1
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Nakai H, Takemura T, Ono J, Nishimura Y. Quantum-Mechanical Molecular Dynamics Simulations on Secondary Proton Transfer in Bacteriorhodopsin Using Realistic Models. J Phys Chem B 2021; 125:10947-10963. [PMID: 34582194 DOI: 10.1021/acs.jpcb.1c06231] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Bacteriorhodopsin (BR) transports a proton from intracellular to extracellular (EC) sites through five proton transfers. The second proton transfer is the release of an excess proton stored in BR into the EC medium, and an atomistic understanding of this whole process has remained unexplored due to its ubiquitous environment. Here, fully quantum mechanical (QM) molecular dynamics (MD) and metadynamics (MTD) simulations for this process were performed at the divide-and-conquer density-functional tight-binding level using realistic models (∼50000 and ∼20000 atoms) based on the time-resolved photointermediate structures from an X-ray free electron laser. Regarding the proton storage process, the QM-MD/MTD simulations confirmed the Glu-shared mechanism, in which an excess proton is stored between Glu194 and Glu204, and clarified that the activation occurs by localizing the proton at Glu204 in the photocycle. Furthermore, the QM-MD/MTD simulations elucidated a release pathway from Glu204 through Ser193 to the EC water molecules and clarified that the proton release starts at ∼250 μs. In the ubiquitous proton diffusion in the EC medium, the transient proton receptors predicted experimentally were assigned to carboxylates in Glu9 and Glu74. Large-scale QM-MD/MTD simulations beyond the conventional sizes, which provided the above findings and confirmations, were possible by adopting our Dcdftbmd program.
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Affiliation(s)
- Hiromi Nakai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.,Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, 1-30 Goryo-Ohara, Nishikyo-ku, Kyoto 615-8245, Japan
| | - Toshiaki Takemura
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Junichi Ono
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan.,Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, 1-30 Goryo-Ohara, Nishikyo-ku, Kyoto 615-8245, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
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2
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Santra M, Seal A, Bhattacharjee K, Chakrabarty S. Structural and dynamical heterogeneity of water trapped inside Na +-pumping KR2 rhodopsin in the dark state. J Chem Phys 2021; 154:215101. [PMID: 34240976 DOI: 10.1063/5.0044904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Photoisomerization in the retinal leads to a channel opening in rhodopsins that triggers translocation or pumping of ions/protons. Crystal structures of rhodopsins contain several structurally conserved water molecules. It has been suggested that water plays an active role in facilitating the ion pumping/translocation process by acting as a lubricant in these systems. In this paper, we systematically investigate the localization, structure, dynamics, and energetics of the water molecules along the channel for the resting/dark state of KR2 rhodopsin. By employing several microseconds long atomistic molecular dynamics simulation of this trans-membrane protein system, we demonstrate the presence of five distinct water containing pockets/cavities separated by gateways controlled by protein side-chains. There exists a strong hydrogen bonded network involving these buried water molecules and functionally important key residues. We present evidence of significant structural and dynamical heterogeneity in the water molecules present in these cavities, with very rare exchange between them. The exchange time scale of such buried water with the bulk has an extremely wide range, from tens of nanoseconds to >1.5 µs. The translational and rotational dynamics of buried water are found to be strongly dependent on the protein cavity size and local interactions with a classic signature of trapped diffusion and rotational anisotropy.
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Affiliation(s)
- Mantu Santra
- School of Chemical and Materials Sciences, Indian Institute of Technology Goa, Ponda, Goa 403401, India
| | - Aniruddha Seal
- School of Chemical Sciences, National Institute of Science Education and Research, Bhubaneswar 752050, Odisha, India
| | - Kankana Bhattacharjee
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India
| | - Suman Chakrabarty
- Department of Chemical, Biological & Macro-Molecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, West Bengal, India
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3
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Yagi K, Sugita Y. Anharmonic Vibrational Calculations Based on Group-Localized Coordinates: Applications to Internal Water Molecules in Bacteriorhodopsin. J Chem Theory Comput 2021; 17:5007-5020. [PMID: 34296615 PMCID: PMC10986902 DOI: 10.1021/acs.jctc.1c00060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
An efficient anharmonic vibrational method is developed exploiting the locality of molecular vibration. Vibrational coordinates localized to a group of atoms are employed to divide the potential energy surface (PES) of a system into intra- and inter-group contributions. Then, the vibrational Schrödinger equation is solved based on a PES, in which the inter-group coupling is truncated at the harmonic level while accounting for the intra-group anharmonicity. The method is applied to a pentagonal hydrogen bond network (HBN) composed of internal water molecules and charged residues in a membrane protein, bacteriorhodopsin. The PES is calculated by the quantum mechanics/molecular mechanics (QM/MM) calculation at the level of B3LYP-D3/aug-cc-pVDZ. The infrared (IR) spectrum is computed using a set of coordinates localized to each water molecule and amino acid residue by second-order vibrational quasi-degenerate perturbation theory (VQDPT2). Benchmark calculations show that the proposed method yields the N-D/O-D stretching frequencies with an error of 7 cm-1 at the cost reduced by more than five times. In contrast, the harmonic approximation results in a severe error of 150 cm-1. Furthermore, the size of QM regions is carefully assessed to find that the QM regions should include not only the pentagonal HBN itself but also its HB partners. VQDPT2 calculations starting from transient structures obtained by molecular dynamics simulations have shown that the structural sampling has a significant impact on the calculated IR spectrum. The incorporation of anharmonicity, sufficiently large QM regions, and structural samplings are of essential importance to reproduce the experimental IR spectrum. The computational spectrum paves the way for decoding the IR signal of strong HBNs and helps elucidate their functional roles in biomolecules.
