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Leighton RE, Frontiera RR. Quantifying Bacteriorhodopsin Activity as a Function of its Local Environment with a Raman-Based Assay. J Phys Chem B 2023; 127:8833-8841. [PMID: 37812499 DOI: 10.1021/acs.jpcb.3c04802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Bacteriorhodopsin (bR) is a transmembrane protein that functions as a light-driven proton pump in halophilic archaea. The bR photocycle has been well-characterized; however, these measurements almost exclusively measured purified bR, outside of its native membrane. To investigate what effect the cellular environment has on the bR photocycle, we have developed a Raman-based assay that can monitor the activity of the bR in a variety of conditions, including in its native membrane. The assay uses two continuous-wave lasers, one to initiate photochemistry and one to monitor bR activity. The excitation leads to the steady-state depletion of ground-state bR, which directly relates to the population of photocycle intermediate states. We have used this assay to monitor bR activity both in vitro and in vivo. Our in vitro measurements confirm that our assay is sensitive to bulk environmental changes reported in the literature. Our in vivo measurements show a decrease in bR activity with increasing extracellular pH for bR in its native membrane. The difference in activity with increasing pH indicates that the native membrane environment affects the function of bR. This assay opens the door to future measurements into understanding how the local environment of this transmembrane protein affects function.
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Affiliation(s)
- Ryan E Leighton
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Renee R Frontiera
- Department of Chemistry, University of Minnesota, Minneapolis, Minnesota 55455, United States
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Ono J, Okada C, Nakai H. Hydroxide Ion Mechanism for Long-Range Proton Pumping in the Third Proton Transfer of Bacteriorhodopsin. Chemphyschem 2022; 23:e202200109. [PMID: 35818319 DOI: 10.1002/cphc.202200109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/21/2022] [Indexed: 11/10/2022]
Abstract
In bacteriorhodopsin, representative light-driven proton pump, five proton transfers yield vectorial active proton translocation, resulting in a proton gradient in microbes. Third proton transfer occurs from Asp96 to the Schiff base on the photocycle, which is expected to be a long-range proton transfer via the Grotthuss mechanism through internal water molecules. Here, large-scale quantum molecular dynamics simulations are performed for the third proton transfer, where all the atoms (~50000 atoms) are treated quantum-mechanically. The simulations demonstrate that two reaction paths exist along the water wire, namely, via hydronium and via hydroxide ions. The free energy analysis confirms that the path via hydroxide ions is considerably favorable and consistent with the observed lifetime of the transient water wire. Therefore, the proposed hydroxide ion mechanism, as in the first proton transfer, is responsible for the third long-range proton transfer.
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Affiliation(s)
- Junichi Ono
- Kyoto University: Kyoto Daigaku, Elements Strategy Initiative for Catalysts & Batteries (ESICB), 1-30 Goryo-Ohara, 615-8245, Nishi-ku, JAPAN
| | - Chika Okada
- Waseda University: Waseda Daigaku, Department of Chemistry and Biochemistry, 3-4-1 Okubo, 169-8555, Shinjuku, JAPAN
| | - Hiromi Nakai
- Waseda University Faculty of Science and Engineering: Waseda Daigaku Riko Gakujutsuin, Department of Chemistry and Biochemistry, 3-4-1 Okubo, 169-8555, Shinjuku, JAPAN
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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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Takaoka T, Mori K, Okimoto N, Neya S, Hoshino T. Prediction of the Structure of Complexes Comprised of Proteins and Glycosaminoglycans Using Docking Simulation and Cluster Analysis. J Chem Theory Comput 2015; 3:2347-56. [PMID: 26636224 DOI: 10.1021/ct700029q] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A typical docking simulation provides information on the structure of ligand-receptor complexes and their binding affinity in terms of a docking energy. We have developed a potent method combining a docking simulation with cluster analysis to extract adequate docking structures from the many possible output structures of the simulation. First, we tried to predict the structure of basic fibroblast growth factor (bFGF) bound to heparin, using the docking simulation program AutoDock 3.0. Two X-ray crystal structures had already been obtained for bFGF. One was a complex of the protein and heparin, a kind of glycosaminoglycan, and the other, only the protein itself, hereafter called a simplex. We docked a heparin molecule onto the protein simplex and generated many trial structures for the bFGF-heparin complex. The structures of those docked complexes were optimized through energy minimization by AMBER8. Although neither the docking energy calculated by AMBER8 nor that calculated by AutoDock 3.0 could be used satisfactorily by themselves to select a proper heparin-binding complex from the output structures, the majority of the structures generated by AutoDock 3.0 were fairly close to each other in atom geometry, and the averaged geometry over these structures was also close to that of the crystal. Hence, we utilized only the atom geometry for evaluation and carried out cluster analysis with the collection of geometries. This procedure enabled selection of a structure considerably close to the crystal's. We applied this approach to two other heparin-binding proteins: antithrombin and annexin V. Two crystal structures, a complex and a simplex, had been elucidated for these proteins as well as for bFGF. Our trials gave an exact prediction of the heparin-binding structures of these proteins, showing the approach in this study is effective in studying the docking of ligands that have a variety of docking conformations due to the presence of multiple rotatable bonds and charged chemical groups.
