 8 in the catalysis of thiol-disulfide exchange by this enzyme, we synthesized the "wild type" enzyme (sGrx3), and four analogues substituting the lysine at position 8 with arginine, ornithine (Orn), citrulline (Cit) and norvaline (Nva). The redox potential and equilibration kinetics with thioredoxin (Trx1) were determined for each enzyme by fluorescence intensity. While minor effects on redox potential were observed, we found that residue 8 had a more marked effect on the catalytic efficiency of this enzyme. Surprisingly, truncation of the functional group resulted in a more efficient enzyme, Lys8Nva, exhibiting rate constants that are an order of magnitude higher than sGrx3 for both forward and reverse reactions. These observations pose the question why would a residue that reduces the rate of enzyme turnover be evolutionarily conserved? The significant changes in the kinetic parameters suggest that this position plays an important role in the thiol-disulfide exchange reaction by affecting the nucleophilic thiolate through electrostatic or hydrogen bonding interactions. Since the reduced Grx has an exposed thiol that could easily be alkylated, either Arg or Lys could act as a gatekeeper that deters unwanted electrophiles from attacking the active site thiolate.
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Affiliation(s)
- Talia Shekhter
- Schulich Faculty of Chemistry and Institute of Catalysis Science and Technology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
- The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
- The Scripps Research Institute, Department of Molecular Biology, the Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Norman Metanis
- Schulich Faculty of Chemistry and Institute of Catalysis Science and Technology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
- The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
- The Scripps Research Institute, Department of Molecular Biology, the Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Philip E. Dawson
- The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
- The Scripps Research Institute, Department of Molecular Biology, Cell Biology and Chemistry and 10550 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Ehud Keinan
- Schulich Faculty of Chemistry and Institute of Catalysis Science and Technology, Technion-Israel Institute of Technology, Technion City, Haifa 32000, Israel
- The Scripps Research Institute, Department of Molecular Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
- The Scripps Research Institute, Department of Molecular Biology, the Skaggs Institute for Chemical Biology, 10550 North Torrey Pines Road, La Jolla, California 92037, USA
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310
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Pan Y, Konermann L. Membrane protein structural insights from chemical labeling and mass spectrometry. Analyst 2010; 135:1191-200. [DOI: 10.1039/b924805f] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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311
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Cracknell JA, Friedrich B, Armstrong FA. Gas pressure effects on the rates of catalytic H2 oxidation by hydrogenases. Chem Commun (Camb) 2010; 46:8463-5. [DOI: 10.1039/c0cc03292a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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312
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Duan C, Wei M, Guo D, He C, Meng Q. Crystal Structures and Properties of Large Protonated Water Clusters Encapsulated by Metal−Organic Frameworks. J Am Chem Soc 2009; 132:3321-30. [DOI: 10.1021/ja907023c] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Chunying Duan
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, P. R. China, and State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Meilin Wei
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, P. R. China, and State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Dong Guo
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, P. R. China, and State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Cheng He
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, P. R. China, and State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Qingjin Meng
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, P. R. China, and State Key Laboratory of Coordination Chemistry, Nanjing University, Nanjing 210093, P. R. China
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313
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Zhang L, Yang Y, Kao YT, Wang L, Zhong D. Protein hydration dynamics and molecular mechanism of coupled water-protein fluctuations. J Am Chem Soc 2009; 131:10677-91. [PMID: 19586028 DOI: 10.1021/ja902918p] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Protein surface hydration is fundamental to its structural stability and flexibility, and water-protein fluctuations are essential to biological function. Here, we report a systematic global mapping of water motions in the hydration layer around a model protein of apomyoglobin in both native and molten globule states. With site-directed mutagenesis, we use intrinsic tryptophan as a local optical probe to scan the protein surface one at a time with single-site specificity. With femtosecond resolution, we examined 16 mutants in two states and observed two types of water-network relaxation with distinct energy and time distributions. The first water motion results from the local collective hydrogen-bond network relaxation and occurs in a few picoseconds. The initial hindered motions, observed in bulk water in femtoseconds, are highly suppressed and drastically slow down due to structured water-network collectivity in the layer. The second water-network relaxation unambiguously results from the lateral cooperative rearrangements in the inner hydration shell and occurs in tens to hundreds of picoseconds. Significantly, this longtime dynamics is the coupled interfacial water-protein motions and is the direct measurement of such cooperative fluctuations. These local protein motions, although highly constrained, are necessary to assist the longtime water-network relaxation. A series of correlations of hydrating water dynamics and coupled fluctuations with local protein's chemical and structural properties were observed. These results are significant and reveal various water behaviors in the hydration layer with wide heterogeneity. We defined a solvation speed and an angular speed to quantify the water-network rigidity and local protein flexibility, respectively. We also observed that the dynamic hydration layer extends to more than 10 A. Finally, from native to molten globule states, the hydration water networks loosen up, and the protein locally becomes more flexible with larger global plasticity and partial unfolding.
