351
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Ricks AM, Douberly GE, Duncan MA. Infrared spectroscopy of the protonated nitrogen dimer: The complexity of shared proton vibrations. J Chem Phys 2009. [DOI: 10.1063/1.3224155] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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352
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Amino acids with an intermolecular proton bond as proton storage site in bacteriorhodopsin. Proc Natl Acad Sci U S A 2008; 105:19672-7. [PMID: 19064907 DOI: 10.1073/pnas.0810712105] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The positions of protons are not available in most high-resolution structural data of biomolecules, thus the identity of proton storage sites in biomolecules that transport proton is generally difficult to determine unambiguously. Using combined quantum mechanical/molecular mechanical computations, we demonstrate that a pair of conserved glutamate residues (Glu 194/204) bonded by a delocalized proton is the proton release group that has been long sought in the proton pump, bacteriorhodopsin. This model is consistent with all available experimental structural and infrared data for both the wild-type bacteriorhodopsin and several mutants. In particular, the continuum infrared band in the 1,800- to 2,000-cm(-1) region is shown to arise due to the partially delocalized nature of the proton between the glutamates in the wild-type bacteriorhodopsin; alternations in the flexibility of the glutamates and electrostatic nature of nearby residues in various mutants modulate the degree of proton delocalization and therefore intensity of the continuum band. The strong hydrogen bond between Glu 194/204 also significantly shifts the carboxylate stretches of these residues well <1,700 cm(-1), which explains why carboxylate spectral shift was not observed experimentally in the typical >1,700-cm(-1) region upon proton release. By contrast, simulations with the proton restrained on the nearby water cluster, as proposed by several recent studies [see, for example, Garezarek K, Gerwert K (2006) Functional waters in intraprotein proton transfer monitored by FTIR difference spectroscopy. Nature 439:109], led to significant structural deviations from available X-ray structures. This study establishes a biological function for strong, low-barrier hydrogen bonds.
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353
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Yoshimoto J, Sandoval CA, Saito S. Aqua-aminoorganoboron Catalyst: Engineering Single Water Molecule to Act as an Acid Catalyst in Nitro Aldol Reaction. CHEM LETT 2008. [DOI: 10.1246/cl.2008.1294] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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354
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Bondar AN, Baudry J, Suhai S, Fischer S, Smith JC. Key Role of Active-Site Water Molecules in Bacteriorhodopsin Proton-Transfer Reactions. J Phys Chem B 2008; 112:14729-41. [DOI: 10.1021/jp801916f] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ana-Nicoleta Bondar
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Jerome Baudry
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Sándor Suhai
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Stefan Fischer
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
| | - Jeremy C. Smith
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, D-69120 Heidelberg, Germany, Molecular Biophysics Department, German Cancer Research Center, Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, University of California at Irvine, Department of Physiology and Biophysics and the Center for Biomembrane Systems, Med. Sci. I, D-374, Irvine, California 92697-4560, University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge
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355
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Crystallographic structure of xanthorhodopsin, the light-driven proton pump with a dual chromophore. Proc Natl Acad Sci U S A 2008; 105:16561-5. [PMID: 18922772 DOI: 10.1073/pnas.0807162105] [Citation(s) in RCA: 180] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Homologous to bacteriorhodopsin and even more to proteorhodopsin, xanthorhodopsin is a light-driven proton pump that, in addition to retinal, contains a noncovalently bound carotenoid with a function of a light-harvesting antenna. We determined the structure of this eubacterial membrane protein-carotenoid complex by X-ray diffraction, to 1.9-A resolution. Although it contains 7 transmembrane helices like bacteriorhodopsin and archaerhodopsin, the structure of xanthorhodopsin is considerably different from the 2 archaeal proteins. The crystallographic model for this rhodopsin introduces structural motifs for proton transfer during the reaction cycle, particularly for proton release, that are dramatically different from those in other retinal-based transmembrane pumps. Further, it contains a histidine-aspartate complex for regulating the pK(a) of the primary proton acceptor not present in archaeal pumps but apparently conserved in eubacterial pumps. In addition to aiding elucidation of a more general proton transfer mechanism for light-driven energy transducers, the structure defines also the geometry of the carotenoid and the retinal. The close approach of the 2 polyenes at their ring ends explains why the efficiency of the excited-state energy transfer is as high as approximately 45%, and the 46 degrees angle between them suggests that the chromophore location is a compromise between optimal capture of light of all polarization angles and excited-state energy transfer.
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356
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357
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Amsden JJ, Kralj JM, Bergo VB, Spudich EN, Spudich JL, Rothschild KJ. Different structural changes occur in blue- and green-proteorhodopsins during the primary photoreaction. Biochemistry 2008; 47:11490-8. [PMID: 18842006 DOI: 10.1021/bi800945t] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We examine the structural changes during the primary photoreaction in blue-absorbing proteorhodopsin (BPR), a light-driven retinylidene proton pump, using low-temperature FTIR difference spectroscopy. Comparison of the light-induced BPR difference spectrum recorded at 80 K to that of green-absorbing proteorhodopsin (GPR) reveals that there are several differences in the BPR and GPR primary photoreactions despite the similar structure of the retinal chromophore and all-trans --> 13-cis isomerization. Strong bands near 1700 cm(-1) assigned previously to a change in hydrogen bonding of Asn230 in GPR are still present in BPR. However, additional bands in the same region are assigned on the basis of site-directed mutagenesis to changes occurring in Gln105. In the amide II region, bands are assigned on the basis of total (15)N labeling to structural changes of the protein backbone, although no such bands were previously observed for GPR. A band at 3642 cm(-1) in BPR, assigned to the OH stretching mode of a water molecule on the basis of H2(18)O substitution, appears at a different frequency than a band at 3626 cm(-1) previously assigned to a water molecule in GPR. However, the substitution of Gln105 for Leu105 in BPR leads to the appearance of both bands at 3642 and 3626 cm(-1), indicating the waters assigned in BPR and GPR exist in separate distinct locations and can coexist in the GPR-like Q105L mutant of BPR. These results indicate that there exist significant differences in the conformational changes occurring in these two types proteorhodopsin during the initial photoreaction despite their similar chromophore structures, which might reflect a different arrangement of water in the active site as well as substitution of a hydrophilic for hydrophobic residue at residue 105.