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Affiliation(s)
- Tsubasa Takaoka
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan, Bioinformatics Group, GSC, RIKEN, Yokohama, Kanagawa 230-0046, Japan, and PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Kenichi Mori
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan, Bioinformatics Group, GSC, RIKEN, Yokohama, Kanagawa 230-0046, Japan, and PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Noriaki Okimoto
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan, Bioinformatics Group, GSC, RIKEN, Yokohama, Kanagawa 230-0046, Japan, and PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Saburo Neya
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan, Bioinformatics Group, GSC, RIKEN, Yokohama, Kanagawa 230-0046, Japan, and PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Tyuji Hoshino
- Graduate School of Pharmaceutical Sciences, Chiba University, Chiba 263-8522, Japan, Bioinformatics Group, GSC, RIKEN, Yokohama, Kanagawa 230-0046, Japan, and PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
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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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Kellie JL, Wetmore SD. Mechanistic and conformational flexibility of the covalent linkage formed during β-lyase activity on an AP-site: application to hOgg1. J Phys Chem B 2012; 116:10786-97. [PMID: 22877319 DOI: 10.1021/jp306344g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The β/δ-lyase activity of bifunctional glycosylases on damaged nucleotides in DNA involves the formation of a covalent linkage between the protein (lysine or N-terminal proline) and DNA (C1' of the damaged nucleotide). In the present study, the conformational and mechanistic flexibility of the cross-link is examined. Repair of 8-oxoguanine damage by hOgg1 is considered as a representative system, and the glycosylase through β-lyase steps are investigated using density functional theory. (PCM/SMD)-M06-2X/6-311+G(2df,2p)//PCM-B3LYP/6-31G(d) energetics were determined for eight unique mechanisms differing in the conformation of the imine linkage (E/Z), the proton (pro-S/R) abstracted during elimination, and whether the ring-opening step is base catalyzed. This initial study used a model system limited to the damaged nucleoside 3'-monophosphate and a model nucleophile to investigate this series of complex reaction steps. The great flexibility exhibited by the linkage and clustered β-elimination energetics indicate sterics will play a large role in predicting the preferred lyase mechanism for a given enzyme. The stationary points identified herein can be overlaid into a protein structure to assist in generating initial guesses for large model systems. By comparing the characterized geometries and enzyme active sites, methods for catalysis of the various chemical steps can be identified, and these possibilities are discussed in detail for hOgg1. Interestingly, the most stable structure on the potential energy surface occurs before elimination of the 3'-phosphate. Hydrolysis of the protein-DNA cross-link at this point would yield an AP-site, which provides support for the recently observed monofunctional activity of hOgg1.