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Affiliation(s)
- Luyuan Zhang
- Department of Physics, Program of Biophysics, The Ohio State University, Columbus, Ohio 43210, USA
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314
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Segura JJ, Verdaguer A, Cobián M, Hernández ER, Fraxedas J. Amphiphillic Organic Crystals. J Am Chem Soc 2009; 131:17853-9. [DOI: 10.1021/ja905961h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- J. J. Segura
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - A. Verdaguer
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - M. Cobián
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - E. R. Hernández
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
| | - J. Fraxedas
- Centre d’Investigació en Nanociència i Nanotecnologia, CIN2 (CSIC-ICN), Edifici CM7, Esfera UAB, Campus de Bellaterra, E-08193 Barcelona, Spain, and Institut de Ciència de Materials de Barcelona ICMAB (CSIC), Campus de Bellaterra, E-08193 Barcelona, Spain
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315
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Simón-Vázquez R, Lazarova T, Perálvarez-Marín A, Bourdelande JL, Padrós E. Cross-Linking of Transmembrane Helices Reveals a Rigid-Body Mechanism in Bacteriorhodopsin Transport. Angew Chem Int Ed Engl 2009; 48:8523-5. [DOI: 10.1002/anie.200904031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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316
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Simón-Vázquez R, Lazarova T, Perálvarez-Marín A, Bourdelande JL, Padrós E. Cross-Linking of Transmembrane Helices Reveals a Rigid-Body Mechanism in Bacteriorhodopsin Transport. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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317
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A G protein-coupled receptor at work: the rhodopsin model. Trends Biochem Sci 2009; 34:540-52. [PMID: 19836958 DOI: 10.1016/j.tibs.2009.07.005] [Citation(s) in RCA: 298] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Revised: 07/17/2009] [Accepted: 07/28/2009] [Indexed: 12/17/2022]
Abstract
G protein-coupled receptors (GPCRs) are ubiquitous signal transducers in cell membranes, as well as important drug targets. Interaction with extracellular agonists turns the seven transmembrane helix (7TM) scaffold of a GPCR into a catalyst for GDP and GTP exchange in heterotrimeric Galphabetagamma proteins. Activation of the model GPCR, rhodopsin, is triggered by photoisomerization of its retinal ligand. From the augmentation of biochemical and biophysical studies by recent high-resolution 3D structures, its activation intermediates can now be interpreted as the stepwise engagement of protein domains. Rearrangement of TM5-TM6 opens a crevice at the cytoplasmic side of the receptor into which the C terminus of the Galpha subunit can bind. The Galpha C-terminal helix is used as a transmission rod to the nucleotide binding site. The mechanism relies on dynamic interactions between conserved residues and could therefore be common to other GPCRs.
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318
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Matsuoka D, Nakasako M. Probability distributions of hydration water molecules around polar protein atoms obtained by a database analysis. J Phys Chem B 2009; 113:11274-92. [PMID: 19621908 DOI: 10.1021/jp902459n] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Hydration structures on protein surfaces are visualized by high-resolution cryogenic X-ray crystallography. We calculated the probability distributions of 4,831,570 hydration water molecules found around the 4,214,227 polar atoms in main chains and hydrophilic side chains from the 17,984 crystal structures in the Protein Data Bank. The structures are refined using the diffraction data collected below 150 K and at resolutions of better than 2.2 A. The calculated distributions were nonrandom but condensed into a few clusters. The clusters were decomposed into the distance and angular distributions by viewing from the polar coordinate system. The major peaks in the clusters were almost located along the directions of the N-H and O-H bonds or the lone pairs of oxygen atoms. The Gaussian fitting method was applied for the distribution profiles to evaluate quantitatively the peak positions and the widths. The parameters characterizing the distributions apparently depended on the hydrogen-bond partners of water molecules and on the modes whether the water molecules acted as donors or acceptors of protons. This led to propose the different roles of NH(n) (n = 1, 3), OH, and CO groups in protein hydration and possible in protein-ligand and protein-protein interaction: While C horizontal lineO groups appear to control the H-bond distances, NH(n) groups likely limit the angular range of H-bonds. The OH groups have both characteristics. In addition, it was also demonstrated that polar protein atoms were arranged to satisfy the tetrahedral hydrogen-bond geometry of water molecules, suggesting essential roles of water molecules in the folding process and in the stabilization of protein structures. These probability distributions are probably one of fundamental data to better understand the roles of hydration water molecules in the folding process and the stability of proteins in solution.