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Affiliation(s)
- Jason J Amsden
- Department of Physics, Photonics Center, and Molecular Biophysics Laboratory, Boston University, Boston, Massachusetts 02215, USA
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358
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Morgan JE, Vakkasoglu AS, Lugtenburg J, Gennis RB, Maeda A. Structural changes due to the deprotonation of the proton release group in the M-photointermediate of bacteriorhodopsin as revealed by time-resolved FTIR spectroscopy. Biochemistry 2008; 47:11598-605. [PMID: 18837559 DOI: 10.1021/bi801405v] [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
One of the steps in the proton pumping cycle of bacteriorhodopsin (BR) is the release of a proton from the proton-release group (PRG) on the extracellular side of the Schiff base. This proton release takes place shortly after deprotonation of the Schiff base (L-to-M transition) and results in an increase in the pKa of Asp85, which is a crucial mechanistic step for one-way proton transfer for the entire photocycle. Deprotonation of the PRG can also be brought about without photoactivation, by raising the pH of the enzyme (pKa of PRG; approximately 9). Thus, comparison of the FTIR difference spectrum for formation of the M intermediate (M minus initial unphotolyzed BR state) at pH 7 to the corresponding spectrum generated at pH 10 may reveal structural changes specifically associated with deprotonation of the PRG. Vibrational bands of BR that change upon M formation are distributed across a broad region between 2120 and 1685 cm(-1). This broad band is made up of two parts. The band above 1780 cm(-1), which is insensitive to C15-deuteration of the retinal, may be due to a proton delocalized in the PRG. The band between 1725 and 1685 cm(-1), on the lower frequency side of the broad band, is sensitive to C15-deuteration. This band may arise from transition dipole coupling of the vibrations of backbone carbonyl groups in helix G with the side chain of Tyr57 and with the C15H of the Schiff base. In M, these broad bands are abolished, and the 3657 cm(-1) band, which is due to the disruption of the hydrogen bonding of a water molecule, probably with Arg82, appears. Loss of the interaction of the backbone carbonyl groups in helix G with Tyr57 and the Schiff base, and separation of Tyr57 from Arg82, may be causes of these spectral changes, leading to the stabilization of the protonated Asp85 in M.
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Affiliation(s)
- Joel E Morgan
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Room 2137, Rensselaer Polytechnic Institute, 110 Eighth Street, Troy, New York 12180, USA
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359
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Nabedryk E, Breton J. Coupling of electron transfer to proton uptake at the QB site of the bacterial reaction center: A perspective from FTIR difference spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1229-48. [DOI: 10.1016/j.bbabio.2008.06.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 01/09/2023]
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360
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Resolving voltage-dependent structural changes of a membrane photoreceptor by surface-enhanced IR difference spectroscopy. Proc Natl Acad Sci U S A 2008; 105:12113-7. [PMID: 18719097 DOI: 10.1073/pnas.0802289105] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Membrane proteins are molecular machines that transport ions, solutes, or information across the cell membrane. Electrophysiological techniques have unraveled many functional aspects of ion channels but suffer from the lack of structural sensitivity. Here, we present spectroelectrochemical data on vibrational changes of membrane proteins derived from a single monolayer. For the seven-helical transmembrane protein sensory rhodopsin II, structural changes of the protein backbone and the retinal cofactor as well as single ion transfer events are resolved by surface-enhanced IR difference absorption spectroscopy (SEIDAS). Angular changes of bonds versus the membrane normal have been determined because SEIDAS monitors only those vibrations whose dipole moment are oriented perpendicular to the solid surface. The application of negative membrane potentials (DeltaV = -0.3 V) leads to the selective halt of the light-induced proton transfer at the stage of D75, the counter ion of the retinal Schiff base. It is inferred that the voltage raises the energy barrier of this particular proton-transfer reaction, rendering the energy deposited in the retinal by light excitation insufficient for charge transfer to occur. The other structural rearrangements that accompany light-induced activity of the membrane protein, are essentially unaffected by the transmembrane electric field. Our results demonstrate that SEIDAS is a generic approach to study processes that depend on the membrane potential, like those in voltage-gated ion channels and transporters, to elucidate the mechanism of ion transfer with unprecedented spatial sensitivity and temporal resolution.
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361
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de la Rica R, Matsui H. Urease as a Nanoreactor for Growing Crystalline ZnO Nanoshells at Room Temperature. Angew Chem Int Ed Engl 2008; 47:5415-7. [DOI: 10.1002/anie.200801181] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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362
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de la Rica R, Matsui H. Urease as a Nanoreactor for Growing Crystalline ZnO Nanoshells at Room Temperature. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801181] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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363
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Morgan JE, Gennis RB, Maeda A. A role for internal water molecules in proton affinity changes in the Schiff base and Asp85 for one-way proton transfer in bacteriorhodopsin. Photochem Photobiol 2008; 84:1038-45. [PMID: 18557823 DOI: 10.1111/j.1751-1097.2008.00377.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Light-induced proton pumping in bacteriorhodospin is carried out through five proton transfer steps. We propose that the proton transfer to Asp85 from the Schiff base in the L-to-M transition is accompanied by the relocation of a water cluster on the cytoplasmic side of the Schiff base from a site close to the Schiff base in L to the Phe219-Thr46 region in M. The water cluster present in L, formed at 170 K, is more rigid than that at room temperature. This may be responsible for blocking the conversion of L to M at 170 K. In the photocycle at room temperature, this water cluster returns to the site close to the Schiff base in N, with a rigid structure similar to that of L at 170 K. The increase in the proton affinity of Asp85, which is a prerequisite for the one-way proton transfer in the M-to-N transition, is suggested to be facilitated by a structural change which disrupts interactions between Asp212 and the Schiff base, and between Asp212 and Arg82. We propose that this liberation of Asp212 is accompanied by a rearrangement of the structure of water molecules between Asp85 and Asp212, stabilizing the protonated Asp85 in M.