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Affiliation(s)
- Kiyoshi Yagi
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yuji Sugita
- Theoretical
Molecular Science Laboratory, RIKEN Cluster
for Pioneering Research, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Computational
Biophysics Research Team, RIKEN Center for
Computational Science, 7-1-26 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
- Laboratory
for Biomolecular Function Simulation, RIKEN
Center for Biosystems Dynamics Research, 1-6-5 Minatojima-Minamimachi,
Chuo-ku, Kobe, Hyogo 650-0047, Japan
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4
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Zhang J, Qi S, Zhang C, Fan Z, Ding Q, Mao S, Dong Z. Controlling Keto–Enol Tautomerism of Ureidopyrimidinone to Generate a Single-Quadruple AADD-DDAA Dimeric Array. Org Lett 2020; 22:7305-7309. [DOI: 10.1021/acs.orglett.0c02644] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jing Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shuaiwei Qi
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Chenyang Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Zengming Fan
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Qinwen Ding
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Shizhong Mao
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
| | - Zeyuan Dong
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, China
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5
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Ono J, Imai M, Nishimura Y, Nakai H. Hydroxide Ion Carrier for Proton Pumps in Bacteriorhodopsin: Primary Proton Transfer. J Phys Chem B 2020; 124:8524-8539. [DOI: 10.1021/acs.jpcb.0c05507] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Junichi Ono
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, 1-30 Goryo-Ohara, Nishikyo-ku, Kyoto 615-8245, Japan
| | - Minori Imai
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering (WISE), Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
- Elements Strategy Initiative for Catalysts & Batteries (ESICB), Kyoto University, 1-30 Goryo-Ohara, Nishikyo-ku, Kyoto 615-8245, Japan
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
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6
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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7
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Tripathi R, Forbert H, Marx D. Settling the Long-Standing Debate on the Proton Storage Site of the Prototype Light-Driven Proton Pump Bacteriorhodopsin. J Phys Chem B 2019; 123:9598-9608. [DOI: 10.1021/acs.jpcb.9b09608] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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8
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Theoretical study on kinetics of ammonia-catalyzed ground-state tautomerization in 2-pyridone: effect of chemical modification. CHEMICAL PAPERS 2019. [DOI: 10.1007/s11696-019-00711-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Gupta PK, Esser A, Forbert H, Marx D. Toward theoretical terahertz spectroscopy of glassy aqueous solutions: partially frozen solute-solvent couplings of glycine in water. Phys Chem Chem Phys 2019; 21:4975-4987. [PMID: 30758388 DOI: 10.1039/c8cp07489e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular-level understanding of THz spectra of aqueous solutions under ambient conditions has been greatly advanced in recent years. Here, we go beyond previous analyses by performing ab initio molecular dynamics simulations of glycine in water with artificially frozen solute or solvent molecules, respectively, while computing the total THz response as well as its decomposition into mode-specific resonances based on the "supermolecular solvation complex" technique. Clamping the water molecules and keeping glycine moving breaks the coupling of glycine to the structural dynamics of the solvent, however, the polarization and dielectric solvation effects in the static solvation cage are still at work since the full electronic structure of the quenched solvent is taken into account. The complementary approach of fixing glycine reveals both the dynamical and electronic response of the solvation cage at the level of its THz response. Moreover, to quantitatively account for the electronic contribution solely due to solvent embedding, the solute species is "vertically desolvated", thus preserving the fully coupled solute-solvent motion in terms of the solute's structural dynamics in solution, while its electronic structure is no longer subject to solute-solvent polarization and charge transfer effects. When referenced to the free simulation of Gly(aq), this three-fold approach allows us to decompose the THz spectral contributions due to the correlated solute-solvent dynamics into entirely structural and purely electronic effects. Beyond providing hitherto unknown insights, the observed systematic changes of THz spectra in terms of peak shifts and lineshape modulations due to conformational freezing and frozen solvation cages might be useful to investigate the solvation of molecules in highly viscous H-bonding solvents such as ionic liquids and even in cryogenic ices as relevant to polar stratospheric and dark interstellar clouds.
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Affiliation(s)
- Prashant Kumar Gupta
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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10
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Inakollu VSS, Yu H. A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function. J Comput Chem 2018; 39:2067-2078. [DOI: 10.1002/jcc.25390] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/04/2018] [Accepted: 06/12/2018] [Indexed: 11/10/2022]
Affiliation(s)
- V. S. Sandeep Inakollu
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2522 Australia
- Molecular Horizons University of Wollongong New South Wales 2522 Australia
| | - Haibo Yu
- School of Chemistry and Molecular Bioscience University of Wollongong Wollongong New South Wales 2522 Australia
- Molecular Horizons University of Wollongong New South Wales 2522 Australia
- Illawarra Health and Medical Research Institute Wollongong New South Wales 2522 Australia
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11
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Theoretical study on the substituent effect of halogen atom at different position of 7-azaindole-water derivatives: relative stability and excited-state proton-transfer mechanism. Struct Chem 2018. [DOI: 10.1007/s11224-018-1119-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Daldrop JO, Saita M, Heyden M, Lorenz-Fonfria VA, Heberle J, Netz RR. Orientation of non-spherical protonated water clusters revealed by infrared absorption dichroism. Nat Commun 2018; 9:311. [PMID: 29358659 PMCID: PMC5778031 DOI: 10.1038/s41467-017-02669-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 12/15/2017] [Indexed: 11/09/2022] Open
Abstract
Infrared continuum bands that extend over a broad frequency range are a key spectral signature of protonated water clusters. They are observed for many membrane proteins that contain internal water molecules, but their microscopic mechanism has remained unclear. Here we compute infrared spectra for protonated and unprotonated water chains, discs, and droplets from ab initio molecular dynamics simulations. The continuum bands of the protonated clusters exhibit significant anisotropy for chains and discs, with increased absorption along the direction of maximal cluster extension. We show that the continuum band arises from the nuclei motion near the excess charge, with a long-ranged amplification due to the electronic polarizability. Our experimental, polarization-resolved light–dark difference spectrum of the light-driven proton pump bacteriorhodopsin exhibits a pronounced dichroic continuum band. Our results suggest that the protonated water cluster responsible for the continuum band of bacteriorhodopsin is oriented perpendicularly to the membrane normal. Protein-bound water clusters play a key role for proton transport and storage in molecular biology. Here, the authors show by simulations and experiments that the orientation of non-spherical protonated water clusters in bacteriorhodopsin is unveiled by polarization-resolved infrared spectroscopy.