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Affiliation(s)
- Daisuke Matsuoka
- Department of Physics, Faculty of Science and Technology, Keio University, Yokohama, Kanagawa 223-8522, Japan
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319
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Alexandre MTA, van Grondelle R, Hellingwerf KJ, Kennis JTM. Conformational heterogeneity and propagation of structural changes in the LOV2/Jalpha domain from Avena sativa phototropin 1 as recorded by temperature-dependent FTIR spectroscopy. Biophys J 2009; 97:238-47. [PMID: 19580761 DOI: 10.1016/j.bpj.2009.03.047] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2008] [Revised: 03/18/2009] [Accepted: 03/26/2009] [Indexed: 12/17/2022] Open
Abstract
Phototropins control phototropism, chloroplast movement, stomatal opening, and leaf expansion in plants. Phototropin 1 (phot1) is composed of a kinase domain linked to two blue light-sensing domains, LOV2 and LOV1, which bind flavin mononucleotide. Disruption of the interaction between the LOV2 domain and a helical segment named Jalpha, joining LOV to the kinase domain, induces the subsequent kinase activity of phototropin 1 and further-downstream signal transduction. Here we study the effects of temperature and hydration on the light-triggered signal propagation in the phot1 LOV2 domain of Avena sativa (AsLOV2/Jalpha), using Fourier transform infrared spectroscopy to unravel part of the molecular mechanism of phototropin 1. We report that AsLOV2/Jalpha shows an intense signal in the amide I and II regions, arising mainly from beta-sheet changes and the unbinding of the Jalpha helix from the Per-ARNT-Sim core and its subsequent partial unfolding. Importantly, these structural changes only occur under conditions of full hydration and at temperatures above 280 K. We characterized a newly isolated low-hydration intermediate that shows a downshift of high-frequency amide I signals and that possibly corresponds to loop tightening, without large beta-sheet or Jalpha structural changes. In addition, we report a heterogeneity in AsLOV2/Jalpha involving two different C(4)=O conformer populations, coexisting in the dark state and characterized by C(4)=O carbonyl frequencies at 1712 cm(-1) and 1694 cm(-1) that are attributable to a single H-bond and two H-bonds at this site, respectively. Such conformers display slightly shifted absorption spectra and cause a splitting of the 475-nm band in the ultraviolet/visible spectra of LOV domains at low temperature.
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Affiliation(s)
- Maxime T A Alexandre
- Department of Biophysics, Faculty of Sciences, Vrije Universiteit, 1081HV Amsterdam, The Netherlands
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320
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Smirnova I, Kasho V, Sugihara J, Choe JY, Kaback HR. Residues in the H+ translocation site define the pKa for sugar binding to LacY. Biochemistry 2009; 48:8852-60. [PMID: 19689129 DOI: 10.1021/bi9011918] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A remarkably high pKa of approximately 10.5 has been determined for sugar-binding affinity to the lactose permease of Escherichia coli (LacY), indicating that, under physiological conditions, substrate binds to fully protonated LacY. We have now systematically tested site-directed replacements for the residues involved in sugar binding, as well as H+ translocation and coupling, in order to determine which residues may be responsible for this alkaline pKa. Mutations in the sugar-binding site (Glu126, Trp151, Glu269) markedly decrease affinity for sugar but do not alter the pKa for binding. In contrast, replacements for residues involved in H+ translocation (Arg302, Tyr236, His322, Asp240, Glu325, Lys319) exhibit pKa values for sugar binding that are either shifted toward neutral pH or independent of pH. Values for the apparent dissociation constant for sugar binding (K(d)(app)) increase greatly for all mutants except neutral replacements for Glu325 or Lys319, which are characterized by remarkably high affinity sugar binding (i.e., low K(d)(app)) from pH 5.5 to pH 11. The pH dependence of the on- and off-rate constants for sugar binding measured directly by stopped-flow fluorometry implicates k(off) as a major factor for the affinity change at alkaline pH and confirms the effects of pH on K(d)(app) inferred from steady-state fluorometry. These results indicate that the high pKa for sugar binding by wild-type LacY cannot be ascribed to any single amino acid residue but appears to reside within a complex of residues involved in H+ translocation. There is structural evidence for water bound in this complex, and the water could be the site of protonation responsible for the pH dependence of sugar binding.