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Affiliation(s)
- Joel E Morgan
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, USA
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364
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Lammers S, Lutz S, Meuwly M. Reactive force fields for proton transfer dynamics. J Comput Chem 2008; 29:1048-63. [PMID: 18072179 DOI: 10.1002/jcc.20864] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A force field-inspired method based on fitted, high-quality multidimensional potential energy surfaces to follow proton transfer (PT) reactions in molecular dynamics simulations is presented. In molecular mechanics with proton transfer (MMPT) a system is partitioned into a region where proton transfer takes place and the remaining degrees of freedom which are treated with a conventional force field. The implementation of the method and applications to specific chemically and biologically relevant scenarios are presented. MMPT is developed in view of two primary areas in mind: to follow the molecular dynamics of proton transfer in the condensed phase on realistic time scales and to adapt the shape (morphing) of the potential energy surface for specific applications. MMPT is applied to PT in protonated ammonia dimer, double proton transfer in 2-pyridone-2-hydroxypyridine, and the first step of PT from a protein side-chain towards a buried [3Fe4S] cluster in ferredoxin I. Specific findings of the work include the fundamental role of the N-N vibration as the gating mode for PT in NH4+...NH3 and the qualitative understanding of PT from the protein to a metastable active-site water molecule in Ferredoxin I.
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Affiliation(s)
- Sven Lammers
- Chemistry Department, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
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365
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Rakhmanov SV, Makeev VJ. Stochastic modeling of noninteracting probes in the protein structure space for construction of knowledge-based potentials for atom-atom interactions. Biophysics (Nagoya-shi) 2008. [DOI: 10.1134/s0006350908030019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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366
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Braun-Sand S, Sharma PK, Chu ZT, Pisliakov AV, Warshel A. The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all. BIOCHIMICA ET BIOPHYSICA ACTA 2008; 1777:441-52. [PMID: 18387356 PMCID: PMC2443747 DOI: 10.1016/j.bbabio.2008.03.001] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2007] [Revised: 02/29/2008] [Accepted: 03/03/2008] [Indexed: 11/26/2022]
Abstract
The light-induced proton transport in bacteriorhodopsin has been considered as a model for other light-induced proton pumps. However, the exact nature of this process is still unclear. For example, it is not entirely clear what the driving force of the initial proton transfer is and, in particular, whether it reflects electrostatic forces or other effects. The present work simulates the primary proton transfer (PT) by a specialized combination of the EVB and the QCFF/PI methods. This combination allows us to obtain sufficient sampling and a quantitative free energy profile for the PT at different protein configurations. The calculated profiles provide new insight about energetics of the primary PT and its coupling to the protein conformational changes. Our finding confirms the tentative analysis of an earlier work (A. Warshel, Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium, Photochem. Photobiol. 30 (1979) 285-290) and determines that the overall PT process is driven by the energetics of the charge separation between the Schiff base and its counterion Asp85. Apparently, the light-induced relaxation of the steric energy of the chromophore leads to an increase in the ion-pair distance, and this drives the PT process. Our use of the linear response approximation allows us to estimate the change in the protein conformational energy and provides the first computational description of the coupling between the protein structural changes and the PT process. It is also found that the PT is not driven by twist-modulated changes of the Schiff base's pKa, changes in the hydrogen bond directionality, or other non-electrostatic effects. Overall, based on a consistent use of structural information as the starting point for converging free energy calculations, we conclude that the primary event should be described as a light-induced formation of an unstable ground state, whose relaxation leads to charge separation and to the destabilization of the ion-pair state. This provides the driving force for the subsequent PT steps.
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Affiliation(s)
- Sonja Braun-Sand
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
- Department of Chemistry, University of Colorado at Colorado Springs (UCCS), Colorado Springs, CO 80918
| | - Pankaz K. Sharma
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Zhen T. Chu
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Andrei V. Pisliakov
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
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367
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The GAP arginine finger movement into the catalytic site of Ras increases the activation entropy. Proc Natl Acad Sci U S A 2008; 105:6260-5. [PMID: 18434546 DOI: 10.1073/pnas.0712095105] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Members of the Ras superfamily of small G proteins play key roles in signal transduction pathways, which they control by GTP hydrolysis. They are regulated by GTPase activating proteins (GAPs). Mutations that prevent hydrolysis cause severe diseases including cancer. A highly conserved "arginine finger" of GAP is a key residue. Here, we monitor the GTPase reaction of the Ras.RasGAP complex at high temporal and spatial resolution by time-resolved FTIR spectroscopy at 260 K. After triggering the reaction, we observe as the first step a movement of the switch-I region of Ras from the nonsignaling "off" to the signaling "on" state with a rate of 3 s(-1). The next step is the movement of the "arginine finger" into the active site of Ras with a rate of k(2) = 0.8 s(-1). Once the arginine points into the binding pocket, cleavage of GTP is fast and the protein-bound P(i) intermediate forms. The switch-I reversal to the "off" state, the release of P(i), and the movement of arginine back into an aqueous environment is observed simultaneously with k(3) = 0.1 s(-1), the rate-limiting step. Arrhenius plots for the partial reactions show that the activation energy for the cleavage reaction is lowered by favorable positive activation entropy. This seems to indicate that protein-bound structured water molecules are pushed by the "arginine finger" movement out of the binding pocket into the bulk water. The proposed mechanism shows how the high activation barrier for phosphoryl transfer can be reduced by splitting into partial reactions separated by a P(i)-intermediate.