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Affiliation(s)
- Jan O Daldrop
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Mattia Saita
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany
| | - Matthias Heyden
- Max-Planck-Institut für Kohlenforschung, 45470, Mülheim an der Ruhr, Germany
| | | | - Joachim Heberle
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany.
| | - Roland R Netz
- Department of Physics, Freie Universität Berlin, 14195, Berlin, Germany.
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13
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Khrenova MG, Kulakova AM, Nemukhin AV. Competition between two cysteines in covalent binding of biliverdin to phytochrome domains. Org Biomol Chem 2018; 16:7518-7529. [DOI: 10.1039/c8ob02262c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this work, we disclose a mechanism of competing chemical reactions of protein assembly for a bacterial phytochrome using modern methods of molecular modeling.
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Affiliation(s)
- Maria G. Khrenova
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow
- Russian Federation
- Federal Research Center of Biotechnology
| | - Anna M. Kulakova
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow
- Russian Federation
| | - Alexander V. Nemukhin
- Department of Chemistry
- Lomonosov Moscow State University
- Moscow
- Russian Federation
- Emanuel Institute of Biochemical Physics
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14
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pH-sensitive vibrational probe reveals a cytoplasmic protonated cluster in bacteriorhodopsin. Proc Natl Acad Sci U S A 2017; 114:E10909-E10918. [PMID: 29203649 DOI: 10.1073/pnas.1707993114] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Infrared spectroscopy has been used in the past to probe the dynamics of internal proton transfer reactions taking place during the functional mechanism of proteins but has remained mostly silent to protonation changes in the aqueous medium. Here, by selectively monitoring vibrational changes of buffer molecules with a temporal resolution of 6 µs, we have traced proton release and uptake events in the light-driven proton-pump bacteriorhodopsin and correlate these to other molecular processes within the protein. We demonstrate that two distinct chemical entities contribute to the temporal evolution and spectral shape of the continuum band, an unusually broad band extending from 2,300 to well below 1,700 cm-1 The first contribution corresponds to deprotonation of the proton release complex (PRC), a complex in the extracellular domain of bacteriorhodopsin where an excess proton is shared by a cluster of internal water molecules and/or ionic E194/E204 carboxylic groups. We assign the second component of the continuum band to the proton uptake complex, a cluster with an excess proton reminiscent to the PRC but located in the cytoplasmic domain and possibly stabilized by D38. Our findings refine the current interpretation of the continuum band and call for a reevaluation of the last proton transfer steps in bacteriorhodopsin.
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15
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Fang H. Ground-State Long-Range Proton Transfer Controlled by Proton-Accepting Ability of Hydrogen-Bonded Chains: A Theoretical Study. PROGRESS IN REACTION KINETICS AND MECHANISM 2017. [DOI: 10.3184/146867817x14954764850487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ground-state triple proton transfer (GSTPT) reactions in HCOOH complexing with H2O, CH3OH, C2H5OH and mixed water–alcohol molecules were studied by quantum mechanical methods in the gas phase and in heptane. The triple proton transfer in HCOOH–S1–S2 (S1, S2 = H2O, CH3OH, C2H5OH) systems all occurred in an asynchronous but concerted protolysis mechanism. The formation pattern of the hydrogen-bonded chain was important to reduce the barrier height of the proton transfer process. When the hydrogen-bonded chain consisted of two identical CH3OH or C2H5OH molecules in the HCOOH–S1–S2 complexes, the GSTPT barrier height of HCOOH–S1–S2 decreased by more than 2 kcal mol−1 compared to that of HCOOH–H2O–H2O both in the gas phase and in heptane, because CH3OH and C2H5OH had larger proton-accepting abilities than had H2O. When the two solvent molecules in the hydrogen-bonded chain in the HCOOH–S1–S2 complexes were different, the barrier height of the proton transfer process varied depending on the proton-accepting ability (basicity) of the hydrogen-bonded chain. The bigger the proton-accepting ability (basicity) of the hydrogen-bonded chain, the lower the barrier height of the proton transfer process. Mixed bridging solvent molecules could accumulate their proton-accepting abilities and thus speeded up proton transfer. The solvent effect evidently decreased the zero point energy-corrected barrier heights of HCOOH clusters and increased the asynchronicity of the proton transfer, while the proton transfer mechanisms did not change in heptane.
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Affiliation(s)
- Hua Fang
- Department of Chemistry and Material Science, College of Science, Nanjing Forestry University, Nanjing 210037, P.R. China
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16
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Yi J, Fang H. Theoretical Study on the Substituent Effect on the Excited-State Proton Transfer in the 7-Azaindole-Water Derivatives. Photochem Photobiol 2017; 94:27-35. [DOI: 10.1111/php.12839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 08/21/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Jiacheng Yi
- Department of Chemistry and Material Science; College of Science; Nanjing Forestry University; Nanjing Jiangsu China
| | - Hua Fang
- Department of Chemistry and Material Science; College of Science; Nanjing Forestry University; Nanjing Jiangsu China
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17
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Ultrafast excited state intermolecular proton transfer dynamics of 2-(4′-Pyridyl)benzimidazole inside the nanocavity of reverse micelles. J Photochem Photobiol A Chem 2017. [DOI: 10.1016/j.jphotochem.2017.07.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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18
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Thirumuruganandham SP, Gómez EA, Lakshmanan S, Hamblin MR. Terahertz Frequency Spectroscopy to Determine Cold Shock Protein Stability upon Solvation and Evaporation - A Molecular Dynamics Study. IEEE TRANSACTIONS ON TERAHERTZ SCIENCE AND TECHNOLOGY 2017; 7:131-143. [PMID: 30881732 PMCID: PMC6419770 DOI: 10.1109/tthz.2016.2637380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Infrared (IR) and Terahertz (THz) spectroscopy simulations were carried out using CHARMM35b2 to determine protein stability. The stabilities of three bacterial cold shock proteins (Csps) originating from mesophiles, thermophiles and hyper- thermophiles respectively were investigated in this study. The three different Csps were investigated by Normal-Mode analysis and Molecular Dynamics simulation of THz spectra using the Hessian matrix for solvated systems, interpreted in the harmonic approximation at optimum near-melting temperatures of each homologue, by incorporating differences in the hydrous and anhydrous states of the Csps. The results show slight variations in the large scale protein motion. However, the IR spectra of Csps observed at the low frequency saddle surface region, clearly distinguishes the thermophilic and mesophilic proteins based on their stability. Further studies on protein stability employing low-frequency collective modes have the potential to reveal functionally important conformational changes that are biologically significant.