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Affiliation(s)
- Irina Smirnova
- Department of Physiology, University of California Los Angeles, Los Angeles, California 90095-7327, USA
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321
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Muthuselvi L, Dhathathreyan A. Understanding dynamics of myoglobin in heterogeneous aqueous environments using coupled water fractions. Adv Colloid Interface Sci 2009; 150:55-62. [PMID: 19442960 DOI: 10.1016/j.cis.2009.04.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2009] [Revised: 04/08/2009] [Accepted: 04/08/2009] [Indexed: 11/19/2022]
Abstract
This work presents an analysis of near environment of myoglobin (Mb) in different aqueous solutions (in the presence of NaCl, sucrose, trehalose, urea, and glycerol) using the coupled water fractions measured using a quartz crystal microbalance (QCM). The secondary structural features of the protein from circular dichroic (CD) spectroscopy and the coupled water fractions give important clues to the overall dynamics of the protein. Using time resolved fluorescence, these leads have been applied to understand the observed lifetime relaxations of Mb. Though the time scales of observation of coupled water and the lifetimes are very different, our study suggests that the trends in coupled water fraction seem to be good indicators for regulation of the relaxation dynamics of the protein. The relaxations generally show a triphasic distribution of time scales. The initial relaxation in the picoseconds time scale represents the local motions of coupled water followed by a slightly slower decay in hundreds of picoseconds attributable to coupled water-'quasi free' water interactions. The third nanosecond lifetime is due to changes in transitions in isomers of hydrated protein. The dynamics of coupled water in Mb with NaCl is the fastest (around 21 ps) and is slowest in glycerol (250 ps). The results strongly indicate that it is the resident times of water molecules that play a dominant role in the overall stability of protein in a particular hydrated isomer and not just always the number of such water molecules in the hydrated protein.
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Affiliation(s)
- L Muthuselvi
- Chemical Lab., CLRI (CSIR), Adyar, Chennai 600 020, India
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322
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Verhoefen MK, Lenz MO, Amarie S, Klare JP, Tittor J, Oesterhelt D, Engelhard M, Wachtveitl J. Primary Reaction of Sensory Rhodopsin II Mutant D75N and the Influence of Azide. Biochemistry 2009; 48:9677-83. [DOI: 10.1021/bi901197c] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mirka-Kristin Verhoefen
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Martin O. Lenz
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Sergiu Amarie
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Johann P. Klare
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Jörg Tittor
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Dieter Oesterhelt
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Martin Engelhard
- Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44139 Dortmund, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Institute of Biophysics, Johann Wolfgang Goethe-University Frankfurt, Max von Laue-Strasse 7, 60438 Frankfurt am Main, Germany
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323
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Park SY, Kwon OH, Lee YS, Jang DJ. Triplet-State Acid−Base Reactions of 1-Methyl-7-oxyquinolinium in Water. J Phys Chem A 2009; 113:10589-92. [DOI: 10.1021/jp907687a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Sun-Young Park
- School of Chemistry, Seoul National University, NS60, Seoul 151-742, Korea
| | - Oh-Hoon Kwon
- School of Chemistry, Seoul National University, NS60, Seoul 151-742, Korea
| | - Young-Shin Lee
- School of Chemistry, Seoul National University, NS60, Seoul 151-742, Korea
| | - Du-Jeon Jang
- School of Chemistry, Seoul National University, NS60, Seoul 151-742, Korea
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324
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The cytochrome ba3 oxygen reductase from Thermus thermophilus uses a single input channel for proton delivery to the active site and for proton pumping. Proc Natl Acad Sci U S A 2009; 106:16169-73. [PMID: 19805275 DOI: 10.1073/pnas.0905264106] [Citation(s) in RCA: 89] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The heme-copper oxygen reductases are redox-driven proton pumps that generate a proton motive force in both prokaryotes and mitochondria. These enzymes have been divided into 3 evolutionarily related groups: the A-, B- and C-families. Most experimental work on proton-pumping mechanisms has been performed with members of the A-family. These enzymes require 2 proton input pathways (D- and K-channels) to transfer protons used for oxygen reduction chemistry and for proton pumping, with the D-channel transporting all pumped protons. In this work we use site-directed mutagenesis to demonstrate that the ba(3) oxygen reductase from Thermus thermophilus, a representative of the B-family, does not contain a D-channel. Rather, it utilizes only 1 proton input channel, analogous to that of the A-family K-channel, and it delivers protons to the active site for both O2 chemistry and proton pumping. Comparison of available subunit I sequences reveals that the only structural elements conserved within the oxygen reductase families that could perform these functions are active-site components, namely the covalently linked histidine-tyrosine, the Cu(B) and its ligands, and the active-site heme and its ligands. Therefore, our data suggest that all oxygen reductases perform the same chemical reactions for oxygen reduction and comprise the essential elements of the proton-pumping mechanism (e.g., the proton-loading and kinetic-gating sites). These sites, however, cannot be located within the D-channel. These results along with structural considerations point to the A-propionate region of the active-site heme and surrounding water molecules as the proton-loading site.