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368
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Abstract
ATP synthases are rotary engines which use the energy stored in a transmembrane electrochemical gradient of protons or sodium ions to catalyze the formation of ATP by ADP and inorganic phosphate. Current models predict that protonation/deprotonation of specific amino acids of the rotating c-ring, extracting protons from one side and delivering them to the other side of the membrane, are at the core of the proton translocation mechanism of these enzymes. In this minireview, an alternative proton binding mechanism is presented, considering hydronium ion coordination as proposed earlier. Biochemical data and structural considerations provide evidence for two different proton binding modes in the c-ring of H+-translocating ATP synthases. Recent investigations in several other proton translocating membrane proteins suggest, that hydronium ion coordination by proteins might display a general principle which was so far underestimated in ATP synthases.
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Affiliation(s)
- Christoph von Ballmoos
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli Strasse 10, CH-8093 Zürich, Switzerland.
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369
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Iftimie R, Thomas V, Plessis S, Marchand P, Ayotte P. Spectral Signatures and Molecular Origin of Acid Dissociation Intermediates. J Am Chem Soc 2008; 130:5901-7. [DOI: 10.1021/ja077846o] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Radu Iftimie
- Départment de Chimie, Université de Montréal, CP 6128, succursale Centre-Ville, Montréal H3C3J7, Canada, and Département de Chimie, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke J1K2R1, Canada
| | - Vibin Thomas
- Départment de Chimie, Université de Montréal, CP 6128, succursale Centre-Ville, Montréal H3C3J7, Canada, and Département de Chimie, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke J1K2R1, Canada
| | - Sylvain Plessis
- Départment de Chimie, Université de Montréal, CP 6128, succursale Centre-Ville, Montréal H3C3J7, Canada, and Département de Chimie, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke J1K2R1, Canada
| | - Patrick Marchand
- Départment de Chimie, Université de Montréal, CP 6128, succursale Centre-Ville, Montréal H3C3J7, Canada, and Département de Chimie, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke J1K2R1, Canada
| | - Patrick Ayotte
- Départment de Chimie, Université de Montréal, CP 6128, succursale Centre-Ville, Montréal H3C3J7, Canada, and Département de Chimie, Université de Sherbrooke, 2500 Boulevard Université, Sherbrooke J1K2R1, Canada
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370
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Lórenz-Fonfría VA, Furutani Y, Kandori H. Active Internal Waters in the Bacteriorhodopsin Photocycle. A Comparative Study of the L and M Intermediates at Room and Cryogenic Temperatures by Infrared Spectroscopy. Biochemistry 2008; 47:4071-81. [DOI: 10.1021/bi7024063] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Víctor A. Lórenz-Fonfría
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Yuji Furutani
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
| | - Hideki Kandori
- Department of Materials Science and Engineering, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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371
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Kralj JM, Bergo VB, Amsden JJ, Spudich EN, Spudich JL, Rothschild KJ. Protonation state of Glu142 differs in the green- and blue-absorbing variants of proteorhodopsin. Biochemistry 2008; 47:3447-53. [PMID: 18284210 DOI: 10.1021/bi7018964] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteorhodopsins are a recently discovered class of microbial rhodopsins, ubiquitous in marine bacteria. Over 4000 variants have thus far been discovered, distributed throughout the oceans of the world. Most variants fall into one of two major groups, green- or blue-absorbing proteorhodopsin (GPR and BPR, respectively), on the basis of both the visible absorption maxima (530 versus 490 nm) and photocycle kinetics ( approximately 20 versus approximately 200 ms). For a well-studied pair, these differences appear to be largely determined by the identity of a single residue at position 105 (leucine/GPR and glutamine/BPR). We find using a combination of visible and infrared spectroscopy that a second difference is the protonation state of a glutamic acid residue located at position 142 on the extracellular side of helix D. In BPR, Glu142 (the GPR numbering system is used) is deprotonated and can act as an alternate proton acceptor, thus explaining the earlier observations that neutralization of the Schiff base counterion, Asp97, does not block the formation of the M intermediate. In contrast, Glu142 in GPR is protonated and cannot act in this state as an alternate proton acceptor for the Schiff base. On the basis of these findings, a mechanism is proposed for proton pumping in BPR. Because the pKa of Glu142 is near the pH of its native marine environment, changes in pH may act to modulate its function in the cell.
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Affiliation(s)
- Joel M Kralj
- Department of Physics, Molecular Biophysics Laboratory and Photonics Center, Boston University, Boston, Massachusetts 02215, USA
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372
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Abstract
Enzymatic catalysis by RNA was discovered 25 years ago, yet mechanistic insights are emerging only slowly. Thought to be metalloenzymes at first, some ribozymes proved more versatile than anticipated when shown to utilize their own functional groups for catalysis. Recent evidence suggests that some may also judiciously place structural water molecules to shuttle protons in acid-base catalyzed reactions.
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Affiliation(s)
- Nils G Walter
- Department of Chemistry, Single Molecule Analysis Group, University of Michigan, 930 North University Avenue, Ann Arbor, MI 48019-1055, USA.