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Affiliation(s)
| | - Edgar A Gómez
- Programa de Física, Universidad del Quindío, Armenia, Colombia
| | - Shanmugamurthy Lakshmanan
- Department of Dermatology, Harvard Medical School, Boston, MA 02114, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Michael R Hamblin
- Department of Dermatology, Harvard Medical School, Boston, MA 02114, USA
- Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA 02114, USA
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19
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Drechsel-Grau C, Marx D. Collective proton transfer in ordinary ice: local environments, temperature dependence and deuteration effects. Phys Chem Chem Phys 2017; 19:2623-2635. [DOI: 10.1039/c6cp05679b] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Ordinary ice at low temperature: what about collective nuclear quantum effects in its chiral six rings?
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Affiliation(s)
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie
- Ruhr-Universität Bochum
- 44780 Bochum
- Germany
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20
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Nair NN, Ribas-Arino J, Staemmler V, Marx D. Magnetostructural Dynamics from Hubbard-U Corrected Spin-Projection: [2Fe-2S] Complex in Ferredoxin. J Chem Theory Comput 2015; 6:569-75. [PMID: 26617310 DOI: 10.1021/ct900547w] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A Hubbard-corrected spin-projected two-determinant approach, EBS+Uscf, is introduced to treat low-spin ground states of antiferromagnetically coupled transition metal complexes. In addition to providing access to total energies, forces, and ab initio simulations, it allows one to readily compute Heisenberg's exchange coupling J(t) on the fly. By studying the binuclear [2Fe-2S] cofactor in a metalloprotein, Anabaena Fd, within this consistent nonempirical procedure in combination with a QM/MM framework, it is illustrated that spin-projection, self-interaction corrections, thermal fluctuations, and protein matrix shifts are crucial in obtaining ⟨J⟩ close to the experiment.
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Affiliation(s)
- Nisanth N Nair
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Jordi Ribas-Arino
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Volker Staemmler
- 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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21
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Feng J, Mertz B. Proteorhodopsin Activation Is Modulated by Dynamic Changes in Internal Hydration. Biochemistry 2015; 54:7132-41. [PMID: 26562497 DOI: 10.1021/acs.biochem.5b00932] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Proteorhodopsin, a member of the microbial rhodopsin family, is a seven-transmembrane α-helical protein that functions as a light-driven proton pump. Understanding the proton-pumping mechanism of proteorhodopsin requires intimate knowledge of the proton transfer pathway via complex hydrogen-bonding networks formed by amino acid residues and internal water molecules. Here we conducted a series of microsecond time scale molecular dynamics simulations on both the dark state and the initial photoactivated state of blue proteorhodopsin to reveal the structural basis for proton transfer with respect to protein internal hydration. A complex series of dynamic hydrogen-bonding networks involving water molecules exists, facilitated by water channels and hydration sites within proteorhodopsin. High levels of hydration were discovered at each proton transfer site-the retinal binding pocket and proton uptake and release sites-underscoring the critical participation of water molecules in the proton-pumping mechanism. Water-bridged interactions and local water channels were also observed and can potentially mediate long-distance proton transfer between each site. The most significant phenomenon is after isomerization of retinal, an increase in water flux occurs that connects the proton release group, a conserved arginine residue, and the retinal binding pocket. Our results provide a detailed description of the internal hydration of the early photointermediates in the proteorhodopsin photocycle under alkaline pH conditions. These results lay the fundamental groundwork for understanding the intimate role that hydration plays in the structure-function relationship underlying the proteorhodopsin proton-pumping mechanism, as well as providing context for the relationship of hydration in proteorhodopsin to other microbial retinal proteins.
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Affiliation(s)
- Jun Feng
- The C. Eugene Bennett Department of Chemistry, West Virginia University , 217 Clark Hall, Morgantown, West Virginia 26506, United States
| | - Blake Mertz
- The C. Eugene Bennett Department of Chemistry, West Virginia University , 217 Clark Hall, Morgantown, West Virginia 26506, United States
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22
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Theoretical study on excited-state proton transfer via hydrogen-bonded ethanol (EtOH) wire for 7AI in the gas phase. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1723-6] [Citation(s) in RCA: 5] [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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23
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Wolf S, Freier E, Gerwert K. A delocalized proton-binding site within a membrane protein. Biophys J 2015; 107:174-84. [PMID: 24988352 DOI: 10.1016/j.bpj.2014.05.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 05/13/2014] [Accepted: 05/14/2014] [Indexed: 11/26/2022] Open
Abstract
The role of protein-bound water molecules in protein function and catalysis is an emerging topic. Here, we studied the solvation of an excess proton by protein-bound water molecules and the contribution of the surrounding amino acid residues at the proton release site of the membrane protein bacteriorhodopsin. It hosts an excess proton within a protein-bound water cluster, which is hydrogen bonded to several surrounding amino acids. Indicative of delocalization is a broad continuum absorbance experimentally observed by time-resolved Fourier transform infrared spectroscopy. In combination with site-directed mutagenesis, the involvement of several amino acids (especially Glu-194 and Glu-204) in the delocalization was elaborated. Details regarding the contributions of the glutamates and water molecules to the delocalization mode in biomolecular simulations are controversial. We carried out quantum mechanics/molecular mechanics (QM/MM) self-consistent charge density functional tight-binding simulations for all amino acids that have been experimentally shown to be involved in solvation of the excess proton, and systematically investigated the influence of the quantum box size. We compared calculated theoretical infrared spectra with experimental ones as a measure for the correct description of excess proton delocalization. A continuum absorbance can only be observed for small quantum boxes containing few amino acids and/or water molecules. Larger quantum boxes, including all experimentally shown involved amino acids, resulted in narrow absorbance bands, indicating protonation of a single binding site in contradiction to experimental results. We conclude that small quantum boxes seem to reproduce representative extreme cases of proton delocalization modes: proton delocalization only on water molecules or only between Glu-194 and Glu-204. Extending the experimental spectral region to lower wave numbers, a water-delocalized proton reproduces the observed continuum absorbance better than a glutamate-shared delocalized proton. However, a full agreement between QM simulations and experimental results on the delocalized excess proton will require a larger quantum box as well as more sophisticated QM/MM methods.