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325
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Structural waters define a functional channel mediating activation of the GPCR, rhodopsin. Proc Natl Acad Sci U S A 2009; 106:14367-72. [PMID: 19706523 DOI: 10.1073/pnas.0901074106] [Citation(s) in RCA: 165] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Structural water molecules may act as prosthetic groups indispensable for proper protein function. In the case of allosteric activation of G protein-coupled receptors (GPCRs), water likely imparts structural plasticity required for agonist-induced signal transmission. Inspection of structures of GPCR superfamily members reveals the presence of conserved embedded water molecules likely important to GPCR function. Coupling radiolytic hydroxyl radical labeling with rapid H(2)O(18) solvent mixing, we observed no exchange of these structural waters with bulk solvent in either ground state or for the Meta II or opsin states. However, the radiolysis approach permitted labeling of selected side chain residues within the transmembrane helices and revealed activation-induced changes in local structural constraints likely mediated by dynamics of both water and protein. These results suggest both a possible general mechanism for water-dependent communication in family A GPCRs based on structural conservation, and a strategy for probing membrane protein structure.
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326
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Zhong D. Hydration Dynamics and Coupled Water-Protein Fluctuations Probed by Intrinsic Tryptophan. ADVANCES IN CHEMICAL PHYSICS 2009. [DOI: 10.1002/9780470508602.ch3] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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327
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Babitzki G, Denschlag R, Tavan P. Polarization Effects Stabilize Bacteriorhodopsin’s Chromophore Binding Pocket: A Molecular Dynamics Study. J Phys Chem B 2009; 113:10483-95. [DOI: 10.1021/jp902428x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- G. Babitzki
- Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - R. Denschlag
- Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - P. Tavan
- Theoretische Biophysik, Lehrstuhl für Biomolekulare Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
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328
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Douberly GE, Ricks AM, Duncan MA. Infrared Spectroscopy of Perdeuterated Protonated Water Clusters in the Vicinity of the Clathrate Cage. J Phys Chem A 2009; 113:8449-53. [DOI: 10.1021/jp9052709] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Gary E. Douberly
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - Allen M. Ricks
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
| | - Michael A. Duncan
- Department of Chemistry, University of Georgia, Athens, Georgia 30602-2556
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329
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Kaneko Y, Hayashi S, Ohmine I. Proton-Transfer Reactions in Reaction Center of Photosynthetic Bacteria Rhodobacter sphaeroides. J Phys Chem B 2009; 113:8993-9003. [DOI: 10.1021/jp9008898] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yu Kaneko
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya 464-8602, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan, and Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraku-machi 34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - Shigehiko Hayashi
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya 464-8602, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan, and Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraku-machi 34-4, Sakyo-ku, Kyoto 606-8103, Japan
| | - Iwao Ohmine
- Department of Chemistry, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya 464-8602, Japan, Department of Chemistry, Graduate School of Science, Kyoto University, Kitashirakawa, Sakyo-ku, Kyoto 606-8502, Japan, and Fukui Institute for Fundamental Chemistry, Kyoto University, Nishihiraku-machi 34-4, Sakyo-ku, Kyoto 606-8103, Japan
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330
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Bondar AN, Smith JC. Water Molecules in Short- and Long-Distance Proton Transfer Steps of Bacteriorhodopsin Proton Pumping. Isr J Chem 2009. [DOI: 10.1560/ijc.49.2.155] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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331
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Andresen ER, Hamm P. Site-specific difference 2D-IR spectroscopy of bacteriorhodopsin. J Phys Chem B 2009; 113:6520-7. [PMID: 19358550 DOI: 10.1021/jp810397u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
We demonstrate the extension of the principle of difference Fourier transform infrared (FTIR) spectroscopy to difference 2D-IR spectroscopy. To this end, we measure difference 2D-IR spectra of the protein bacteriorhodopsin in its early J- and K-intermediates. By comparing with the static 2D-IR spectrum of the protonated Schiff base of all-trans retinal, we demonstrate that the 2D-IR spectrum of the all-trans retinal chromophore in bacteriorhodopsin can be measured with the background from the remainder of the protein completely suppressed. We discuss several models to interpret the detailed line shape of the difference 2D-IR spectrum.