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373
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Michaux C, Wouters J, Perpète EA, Jacquemin D. Microhydration of Protonated Glycine: An ab initio Family Tree. J Phys Chem B 2008; 112:2430-8. [DOI: 10.1021/jp710034r] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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374
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Li Q, Wang N, Zhou Q, Sun S, Yu Z. Excess infrared absorption spectroscopy and its applications in the studies of hydrogen bonds in alcohol-containing binary mixtures. APPLIED SPECTROSCOPY 2008; 62:166-170. [PMID: 18284791 DOI: 10.1366/000370208783575663] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Excess infrared (IR) absorption spectroscopy, a new concept brought forward by applying the idea of excess thermodynamic functions to infrared spectroscopy, is shown to be a potential method to study hydrogen bonds. It can be applied to enhance spectral resolution of complexed IR bands, to evaluate nonideality of liquid mixtures, and to estimate selective molecular interactions. The sign of the excess infrared absorption coefficient is also of importance in providing information on molecular interactions. The results demonstrate that excess infrared absorption spectroscopy can unveil new information on hydrogen bonding in condensed phases.
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Affiliation(s)
- Qingzhong Li
- Key Laboratory of Bioorganic Phosphorous Chemistry and Chemical Biology (Ministry of Education), Department of Chemistry, Tsinghua University, Beijing 100084, China
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375
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Park SY, Lee YS, Jang DJ. Excited-state proton-transfer dynamics of 1-methyl-6-hydroxyquinolinium embedded in a solid matrix of poly(2-hydroxyethyl methacrylate). Phys Chem Chem Phys 2008; 10:6703-7. [DOI: 10.1039/b811180d] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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376
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Yu H, Cui Q. The vibrational spectra of protonated water clusters: A benchmark for self-consistent-charge density-functional tight binding. J Chem Phys 2007; 127:234504. [DOI: 10.1063/1.2806992] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
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377
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Affiliation(s)
- Philip Ball
- Nature, 4-6 Crinan Street, London N1 9XW, U.K
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378
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Brown MF, Heyn MP, Job C, Kim S, Moltke S, Nakanishi K, Nevzorov AA, Struts AV, Salgado GFJ, Wallat I. Solid-state 2H NMR spectroscopy of retinal proteins in aligned membranes. BIOCHIMICA ET BIOPHYSICA ACTA 2007; 1768:2979-3000. [PMID: 18021739 PMCID: PMC5233718 DOI: 10.1016/j.bbamem.2007.10.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2007] [Revised: 10/10/2007] [Accepted: 10/10/2007] [Indexed: 11/21/2022]
Abstract
Solid-state 2H NMR spectroscopy gives a powerful avenue to investigating the structures of ligands and cofactors bound to integral membrane proteins. For bacteriorhodopsin (bR) and rhodopsin, retinal was site-specifically labeled by deuteration of the methyl groups followed by regeneration of the apoprotein. 2H NMR studies of aligned membrane samples were conducted under conditions where rotational and translational diffusion of the protein were absent on the NMR time scale. The theoretical lineshape treatment involved a static axial distribution of rotating C-C2H3 groups about the local membrane frame, together with the static axial distribution of the local normal relative to the average normal. Simulation of solid-state 2H NMR lineshapes gave both the methyl group orientations and the alignment disorder (mosaic spread) of the membrane stack. The methyl bond orientations provided the angular restraints for structural analysis. In the case of bR the retinal chromophore is nearly planar in the dark- and all-trans light-adapted states, as well upon isomerization to 13-cis in the M state. The C13-methyl group at the "business end" of the chromophore changes its orientation to the membrane upon photon absorption, moving towards W182 and thus driving the proton pump in energy conservation. Moreover, rhodopsin was studied as a prototype for G protein-coupled receptors (GPCRs) implicated in many biological responses in humans. In contrast to bR, the retinal chromophore of rhodopsin has an 11-cis conformation and is highly twisted in the dark state. Three sites of interaction affect the torsional deformation of retinal, viz. the protonated Schiff base with its carboxylate counterion; the C9-methyl group of the polyene; and the beta-ionone ring within its hydrophobic pocket. For rhodopsin, the strain energy and dynamics of retinal as established by 2H NMR are implicated in substituent control of activation. Retinal is locked in a conformation that is twisted in the direction of the photoisomerization, which explains the dark stability of rhodopsin and allows for ultra-fast isomerization upon absorption of a photon. Torsional strain is relaxed in the meta I state that precedes subsequent receptor activation. Comparison of the two retinal proteins using solid-state 2H NMR is thus illuminating in terms of their different biological functions.
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Affiliation(s)
- Michael F Brown
- Department of Chemistry, University of Arizona, Tucson, Arizona 85721, USA.
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379
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Kawamura I, Ohmine M, Tanabe J, Tuzi S, Saitô H, Naito A. Dynamic aspects of extracellular loop region as a proton release pathway of bacteriorhodopsin studied by relaxation time measurements by solid state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3090-7. [DOI: 10.1016/j.bbamem.2007.11.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2007] [Revised: 11/02/2007] [Accepted: 11/05/2007] [Indexed: 11/30/2022]
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380
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Abstract
Protein surface hydration is fundamental to its structure and activity. We report here the direct mapping of global hydration dynamics around a protein in its native and molten globular states, using a tryptophan scan by site-specific mutations. With 16 tryptophan mutants and in 29 different positions and states, we observed two robust, distinct water dynamics in the hydration layer on a few ( approximately 1-8 ps) and tens to hundreds of picoseconds ( approximately 20-200 ps), representing the initial local relaxation and subsequent collective network restructuring, respectively. Both time scales are strongly correlated with protein's structural and chemical properties. These results reveal the intimate relationship between hydration dynamics and protein fluctuations and such biologically relevant water-protein interactions fluctuate on picosecond time scales.