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Affiliation(s)
- Steffen Wolf
- Department of Biophysics, Chinese Academy of Sciences-Max-Planck-Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, P.R. China
| | - Erik Freier
- Department of Biophysics, University of Bochum, Bochum, Germany
| | - Klaus Gerwert
- Department of Biophysics, Chinese Academy of Sciences-Max-Planck-Gesellschaft Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Shanghai, P.R. China; Department of Biophysics, University of Bochum, Bochum, Germany.
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24
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Kang B, Jang DJ, Lee JY. Concerted and asynchronous mechanism of ground state proton transfer in alcohol mediated 7-hydroxyquinoline. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.04.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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25
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Vener MV, Odinokov AV, Wehmeyer C, Sebastiani D. The structure and IR signatures of the arginine-glutamate salt bridge. Insights from the classical MD simulations. J Chem Phys 2015; 142:215106. [DOI: 10.1063/1.4922165] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M. V. Vener
- Mendeleev University of Chemical Technology, Moscow, Russia
| | - A. V. Odinokov
- Photochemistry Center of the Russian Academy of Sciences, Moscow, Russia
| | | | - D. Sebastiani
- Martin-Luther-Universität Halle-Wittenberg, Halle, Germany
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26
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Basarić N, Thomas SS, Bregović VB, Cindro N, Bohne C. Phototautomerization in Pyrrolylphenylpyridine Terphenyl Systems. J Org Chem 2015; 80:4430-42. [DOI: 10.1021/acs.joc.5b00275] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Nikola Basarić
- Department
of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Suma S. Thomas
- Department
of Chemistry, University of Victoria, Box 3065 STN CSC, Victoria, BC V8W 3 V6, Canada
| | - Vesna Blažek Bregović
- Department
of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Nikola Cindro
- Department
of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10 000 Zagreb, Croatia
| | - Cornelia Bohne
- Department
of Chemistry, University of Victoria, Box 3065 STN CSC, Victoria, BC V8W 3 V6, Canada
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27
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Fang H, Mai BK, Kim Y. Excited-State Multiple Proton Transfer Depending on the Acidity and Basicity of Mediating Alcohols in 7-Azaindole-(ROH)2(R=H, CH3) Complexes: A Theoretical Study. Photochem Photobiol 2015; 91:306-14. [DOI: 10.1111/php.12417] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 12/29/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Hua Fang
- Department of Applied Chemistry and Institute of Natural Sciences; Kyung Hee University; Yongin-Si Gyeonggi-Do Korea
| | - Binh Khanh Mai
- Department of Applied Chemistry and Institute of Natural Sciences; Kyung Hee University; Yongin-Si Gyeonggi-Do Korea
| | - Yongho Kim
- Department of Applied Chemistry and Institute of Natural Sciences; Kyung Hee University; Yongin-Si Gyeonggi-Do Korea
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28
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Pinto da Silva L, Esteves da Silva JCG. A theoretical analysis of the potential role of π-π stacking interactions in the photoprotolytic cycle of firefly luciferin. Chemphyschem 2014; 15:3761-7. [PMID: 25236293 DOI: 10.1002/cphc.201402558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2014] [Indexed: 11/10/2022]
Abstract
Firefly oxyluciferin is a photoacid that presents a pH-sensitive fluorescence, which results from pH-dependent changes on the conformation of self-aggregated π-π stacking complexes. Luciferin is a derivative of oxyluciferin with very similar fluorescence and photoacidic properties. This similarity indicates that luciferin is also expected to be able to form π-π stacking complexes, but no pH-sensitive fluorescence is found for this compound. Here, a theoretical approach is used to rationalize this finding. We have found that luciferin only forms π-π stacking complexes in the ground state at acidic pH. At basic pH and in the excited state, luciferin is present as a dianion. This species is not able to self-aggregate, owing to repulsive electrostatic interactions. Thus, this emissive species is not subject to π-π stacking interactions; this explains its pH-insensitive fluorescence.
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Affiliation(s)
- Luís Pinto da Silva
- Centro de Investigação em Química (CIQ-UP), Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, R. Campo Alegre 697, 4169-007 Porto (Portugal)
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29
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Drechsel-Grau C, Marx D. Exceptional Isotopic-Substitution Effect: Breakdown of Collective Proton Tunneling in Hexagonal Ice due to Partial Deuteration. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405989] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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30
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Drechsel-Grau C, Marx D. Exceptional isotopic-substitution effect: breakdown of collective proton tunneling in hexagonal ice due to partial deuteration. Angew Chem Int Ed Engl 2014; 53:10937-40. [PMID: 25154597 DOI: 10.1002/anie.201405989] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Indexed: 11/09/2022]
Abstract
Multiple proton transfer controls many chemical reactions in hydrogen-bonded networks. However, in contrast to well-understood single proton transfer, the mechanisms of correlated proton transfer and of correlated proton tunneling in particular have remained largely elusive. Herein, fully quantized ab initio simulations are used to investigate H/D isotopic-substitution effects on the mechanism of the collective tunneling of six protons within proton-ordered cyclic water hexamers that are contained in proton-disordered ice, a prototypical hydrogen-bonded network. At the transition state, isotopic substitution leads to a Zundel-like complex, [HO⋅⋅⋅D⋅⋅⋅OH], which localizes ionic defects and thus inhibits perfectly correlated proton tunneling. These insights into fundamental aspects of collective proton tunneling not only rationalize recent neutron-scattering experiments, but also stimulate investigations into multiple proton transfer in hydrogen-bonded networks much beyond ice.