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Affiliation(s)
- Jennifer L Kellie
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta, T1K 3M4, Canada
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A QM/MM-based computational investigation on the catalytic mechanism of saccharopine reductase. Molecules 2011; 16:8569-89. [PMID: 21993247 PMCID: PMC6264447 DOI: 10.3390/molecules16108569] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 09/27/2011] [Accepted: 09/30/2011] [Indexed: 11/17/2022] Open
Abstract
Saccharopine reductase from Magnaporthe grisea, an NADPH-containing enzyme in the α-aminoadipate pathway, catalyses the formation of saccharopine, a precursor to L-lysine, from the substrates glutamate and α-aminoadipate-δ-semialdehyde. Its catalytic mechanism has been investigated using quantum mechanics/molecular mechanics (QM/MM) ONIOM-based approaches. In particular, the overall catalytic pathway has been elucidated and the effects of electron correlation and the anisotropic polar protein environment have been examined via the use of the ONIOM(HF/6-31G(d):AMBER94) and ONIOM(MP2/6-31G(d)//HF/6-31G(d):AMBER94) methods within the mechanical embedding formulism and ONIOM(MP2/6-31G(d)//HF/6-31G(d):AMBER94) and ONIOM(MP2/6-311G(d,p)//HF/6-31G(d):AMBER94) within the electronic embedding formulism. The results of the present study suggest that saccharopine reductase utilises a substrate-assisted catalytic pathway in which acid/base groups within the cosubstrates themselves facilitate the mechanistically required proton transfers. Thus, the enzyme appears to act most likely by binding the three required reactant molecules glutamate, α-aminoadipate-δ-semialdehyde and NADPH in a manner and polar environment conducive to reaction.
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Abstract
Combined quantum-mechanics/molecular-mechanics (QM/MM) approaches have become the method of choice for modeling reactions in biomolecular systems. Quantum-mechanical (QM) methods are required for describing chemical reactions and other electronic processes, such as charge transfer or electronic excitation. However, QM methods are restricted to systems of up to a few hundred atoms. However, the size and conformational complexity of biopolymers calls for methods capable of treating up to several 100,000 atoms and allowing for simulations over time scales of tens of nanoseconds. This is achieved by highly efficient, force-field-based molecular mechanics (MM) methods. Thus to model large biomolecules the logical approach is to combine the two techniques and to use a QM method for the chemically active region (e.g., substrates and co-factors in an enzymatic reaction) and an MM treatment for the surroundings (e.g., protein and solvent). The resulting schemes are commonly referred to as combined or hybrid QM/MM methods. They enable the modeling of reactive biomolecular systems at a reasonable computational effort while providing the necessary accuracy.
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Affiliation(s)
- Hans Martin Senn
- Department of Chemistry, WestCHEM and University of Glasgow, Glasgow G12 8QQ, UK.
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Wu J, Ma D, Wang Y, Ming M, Balashov SP, Ding J. Efficient Approach to Determine the pKa of the Proton Release Complex in the Photocycle of Retinal Proteins. J Phys Chem B 2009; 113:4482-91. [DOI: 10.1021/jp804838h] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jia Wu
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Advanced Materials Laboratory, Fudan University, Shanghai 200433, China and Department of Physiology and Biophysics, University of California, Irvine 92697, USA
| | - Dewang Ma
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Advanced Materials Laboratory, Fudan University, Shanghai 200433, China and Department of Physiology and Biophysics, University of California, Irvine 92697, USA
| | - Yazhuo Wang
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Advanced Materials Laboratory, Fudan University, Shanghai 200433, China and Department of Physiology and Biophysics, University of California, Irvine 92697, USA
| | - Ming Ming
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Advanced Materials Laboratory, Fudan University, Shanghai 200433, China and Department of Physiology and Biophysics, University of California, Irvine 92697, USA
| | - Sergei P. Balashov
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Advanced Materials Laboratory, Fudan University, Shanghai 200433, China and Department of Physiology and Biophysics, University of California, Irvine 92697, USA
| | - Jiandong Ding
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Advanced Materials Laboratory, Fudan University, Shanghai 200433, China and Department of Physiology and Biophysics, University of California, Irvine 92697, USA
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FUKUZAWA K, NAKANO T, KATO A, MOCHIZUKI Y, TANAKA S. Applications of the Fragment Molecular Orbital Method for Bio-Macromolecules. ACTA ACUST UNITED AC 2007. [DOI: 10.2477/jccj.6.185] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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