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381
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382
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Przybylski P, Gierczyk B, Schroeder G, Zundel G, Brzezinski B, Bartl F. Spectroscopic and PM5 semiempirical studies of the proton accepting properties of 1,8-bis(tetramethylguanidino)naphthalene. J Mol Struct 2007. [DOI: 10.1016/j.molstruc.2007.03.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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383
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Fonari MS, Simonov YA, Wang WJ, Tang SW, Ganin EV, Gelmboldt VO, Chernaya TS, Alekseeva OA, Furmanova NG. Structure of oxonium hexafluoroniobate and hexafluorotantalate complexes with crown ethers of different dimensionality. Polyhedron 2007. [DOI: 10.1016/j.poly.2007.07.037] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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384
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Klare JP, Chizhov I, Engelhard M. Microbial rhodopsins: scaffolds for ion pumps, channels, and sensors. Results Probl Cell Differ 2007; 45:73-122. [PMID: 17898961 DOI: 10.1007/400_2007_041] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Microbial rhodopsins have been intensively researched for the last three decades. Since the discovery of bacteriorhodopsin, the scope of microbial rhodopsins has been considerably extended, not only in view of the large number of family members, but also their functional properties as pumps, sensors, and channels. In this review, we give a short overview of old and newly discovered microbial rhodopsins, the mechanism of signal transfer and ion transfer, and we discuss structural and mechanistic aspects of phototaxis.
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Affiliation(s)
- Johann P Klare
- Fachbereich Physik, University Osnabrück, Barbarastrasse 7, 49069, Osnabrück, Germany
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385
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Fontecilla-Camps JC, Volbeda A, Cavazza C, Nicolet Y. Structure/function relationships of [NiFe]- and [FeFe]-hydrogenases. Chem Rev 2007; 107:4273-303. [PMID: 17850165 DOI: 10.1021/cr050195z] [Citation(s) in RCA: 1004] [Impact Index Per Article: 59.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Juan C Fontecilla-Camps
- Laboratoire de Cristallographie et Cristallogenèse des Proteines, Institut de Biologie Structurale J. P. Ebel, CEA, CNRS, Universitè Joseph Fourier, 41 rue J. Horowitz, 38027 Grenoble Cedex 1, France.
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386
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Barth A. Infrared spectroscopy of proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:1073-101. [PMID: 17692815 DOI: 10.1016/j.bbabio.2007.06.004] [Citation(s) in RCA: 2820] [Impact Index Per Article: 165.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2007] [Revised: 06/18/2007] [Accepted: 06/19/2007] [Indexed: 12/12/2022]
Abstract
This review discusses the application of infrared spectroscopy to the study of proteins. The focus is on the mid-infrared spectral region and the study of protein reactions by reaction-induced infrared difference spectroscopy.
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Affiliation(s)
- Andreas Barth
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, S-106 91 Stockholm, Sweden.
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387
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Marx D. Proton transfer 200 years after von Grotthuss: insights from ab initio simulations. Chemphyschem 2007; 7:1848-70. [PMID: 16929553 DOI: 10.1002/cphc.200600128] [Citation(s) in RCA: 601] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In the last decade, ab initio simulations and especially Car-Parrinello molecular dynamics have significantly contributed to the improvement of our understanding of both the physical and chemical properties of water, ice, and hydrogen-bonded systems in general. At the heart of this family of in silico techniques lies the crucial idea of computing the many-body interactions by solving the electronic structure problem "on the fly" as the simulation proceeds, which circumvents the need for pre-parameterized potential models. In particular, the field of proton transfer in hydrogen-bonded networks greatly benefits from these technical advances. Here, several systems of seemingly quite different nature and of increasing complexity, such as Grotthuss diffusion in water, excited-state proton-transfer in solution, phase transitions in ice, and protonated water networks in the membrane protein bacteriorhodopsin, are discussed in the realms of a unifying viewpoint.
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Affiliation(s)
- Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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388
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Mizuse K, Fujii A, Mikami N. Long range influence of an excess proton on the architecture of the hydrogen bond network in large-sized water clusters. J Chem Phys 2007; 126:231101. [PMID: 17600397 DOI: 10.1063/1.2750669] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Infrared spectra of completely size-selected protonated water clusters H+(H2O)n are reported for clusters ranging from n=15 to 100. The behavior of the dangling OH stretch bands shows that the hydrogen bond structure in H+(H2O)n is uniquely different to that of (H2O)n up to the size of n=100, at least. This finding indicates that the presence of an excess proton creates a characteristic morphology in the hydrogen bond network architecture of more than 100 surrounding water molecules.
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Affiliation(s)
- Kenta Mizuse
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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389
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A nanostructured titania bioceramic implantable device capable of drug delivery to the temporal lobe of the brain. Colloids Surf A Physicochem Eng Asp 2007. [DOI: 10.1016/j.colsurfa.2006.10.060] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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390
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Mohammed OF, Pines D, Nibbering ETJ, Pines E. Base-induced solvent switches in acid-base reactions. Angew Chem Int Ed Engl 2007; 46:1458-61. [PMID: 17212371 DOI: 10.1002/anie.200603383] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Omar F Mohammed
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, Max-Born-Strasse 2A, 12489 Berlin, Germany
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391
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Maeda A, Morgan JE, Gennis RB, Ebrey TG. Water as a cofactor in the unidirectional light-driven proton transfer steps in bacteriorhodopsin. Photochem Photobiol 2007; 82:1398-405. [PMID: 16634652 DOI: 10.1562/2006-01-16-ir-779] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Recent evidence for involvement of internal water molecules in the mechanism of bacteriorhodopsin is reviewed. Water O-H stretching vibration bands in the Fourier transform IR difference spectra of the L, M and N intermediates of bacteriorhodopsin were analyzed by photoreactions at cryogenic temperatures. A broad vibrational band in L was shown to be due to formation of a structure of water molecules connecting the Schiff base to the Thr46-Asp96 region. This structure disappears in the M intermediate, suggesting that it is involved in transient stabilization of the L intermediate prior to proton transfer from the Schiff base to Asp85. The interaction of the Schiff base with a water molecule is restored in the N intermediate. We propose that water is a critical mobile component of bacteriorhodopsin, forming organized structures in the transient intermediates during the photocycle and, to a large extent, determining the chemical behavior of these transient states.