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31
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Koninti RK, Gavvala K, Sengupta A, Hazra P. Excited State Proton Transfer Dynamics of Topotecan Inside Biomimicking Nanocavity. J Phys Chem B 2014; 119:2363-71. [DOI: 10.1021/jp5066902] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Raj Kumar Koninti
- Department
of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India
| | - Krishna Gavvala
- Department
of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India
| | - Abhigyan Sengupta
- Department
of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India
| | - Partha Hazra
- Department
of Chemistry, Indian Institute of Science Education and Research (IISER), Pune 411008, Maharashtra, India
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32
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Pinto da Silva L, Esteves da Silva JCG. Chemiexcitation Induced Proton Transfer: Enolate Oxyluciferin as the Firefly Bioluminophore. J Phys Chem B 2014; 119:2140-8. [DOI: 10.1021/jp5036458] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Luís Pinto da Silva
- Centro de Investigação
em Química, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, 4169-007 Porto, Portugal
| | - Joaquim C. G. Esteves da Silva
- Centro de Investigação
em Química, Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, R. Campo Alegre 687, 4169-007 Porto, Portugal
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33
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Drechsel-Grau C, Marx D. Quantum simulation of collective proton tunneling in hexagonal ice crystals. PHYSICAL REVIEW LETTERS 2014; 112:148302. [PMID: 24766024 DOI: 10.1103/physrevlett.112.148302] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Indexed: 06/03/2023]
Abstract
The effect of proton tunneling on many-body correlated proton transfer in hexagonal ice is investigated by quantum simulation. Classical single-particle hopping along individual hydrogen bonds leads to charge defects at high temperature, whereas six protons in ringlike topologies can move concertedly as a delocalized quasiparticle via collective tunneling at low temperature, thus preventing the creation of high-energy topological defects. Our findings rationalize many-body quantum tunneling in hydrogen-bonded networks and suggest that this phenomenon might be more widespread than previously thought.
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Affiliation(s)
| | - Dominik Marx
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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34
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Gerwert K, Freier E, Wolf S. The role of protein-bound water molecules in microbial rhodopsins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2013; 1837:606-13. [PMID: 24055285 DOI: 10.1016/j.bbabio.2013.09.006] [Citation(s) in RCA: 105] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2013] [Revised: 09/08/2013] [Accepted: 09/10/2013] [Indexed: 02/06/2023]
Abstract
Protein-bound internal water molecules are essential features of the structure and function of microbial rhodopsins. Besides structural stabilization, they act as proton conductors and even proton storage sites. Currently, the most understood model system exhibiting such features is bacteriorhodopsin (bR). During the last 20 years, the importance of water molecules for proton transport has been revealed through this protein. It has been shown that water molecules are as essential as amino acids for proton transport and biological function. In this review, we present an overview of the historical development of this research on bR. We furthermore summarize the recently discovered protein-bound water features associated with proton transport. Specifically, we discuss a pentameric water/amino acid arrangement close to the protonated Schiff base as central proton-binding site, a protonated water cluster as proton storage site at the proton-release site, and a transient linear water chain at the proton uptake site. We highlight how protein conformational changes reposition or reorient internal water molecules, thereby guiding proton transport. Last, we compare the water positions in bR with those in other microbial rhodopsins to elucidate how protein-bound water molecules guide the function of microbial rhodopsins. This article is part of a Special Issue entitled: Retinal Proteins - You can teach an old dog new tricks.
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Affiliation(s)
- Klaus Gerwert
- Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany; Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China.
| | - Erik Freier
- Department of Biophysics, University of Bochum, ND 04 North, 44780 Bochum, Germany
| | - Steffen Wolf
- Department of Biophysics, Chinese Academy of Sciences-Max-Planck Partner Institute for Computational Biology (PICB), Shanghai Institutes for Biological Sciences (SIBS), 320 Yue Yang Lu, 200031 Shanghai, PR China
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35
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Nanoconfinement effects on hydrated excess protons in layered materials. Nat Commun 2013; 4:2349. [DOI: 10.1038/ncomms3349] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Accepted: 07/24/2013] [Indexed: 01/26/2023] Open
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36
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Gunner MR, Amin M, Zhu X, Lu J. Molecular mechanisms for generating transmembrane proton gradients. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:892-913. [PMID: 23507617 PMCID: PMC3714358 DOI: 10.1016/j.bbabio.2013.03.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 01/28/2013] [Accepted: 03/01/2013] [Indexed: 01/02/2023]
Abstract
Membrane proteins use the energy of light or high energy substrates to build a transmembrane proton gradient through a series of reactions leading to proton release into the lower pH compartment (P-side) and proton uptake from the higher pH compartment (N-side). This review considers how the proton affinity of the substrates, cofactors and amino acids are modified in four proteins to drive proton transfers. Bacterial reaction centers (RCs) and photosystem II (PSII) carry out redox chemistry with the species to be oxidized on the P-side while reduction occurs on the N-side of the membrane. Terminal redox cofactors are used which have pKas that are strongly dependent on their redox state, so that protons are lost on oxidation and gained on reduction. Bacteriorhodopsin is a true proton pump. Light activation triggers trans to cis isomerization of a bound retinal. Strong electrostatic interactions within clusters of amino acids are modified by the conformational changes initiated by retinal motion leading to changes in proton affinity, driving transmembrane proton transfer. Cytochrome c oxidase (CcO) catalyzes the reduction of O2 to water. The protons needed for chemistry are bound from the N-side. The reduction chemistry also drives proton pumping from N- to P-side. Overall, in CcO the uptake of 4 electrons to reduce O2 transports 8 charges across the membrane, with each reduction fully coupled to removal of two protons from the N-side, the delivery of one for chemistry and transport of the other to the P-side.
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Affiliation(s)
- M R Gunner
- Department of Physics, City College of New York, New York, NY 10031, USA.