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Affiliation(s)
- Esben Ravn Andresen
- Physikalisch-Chemisches Institut, Universitat Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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332
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Bhate MP, Woodard JC, Mehta MA. Solvation and Hydrogen Bonding in Alanine- and Glycine-Containing Dipeptides Probed Using Solution- and Solid-State NMR Spectroscopy. J Am Chem Soc 2009; 131:9579-89. [DOI: 10.1021/ja902917s] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manasi P. Bhate
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074
| | - Jaie C. Woodard
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074
| | - Manish A. Mehta
- Department of Chemistry and Biochemistry, Oberlin College, Oberlin, Ohio 44074
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333
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Groff D, Thielges MC, Cellitti S, Schultz PG, Romesberg FE. Efforts toward the direct experimental characterization of enzyme microenvironments: tyrosine100 in dihydrofolate reductase. Angew Chem Int Ed Engl 2009; 48:3478-81. [PMID: 19347910 DOI: 10.1002/anie.200806239] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
State secrets: Site-specific deuteration and FTIR studies reveal that Tyr100 in dihydrofolate reductase plays an important role in catalysis, with a strong electrostatic coupling occurring between Tyr100 and the charge that develops in the hydride-transfer transition state (see picture, NADP(+) purple, Tyr100 green). However, relaying correlated motions that facilitate catalysis from distal sites of the protein to the hydride donor may also be involved.
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Affiliation(s)
- Dan Groff
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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334
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Phatak P, Frähmcke JS, Wanko M, Hoffmann M, Strodel P, Smith J, Suhai S, Bondar AN, Elstner M. Long-distance proton transfer with a break in the bacteriorhodopsin active site. J Am Chem Soc 2009; 131:7064-78. [PMID: 19405533 PMCID: PMC2746972 DOI: 10.1021/ja809767v] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteriorhodopsin is a proton-pumping membrane protein found in the plasma membrane of the archaeon Halobacterium salinarium. Light-induced isomerization of the retinal chromophore from all-trans to 13-cis leads to a sequence of five conformation-coupled proton transfer steps and the net transport of one proton from the cytoplasmic to the extracellular side of the membrane. The mechanism of the long-distance proton transfer from the primary acceptor Asp85 to the extracellular proton release group during the O --> bR is poorly understood. Experiments suggest that this long-distance transfer could involve a transient state [O] in which the proton resides on the intermediate carrier Asp212. To assess whether the transient protonation of Asp212 participates in the deprotonation of Asp85, we performed hybrid Quantum Mechanics/Molecular Mechanics proton transfer calculations using different protein structures and with different retinal geometries and active site water molecules. The structural models were assessed by computing UV-vis excitation energies and C=O vibrational frequencies. The results indicate that a transient [O] conformer with protonated Asp212 could indeed be sampled during the long-distance proton transfer to the proton release group. Our calculations suggest that, in the starting proton transfer state O, the retinal is strongly twisted and at least three water molecules are present in the active site.
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Affiliation(s)
- Prasad Phatak
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Jan S. Frähmcke
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
| | - Marius Wanko
- BCCMS, Universität Bremen, D-28334 Bremen, Germany
| | | | - Paul Strodel
- Accelrys Ltd., Cambridge CB4 0WN, United Kingdom
| | - Jeremy Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany
- Center for Molecular Biophysics, Oak Ridge National Laboratory, PO BOX 2008 MS6164, Oak Ridge, Tennessee 37831, USA
- Department of Biochemistry and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Ave, Knoxville Tennessee 37996, USA
| | - Sándor Suhai
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
| | - Ana-Nicoleta Bondar
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120, Heidelberg, Germany
- Department of Physiology and Biophysics and the Center for Biomembrane Systems, University of California at Irvine, Med. Sci. I, D-347, Irvine, CA 92697, USA
| | - Marcus Elstner
- Institute of Physical and Theoretical Chemistry, TU Braunschweig, D-38106 Braunschweig, Germany
- Molecular Biophysics Department, German Cancer Research Institute, Im Neuheimer Feld 280, D-69120, Heidelberg, Germany
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335
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Conformations of NhaA, the Na+/H+ exchanger from Escherichia coli, in the pH-activated and ion-translocating states. J Mol Biol 2009; 388:659-72. [PMID: 19396973 DOI: 10.1016/j.jmb.2009.03.010] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
NhaA, the main sodium-proton exchanger in the inner membrane of Escherichia coli, regulates the cytosolic concentrations of H+ and Na+. It is inactive at acidic pH, becomes active between pH 6 and pH 7, and reaches maximum activity at pH 8. By cryo-electron microscopy of two-dimensional crystals grown at pH 4 and incubated at higher pH, we identified two sequential conformational changes in the protein in response to pH or substrate ions. The first change is induced by a rise in pH from 6 to 7 and marks the transition from the inactive state to the pH-activated state. pH activation, which precedes the ion-induced conformational change, is accompanied by an overall expansion of the NhaA monomer and a local ordering of the N-terminus. The second conformational change is induced by the substrate ions Na+ and Li+ at pH above 7 and involves a 7-A displacement of helix IVp. This movement would cause a charge imbalance at the ion-binding site that may trigger the release of the substrate ion and open a periplasmic exit channel.