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Affiliation(s)
- Akio Maeda
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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392
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Mathias G, Marx D. Structures and spectral signatures of protonated water networks in bacteriorhodopsin. Proc Natl Acad Sci U S A 2007; 104:6980-5. [PMID: 17438299 PMCID: PMC1855365 DOI: 10.1073/pnas.0609229104] [Citation(s) in RCA: 130] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2006] [Indexed: 11/18/2022] Open
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.
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Affiliation(s)
- Gerald Mathias
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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393
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Yan S, Zhang L, Cukier RI, Bu Y. Exploration on Regulating Factors for Proton Transfer along Hydrogen-Bonded Water Chains. Chemphyschem 2007; 8:944-54. [PMID: 17387667 DOI: 10.1002/cphc.200600674] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Proton transfer along a single-file hydrogen-bonded water chain is elucidated with a special emphasis on the investigation of chain length, side water, and solvent effects, as well as the temperature and pressure dependences. The number of water molecules in the chain varies from one to nine. The proton can be transported to the acceptor fragment through the single-file hydrogen-bonded water wire which contains at most five water molecules. If the number of water molecule is more than five, the proton is trapped by the chain in the hydroxyl-centered H(7)O(3) (+) state. The farthest water molecule involved in the formation of H(7)O(3) (+) is the fifth one away from the donor fragment. These phenomena reappear in the molecular dynamics simulations. The energy of the system is reduced along with the proton conduction. The proton transfer mechanism can be altered by excess proton. The augmentation of the solvent dielectric constant weakens the stability of the system, but favors the proton transfer. NMR spin-spin coupling constants can be used as a criterion in judging whether the proton is transferred or not. The enhancement of temperature increases the thermal motion of the molecule, augments the internal energy of the system, and favors the proton transfer. The lengthening of the water wire increases the entropy of the system, concomitantly, the temperature dependence of the Gibbs free energy increases. The most favorable condition for the proton transfer along the H-bonded water wire is the four-water contained chain with side water attached near to the acceptor fragment in polar solvent under higher temperature.
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Affiliation(s)
- Shihai Yan
- Institute of Theoretical Chemistry, Shandong University, Jinan, 250100, P. R. China
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394
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Abstract
A proton shared between two closed-shell molecules, [A.H+.B], constitutes a ubiquitous soft binding motif in biological processes. The vibrational transitions associated with the shared proton, which provide a direct probe of this interaction, have been extensively studied in the condensed phase but have yielded only limited detailed information because of their diffuse character. We exploited recent advances in gas-phase ion spectroscopy to identify sharp spectral features that can be assigned to both the shared proton and the two tethered molecules in a survey of 18 cold, isolated [A.H+.B] ions. These data yield a picture of the intermolecular proton bond at a microscopic scale, facilitating analysis of its properties within the context of a floppy polyatomic molecule.
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Affiliation(s)
- J R Roscioli
- Sterling Chemistry Laboratory, Yale University, Post Office Box 208107, New Haven, CT 06520, USA
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395
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Rakhmanov SV, Makeev VJ. Atomic hydration potentials using a Monte Carlo Reference State (MCRS) for protein solvation modeling. BMC STRUCTURAL BIOLOGY 2007; 7:19. [PMID: 17397537 PMCID: PMC1852318 DOI: 10.1186/1472-6807-7-19] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2006] [Accepted: 03/30/2007] [Indexed: 11/10/2022]
Abstract
Background Accurate description of protein interaction with aqueous solvent is crucial for modeling of protein folding, protein-protein interaction, and drug design. Efforts to build a working description of solvation, both by continuous models and by molecular dynamics, yield controversial results. Specifically constructed knowledge-based potentials appear to be promising for accounting for the solvation at the molecular level, yet have not been used for this purpose. Results We developed original knowledge-based potentials to study protein hydration at the level of atom contacts. The potentials were obtained using a new Monte Carlo reference state (MCRS), which simulates the expected probability density of atom-atom contacts via exhaustive sampling of structure space with random probes. Using the MCRS allowed us to calculate the expected atom contact densities with high resolution over a broad distance range including very short distances. Knowledge-based potentials for hydration of protein atoms of different types were obtained based on frequencies of their contacts at different distances with protein-bound water molecules, in a non-redundant training data base of 1776 proteins with known 3D structures. Protein hydration sites were predicted in a test set of 12 proteins with experimentally determined water locations. The MCRS greatly improves prediction of water locations over existing methods. In addition, the contribution of the energy of macromolecular solvation into total folding free energy was estimated, and tested in fold recognition experiments. The correct folds were preferred over all the misfolded decoys for the majority of proteins from the improved Rosetta decoy set based on the structure hydration energy alone. Conclusion MCRS atomic hydration potentials provide a detailed distance-dependent description of hydropathies of individual protein atoms. This allows placement of water molecules on the surface of proteins and in protein interfaces with much higher precision. The potentials provide a means to estimate the total solvation energy for a protein structure, in many cases achieving a successful fold recognition. Possible applications of atomic hydration potentials to structure verification, protein folding and stability, and protein-protein interactions are discussed.
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Affiliation(s)
- Sergei V Rakhmanov
- Institute of Genetics and Selection of Industrial Microorganisms, State Research Centre GosNIIgenetika, 1Dorozhny proezd, 1, Moscow, Russia
| | - Vsevolod J Makeev
- Institute of Genetics and Selection of Industrial Microorganisms, State Research Centre GosNIIgenetika, 1Dorozhny proezd, 1, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova str. 32, Moscow, Russia
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396
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Groot ML, van Wilderen LJGW, Di Donato M. Time-resolved methods in biophysics. 5. Femtosecond time-resolved and dispersed infrared spectroscopy on proteins. Photochem Photobiol Sci 2007; 6:501-7. [PMID: 17487299 DOI: 10.1039/b613023b] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
In this contribution we describe how femtosecond time-resolved infrared spectroscopy provides insight into the function and dynamics of pigment-protein complexes, and what the technical requirements are to perform such experiments. We further discuss a few examples of experiments performed on the photoactive yellow protein and photosynthetic complexes in more detail.