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37
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Wang T, Sessions AO, Lunde CS, Rouhani S, Glaeser RM, Duan Y, Facciotti MT. Deprotonation of D96 in bacteriorhodopsin opens the proton uptake pathway. Structure 2013; 21:290-7. [PMID: 23394942 DOI: 10.1016/j.str.2012.12.018] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Revised: 12/08/2012] [Accepted: 12/12/2012] [Indexed: 11/18/2022]
Abstract
Despite extensive investigation, the precise mechanism controlling the opening of the cytoplasmic proton uptake pathway in bacteriorhodopsin (bR) has remained a mystery. From an analysis of the X-ray structure of the D96G/F171C/F219L triple mutant of bR and 60 independent molecular dynamics simulations of bR photointermediates, we report that the deprotonation of D96, a key residue in proton transfer reactions, serves two roles that occur sequentially. First, D96 donates a proton to the Schiff base. Subsequently, the deprotonation of D96 serves to "unlatch" the cytoplasmic side. The latching function of D96 appears to be remarkably robust, functioning to open hydration channels in all photointermediate structures. These results suggest that the protonation state of D96 may be the critical biophysical cue controlling the opening and closing of the cytoplasmic half-channel in bR. We suspect that this protonation-switch mechanism could also be utilized in other proton pumps to minimize backflow and reinforce directionality.
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Affiliation(s)
- Ting Wang
- Genome Center and Department of Biomedical Engineering, University of California at Davis, One Shields Avenue, Davis, CA 95616, USA
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38
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Fang H, Kim Y. Excited-State Tautomerization of 7-Azaindole in Nonpolar Solution: A Theoretical Study Based on Liquid-Phase Potential Surfaces of Mean Force. J Chem Theory Comput 2013; 9:3557-66. [DOI: 10.1021/ct3010694] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hua Fang
- Department of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Republic of Korea
| | - Yongho Kim
- Department of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Republic of Korea
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39
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Dreyer J, Zhang C, Ippoliti E, Carloni P. Role of the Membrane Dipole Potential for Proton Transport in Gramicidin A Embedded in a DMPC Bilayer. J Chem Theory Comput 2013; 9:3826-31. [PMID: 26584128 DOI: 10.1021/ct400374n] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The membrane potential at the water/phospholipid interfaces may play a key role for proton conduction of gramicidin A (gA). Here we address this issue by Density Functional Theory-based molecular dynamics and metadynamics simulations. The calculations, performed on gA embedded in a solvated 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) model membrane environment (about 2,000 atoms), indicate that (i) the membrane dipole potential rises at the channel mouth by ∼0.4 V. A similar value has been measured for gA embedded in a DMPC monolayer; (ii) the calculated free energy barrier is located at the channel entrance, consistent with experiments comparing gA proton conduction in different bilayers. The electronic structures of the proton ligands (water molecules and peptide units) are similar to those in the bulk solvent. Based on these results, we suggest an important role of the membrane dipole potential for the free energy barrier of proton permeation of gA. This may provide a rationale for the large increase in the rate of proton conduction under application of a transmembrane voltage, as observed experimentally. Our calculations might suggest also a role for proton desolvation for the permeation process. This role has already emerged from EVB calculations on gA embedded in a model membrane.
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Affiliation(s)
- Jens Dreyer
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Chao Zhang
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Emiliano Ippoliti
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Paolo Carloni
- Computational Biophysics, German Research School for Simulation Sciences, Joint venture of RWTH Aachen University and Forschungszentrum Jülich , Germany, D-52425 Jülich, Germany.,IAS-5, Computational Biomedicine, Institute for Advanced Simulation , Forschungszentrum Jülich, D-52425 Jülich, Germany
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40
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Detection of an intermediary, protonated water cluster in photosynthetic oxygen evolution. Proc Natl Acad Sci U S A 2013; 110:10634-9. [PMID: 23757501 DOI: 10.1073/pnas.1306532110] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In photosynthesis, photosystem II evolves oxygen from water by the accumulation of photooxidizing equivalents at the oxygen-evolving complex (OEC). The OEC is a Mn4CaO5 cluster, and its sequentially oxidized states are termed the Sn states. The dark-stable state is S1, and oxygen is released during the transition from S3 to S0. In this study, a laser flash induces the S1 to S2 transition, which corresponds to the oxidation of Mn(III) to Mn(IV). A broad infrared band, at 2,880 cm(-1), is produced during this transition. Experiments using ammonia and (2)H2O assign this band to a cationic cluster of internal water molecules, termed "W5(+)." Observation of the W5(+) band is dependent on the presence of calcium, and flash dependence is observed. These data provide evidence that manganese oxidation during the S1 to S2 transition results in a coupled proton transfer to a substrate-containing, internal water cluster in the OEC hydrogen-bonded network.
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41
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Rovira C. The description of electronic processes inside proteins from Car-Parrinello molecular dynamics: chemical transformations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1153] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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42
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Ivanov SD, Witt A, Marx D. Theoretical spectroscopy using molecular dynamics: theory and application to CH5+ and its isotopologues. Phys Chem Chem Phys 2013; 15:10270-99. [DOI: 10.1039/c3cp44523b] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Mai BK, Park K, Duong MPT, Kim Y. Proton Transfer Dependence on Hydrogen-Bonding of Solvent to the Water Wire: A Theoretical Study. J Phys Chem B 2012; 117:307-15. [DOI: 10.1021/jp310724g] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Binh Khanh Mai
- Department
of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Korea
| | - Kisoo Park
- Department
of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Korea
| | - My Phu Thi Duong
- Department
of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Korea
| | - Yongho Kim
- Department
of Applied Chemistry, Kyung Hee University, 1 Seochun-Dong,
Giheung-Gu, Yongin-Si, Gyeonggi-Do, 446-701, Korea
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Park SY, Kim HB, Yoo BK, Jang DJ. Direct Observation of Conformation-Dependent Pathways in the Excited-State Proton Transfer of 7-Hydroxyquinoline in Bulk Alcohols. J Phys Chem B 2012; 116:14153-8. [DOI: 10.1021/jp309138w] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sun-Young Park
- School of Chemistry, Seoul National University, NS60, Seoul
151-742, Korea
| | - Hyung-Bae Kim
- School of Chemistry, Seoul National University, NS60, Seoul
151-742, Korea