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336
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Groff D, Thielges M, Cellitti S, Schultz P, Romesberg F. Efforts Toward the Direct Experimental Characterization of Enzyme Microenvironments: Tyrosine100 in Dihydrofolate Reductase. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200806239] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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337
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338
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Lórenz-Fonfría VA, Kandori H. Spectroscopic and Kinetic Evidence on How Bacteriorhodopsin Accomplishes Vectorial Proton Transport under Functional Conditions. J Am Chem Soc 2009; 131:5891-901. [DOI: 10.1021/ja900334c] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Víctor A. Lórenz-Fonfría
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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339
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Bergo VB, Spudich EN, Spudich JL, Rothschild KJ. Active water in protein-protein communication within the membrane: the case of SRII-HtrII signal relay. Biochemistry 2009; 48:811-3. [PMID: 19187030 DOI: 10.1021/bi802180a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We detect internal water molecules in a membrane-embedded receptor-transducer complex and demonstrate water structure changes during formation of the signaling state. Time-resolved FTIR spectroscopy reveals stimulus-induced repositioning of one or more structurally active water molecules to a significantly more hydrophobic environment in the signaling state of the sensory rhodopsin II (SRII)-transducer (HtrII) complex. These waters, distinct from bound water molecules within the SRII receptor, appear to be in the middle of the transmembrane interface region near the Tyr199(SRII)-Asn74(HtrII) hydrogen bond. We conclude that water potentially plays an important role in the SRII --> HtrII signal transfer mechanism in the membrane's hydrophobic core.
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Affiliation(s)
- Vladislav B Bergo
- Department of Physics, Molecular Biophysics Laboratory, and Center for Photonics, Boston University, Boston, Massachusetts 02215, USA
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340
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Verhoefen MK, Neumann K, Weber I, Glaubitz C, Wachtveitl J. Primary Reaction Dynamics of Proteorhodopsin Mutant D97N Observed by Femtosecond Infrared and Visible Spectroscopy. Photochem Photobiol 2009; 85:540-6. [DOI: 10.1111/j.1751-1097.2008.00513.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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341
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Tóth-Boconádi R, Dér A, Fábián L, Taneva SG, Keszthelyi L. Excitation of the M Intermediates of Bacteriorhodopsin. Photochem Photobiol 2009; 85:609-13. [DOI: 10.1111/j.1751-1097.2008.00521.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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342
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Kawamura I, Tanabe J, Ohmine M, Yamaguchi S, Tuzi S, Naito A. Participation of the BC Loop in the Correct Folding of Bacteriorhodopsin as Revealed by Solid-state NMR. Photochem Photobiol 2009; 85:624-30. [DOI: 10.1111/j.1751-1097.2009.00536.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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343
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Wassenaar TA, Daura X, Padrós E, Mark AE. Calcium binding to the purple membrane: A molecular dynamics study. Proteins 2009; 74:669-81. [PMID: 18704943 DOI: 10.1002/prot.22182] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The purple membrane (PM) is a specialized membrane patch found in halophilic archaea, containing the photoreceptor bacteriorhodopsin (bR). It is long known that calcium ions bind to the PM, but their position and role remain elusive to date. Molecular dynamics simulations in conjunction with a highly detailed model of the PM have been used to investigate the stability of calcium ions placed at three proposed cation binding sites within bR, one near the Schiff base, one in the region of the proton release group, and one near Glu9. The simulations suggest that, of the sites investigated, the binding of calcium ions was most likely at the proton release group. Binding in the region of the Schiff base, while possible, was associated with significant changes in local geometry. Calcium ions placed near Glu9 in the interior of bR (simultaneously to a Ca(2+) near the Schiff base and another one near the Glu194-Glu204 site) were not stable. The results obtained are discussed in relation to recent experimental observations and theoretical considerations.