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Affiliation(s)
- Marie Louise Groot
- Department of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit, De Boelelaan 1081, 1081 HV, Amsterdam, The Netherlands.
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397
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Bondar AN, Suhai S, Fischer S, Smith JC, Elstner M. Suppression of the back proton-transfer from Asp85 to the retinal Schiff base in bacteriorhodopsin: A theoretical analysis of structural elements. J Struct Biol 2007; 157:454-69. [PMID: 17189704 DOI: 10.1016/j.jsb.2006.10.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2006] [Revised: 09/26/2006] [Accepted: 10/03/2006] [Indexed: 11/15/2022]
Abstract
The transfer of a proton from the retinal Schiff base to the nearby Asp85 protein group is an essential step in the directional proton-pumping by bacteriorhodopsin. To avoid the wasteful back reprotonation of the Schiff base from Asp85, the protein must ensure that, following Schiff base deprotonation, the energy barrier for back proton-transfer from Asp85 to the Schiff base is larger than that for proton-transfer from the Schiff base to Asp85. Here, three structural elements that may contribute to suppressing the back proton-transfer from Asp85 to the Schiff base are investigated: (i) retinal twisting; (ii) hydrogen-bonding distances in the active site; and (iii) the number and location of internal water molecules. The impact of the pattern of bond twisting on the retinal deprotonation energy is dissected by performing an extensive set of quantum-mechanical calculations. Structural rearrangements in the active site, such as changes of the Thr89:Asp85 distance and relocation of water molecules hydrogen-bonding to the Asp85 acceptor group, may participate in the mechanism which ensures that following the transfer of the Schiff base proton to Asp85 the protein proceeds with the subsequent photocycle steps, and not with back proton transfer from Asp85 to the Schiff base.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Computational Molecular Biophysics, IWR, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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398
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Xu J, Sharpe MA, Qin L, Ferguson-Miller S, Voth GA. Storage of an excess proton in the hydrogen-bonded network of the d-pathway of cytochrome C oxidase: identification of a protonated water cluster. J Am Chem Soc 2007; 129:2910-3. [PMID: 17309257 PMCID: PMC2556150 DOI: 10.1021/ja067360s] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The mechanism of proton transport in the D-pathway of cytochrome c oxidase (CcO) is further elucidated through examining a protonated water/hydroxyl cluster inside the channel. The second generation multi-state empirical valence bond (MS-EVB2) model was employed in a molecular dynamics study based on a high-resolution X-ray structure to simulate the interaction of the excess proton with the channel environment. Our results indicate that a hydrogen-bonded network consisting of about 5 water molecules surrounded by three side chains and two backbone groups (S197, S200, S201, F108) is involved in storage and translocation of an excess proton to the extracellular side of CcO.
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Affiliation(s)
- Jiancong Xu
- Department of Chemistry and Center for Biophysical Modeling and Simulation, 315 South 1400 East Room 2020, University of Utah, Salt Lake City, UT 84112-0850, USA
| | - Martyn A. Sharpe
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
| | - Ling Qin
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
| | - Shelagh Ferguson-Miller
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, Michigan 48824-1319, USA
| | - Gregory A. Voth
- Department of Chemistry and Center for Biophysical Modeling and Simulation, 315 South 1400 East Room 2020, University of Utah, Salt Lake City, UT 84112-0850, USA
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399
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Riccardi D, König P, Prat-Resina X, Yu H, Elstner M, Frauenheim T, Cui Q. "Proton holes" in long-range proton transfer reactions in solution and enzymes: A theoretical analysis. J Am Chem Soc 2007; 128:16302-11. [PMID: 17165785 PMCID: PMC2561195 DOI: 10.1021/ja065451j] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Proton transfers are fundamental to chemical processes in solution and biological systems. Often, the well-known Grotthuss mechanism is assumed where a series of sequential "proton hops" initiates from the donor and combines to produce the net transfer of a positive charge over a long distance. Although direct experimental evidence for the sequential proton hopping has been obtained recently, alternative mechanisms may be possible in complex molecular systems. To understand these events, all accessible protonation states of the mediating groups should be considered. This is exemplified by transfers through water where the individual water molecules can exist in three protonation states (water, hydronium, and hydroxide); as a result, an alternative to the Grotthuss mechanism for a proton transfer through water is to generate a hydroxide by first protonating the acceptor and then transfer the hydroxide toward the donor through water. The latter mechanism can be most generally described as the transfer of a "proton hole" from the acceptor to the donor where the "hole" characterizes the deprotonated state of any mediating molecule. This pathway is distinct and is rarely considered in the discussion of proton-transfer processes. Using a calibrated quantum mechanical/molecular mechanical (QM/MM) model and an effective sampling technique, we study proton transfers in two solution systems and in Carbonic Anhydrase II. Although the relative weight of the "proton hole" and Grotthuss mechanisms in a specific system is difficult to determine precisely using any computational approach, the current study establishes an energetics motivated framework that hinges on the donor/acceptor pKa values and electrostatics due to the environment to argue that the "proton hole" transfer is likely as important as the classical Grotthuss mechanism for proton transport in many complex molecular systems.
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Affiliation(s)
- Demian Riccardi
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, Madison, Wisconsin 53706, USA
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400
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Mohammed O, Pines D, Nibbering E, Pines E. Base-Induced Solvent Switches in Acid–Base Reactions. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603383] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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