| | - Byung Kuk Yoo
- 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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45
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Park SY, Yoo BK, Pyo JY, Kim MS, Jang DJ. Anomalous Acid-Base Equilibria in Biologically Relevant Water Nanopools. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.10.3493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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46
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Basarić N, Došlić N, Ivković J, Wang YH, Veljković J, Mlinarić-Majerski K, Wan P. Excited State Intramolecular Proton Transfer (ESIPT) from Phenol to Carbon in Selected Phenylnaphthols and Naphthylphenols. J Org Chem 2012; 78:1811-23. [DOI: 10.1021/jo301456y] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Nikola Basarić
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta
54, 10000 Zagreb, Croatia
| | - Nađa Došlić
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb,
Croatia
| | - Jakov Ivković
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta
54, 10000 Zagreb, Croatia
| | - Yu-Hsuan Wang
- Department of Chemistry, University of Victoria, Box 3065 Stn CSC, Victoria
BC, V8W 3 V6, Canada
| | - Jelena Veljković
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta
54, 10000 Zagreb, Croatia
| | - Kata Mlinarić-Majerski
- Department of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta
54, 10000 Zagreb, Croatia
| | - Peter Wan
- Department of Chemistry, University of Victoria, Box 3065 Stn CSC, Victoria
BC, V8W 3 V6, Canada
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Molecular dynamics simulations reveal proton transfer pathways in cytochrome C-dependent nitric oxide reductase. PLoS Comput Biol 2012; 8:e1002674. [PMID: 22956904 PMCID: PMC3431322 DOI: 10.1371/journal.pcbi.1002674] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2012] [Accepted: 07/22/2012] [Indexed: 01/25/2023] Open
Abstract
Nitric oxide reductases (NORs) are membrane proteins that catalyze the reduction of nitric oxide (NO) to nitrous oxide (N2O), which is a critical step of the nitrate respiration process in denitrifying bacteria. Using the recently determined first crystal structure of the cytochrome c-dependent NOR (cNOR) [Hino T, Matsumoto Y, Nagano S, Sugimoto H, Fukumori Y, et al. (2010) Structural basis of biological N2O generation by bacterial nitric oxide reductase. Science 330: 1666–70.], we performed extensive all-atom molecular dynamics (MD) simulations of cNOR within an explicit membrane/solvent environment to fully characterize water distribution and dynamics as well as hydrogen-bonded networks inside the protein, yielding the atomic details of functionally important proton channels. Simulations reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side were found, consistently with the experimental observations that cNOR is not a proton pump. One of the pathways, which was newly identified in the MD simulation, is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb3 oxidase, which illustrates that the two enzymes share some elements of the proton transfer mechanisms and confirms a close evolutionary relation between NORs and C-type oxidases. Several mechanisms of the critical proton transfer steps near the catalytic center are proposed. Denitrification is an anaerobic process performed by several bacteria as an alternative to aerobic respiration. A key intermediate step is catalyzed by the nitric oxide reductase (NOR) enzyme, which is situated in the cytoplasmic membrane. Proton delivery to the catalytic site inside NOR is an important part of its functioning. In this work we use molecular dynamics simulations to describe water distribution and to identify proton transfer pathways in cNOR. Our results reveal two channels from the periplasmic side of the membrane and none from the cytoplasmic side, indicating that cNOR is not a proton pump. It is our hope that these results will provide a basis for further experimental and computational studies aimed to understand details of the NOR mechanism. Furthermore, this work sheds light on the molecular evolution of respiratory enzymes.
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Park SY, Kim Y, Lee JY, Jang DJ. Ground-State Proton Transport along a Blended-Alcohol Chain: Accelerated by Accumulated Proton-Donating Ability. J Phys Chem B 2012; 116:10915-21. [DOI: 10.1021/jp305769n] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Sun-Young Park
- School of Chemistry, Seoul National University, NS60, Seoul
151-742, Korea
| | - Yeonho Kim
- School of Chemistry, Seoul National University, NS60, Seoul
151-742, Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 440-746, Korea
| | - Du-Jeon Jang
- School of Chemistry, Seoul National University, NS60, Seoul
151-742, Korea
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49
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A comparative DFT study of the Schiff base formation from acetaldehyde and butylamine, glycine and phosphatidylethanolamine. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1263-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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50
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Hayashi T, Matsuura A, Sato H, Sakurai M. Full-Quantum chemical calculation of the absorption maximum of bacteriorhodopsin: a comprehensive analysis of the amino acid residues contributing to the opsin shift. Biophysics (Nagoya-shi) 2012; 8:115-25. [PMID: 27493528 PMCID: PMC4629650 DOI: 10.2142/biophysics.8.115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 06/14/2012] [Indexed: 12/01/2022] Open
Abstract
Herein, the absorption maximum of bacteriorhodopsin (bR) is calculated using our recently developed method in which the whole protein can be treated quantum mechanically at the level of INDO/S-CIS//ONIOM (B3LYP/6-31G(d,p): AMBER). The full quantum mechanical calculation is shown to reproduce the so-called opsin shift of bR with an error of less than 0.04 eV. We also apply the same calculation for 226 different bR mutants, each of which was constructed by replacing any one of the amino acid residues of the wild-type bR with Gly. This substitution makes it possible to elucidate the extent to which each amino acid contributes to the opsin shift and to estimate the inter-residue synergistic effect. It was found that one of the most important contributions to the opsin shift is the electron transfer from Tyr185 to the chromophore upon excitation. We also indicate that some aromatic (Trp86, Trp182) and polar (Ser141, Thr142) residues, located in the vicinity of the retinal polyene chain and the β-ionone ring, respectively, play an important role in compensating for the large blue-shift induced by both the counterion residues (Asp85, Asp212) and an internal water molecule (W402) located near the Schiff base linkage. In particular, the effect of Trp86 is comparable to that of Tyr185. In addition, Ser141 and Thr142 were found to contribute to an increase in the dipole moment of bR in the excited state. Finally, we provide a complete energy diagram for the opsin shift together with the contribution of the chromophore-protein steric interaction.
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Affiliation(s)
- Tomohiko Hayashi
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Azuma Matsuura
- Fujitsu Laboratories, Ltd., 10-1 Morinosato-Wakamiya, Atsugi 243-0197, Japan
| | - Hiroyuki Sato
- Fujitsu Laboratories, Ltd., 10-1 Morinosato-Wakamiya, Atsugi 243-0197, Japan
| | - Minoru Sakurai
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, B-62 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
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