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Affiliation(s)
- Tsjerk A Wassenaar
- Department of Biophysical Chemistry, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, 9747 AG Groningen, The Netherlands
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344
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Conformations of NhaA, the Na/H Exchanger from Escherichia coli, in the pH-Activated and Ion-Translocating States. J Mol Biol 2009; 386:351-65. [DOI: 10.1016/j.jmb.2008.12.042] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2008] [Revised: 12/11/2008] [Accepted: 12/15/2008] [Indexed: 12/25/2022]
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345
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Kitade Y, Furutani Y, Kamo N, Kandori H. Proton Release Group of pharaonis Phoborhodopsin Revealed by ATR-FTIR Spectroscopy. Biochemistry 2009; 48:1595-603. [DOI: 10.1021/bi801984u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuya Kitade
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Yuji Furutani
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Naoki Kamo
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan, and Graduate School of Pharmaceutical Sciences, Hokkaido University, Sapporo 060-0810, Japan
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346
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Wolf S, Freier E, Gerwert K. How does a membrane protein achieve a vectorial proton transfer via water molecules? Chemphyschem 2009; 9:2772-8. [PMID: 19072873 DOI: 10.1002/cphc.200800703] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We present a detailed mechanism for the proton transfer from a protein-bound protonated water cluster to the bulk water directed by protein side chains in the membrane protein bacteriorhodopsin. We use a combined approach of time-resolved Fourier transform infrared spectroscopy, molecular dynamics simulations, and X-ray structure analysis to elucidate the functional role of a hydrogen bond between Ser193 and Glu204. These two residues seal the internal protonated water cluster from the bulk water and the protein surface. During the photocycle of bacteriorhodopsin, a transient protonation of Glu204 leads to a breaking of this hydrogen bond. This breaking opens the gate to the extracellular bulk water, leading to a subsequent proton release from the protonated water cluster. We show in detail how the protein achieves vectorial proton transfer via protonated water clusters in contrast to random proton transfer in liquid water.
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Affiliation(s)
- Steffen Wolf
- Department of Biophysics, ND 04 North, Ruhr-University BochumD-44780 Bochum, Germany
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347
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Baer M, Mathias G, Kuo IFW, Tobias DJ, Mundy CJ, Marx D. Spectral signatures of the pentagonal water cluster in bacteriorhodopsin. Chemphyschem 2009; 9:2703-7. [PMID: 19025752 DOI: 10.1002/cphc.200800473] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Marcel Baer
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.
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348
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Abstract
The protein bacteriorhodopsin pumps protons across a bacterial membrane; its pumping cycle is triggered by the photoisomerization of a retinal cofactor and involves multiple proton-transfer reactions between intermittent protonation sites. These transfers are either direct or mediated by hydrogen-bonded networks, which may include internal water molecules. The terminal step of the proton-transfer sequence is the proton release from a pocket near Glu194 and Glu204 to the extracellular bulk during the transition from the L to the M photointermediate states. The polar and charged side chains connecting these two regions in the crystal structures show no structural changes between the initial bR state and the L/M states, and no intermittent protonation changes have been detected so far in this region. Based on biomolecular simulations, we propose two potential proton-release channels, which connect the release pocket to the extracellular medium. In simulations of the L photointermediate we observe bulk water entering these channels and forming transient hydrogen-bonded networks, which could serve as fast deprotonation pathways from the release pocket to the bulk via a Grotthuss mechanism. For the first channel, we find that the triple Arg7, Glu9, and Tyr79 acts as a valve, thereby gating water uptake and release. The second channel has two release paths, which split at the position Asn76/Pro77 underneath the release group. Here, water molecules either exchange directly with the bulk or diffuse within the protein towards Arg 134/Lys129, where the exchange with the bulk occurs.
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Affiliation(s)
- Alain Chaumont
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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349
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Abstract
The role of water molecules in spectral tuning of proteins has been left largely unexplored. This topic is important because changing hydrogen bond patterns during the activation process may lead to spectral shifts which can be of diagnostic value for the underlying structures. Arguments put forward in this article are based on spectral shift calculations of the rhodopsin and bathorhodopsin chromophore due to wat2a and 2b in the presence and absence of the counterion and of the amino acids lining the rhodopsin binding pocket. They show, among others, that a single water molecule can shift the absorbance by up to 0.1 eV or 34 nm depending on the environment of the chromophore.
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350
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Radu I, Schleeger M, Bolwien C, Heberle J. Time-resolved methods in biophysics. 10. Time-resolved FT-IR difference spectroscopy and the application to membrane proteins. Photochem Photobiol Sci 2009; 8:1517-28. [DOI: 10.1039/b9pp00050j] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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