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Nachliel E, Gutman M. Reaction within the coulomb-cage; science in retrospect. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2023; 1865:184071. [PMID: 36244436 DOI: 10.1016/j.bbamem.2022.184071] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 08/01/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
The Coulomb-cage is defined as the space where the electrostatic interaction between two bodies is more intensive than the thermal energy (kBT). For small molecule, the Coulomb-cage is a small sphere, extending only few water molecules towards the bulk and its radius is sensitive to the ionic strength of the solution. For charged proteins or membranal structures, the Coulomb-cage can engulf large fraction of the surface and provides a preferred pathway for ion propagation along the surface. Similarly, electrostatic potential at the inner space of a channel can form preferential trajectories passage for ions. The dynamics of ions inside the Coulomb-cage of ions was formulated by the studies of proton-anion recombination of excited photoacids. In the present article, we recount the study of intra- Coulomb-cage reaction taking place on the surface of macro-molecular bodies like micelles, membranes, proteins and intra-protein cavities. The study progressed stepwise, tracing the dynamics of a proton ejected from a photo-acid molecule located at defined sites (on membrane, inter-membrane space, active site of enzyme, inside Large Pore Channels etc.). Accumulation of experimental observations encouraged us to study of the reaction mechanism by molecular dynamics simulations of ions within the Coulomb-cage of proteins surface or inside large pores. The intra-Coulomb-cage proton transfer events follows closely the fine structure of the electrostatic field inside the cage and reflects the shape of nearby dielectric boundaries, the temporal ordering of the solvent molecules and the structural fluctuations of the charged side chains. The article sums some 40 years of research, which in retrospect clarifies the intra-Coulomb-cage reaction mechanism.
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Affiliation(s)
- E Nachliel
- Laser Laboratory for Fast Reactions, Dep. Of Biochemistry and Molecular Biology, Life Sciences, Tel Aviv University, Israel
| | - M Gutman
- Laser Laboratory for Fast Reactions, Dep. Of Biochemistry and Molecular Biology, Life Sciences, Tel Aviv University, Israel.
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2
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Friedman R. Simulations of Biomolecules in Electrolyte Solutions. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800163] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Ran Friedman
- Department of Chemistry and Biomedical SciencesLinnæus UniversityKalmar SE‐391 82 Sweden
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3
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Ahlstrand E, Zukerman Schpector J, Friedman R. Computer simulations of alkali-acetate solutions: Accuracy of the forcefields in difference concentrations. J Chem Phys 2018; 147:194102. [PMID: 29166095 DOI: 10.1063/1.4985919] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
When proteins are solvated in electrolyte solutions that contain alkali ions, the ions interact mostly with carboxylates on the protein surface. Correctly accounting for alkali-carboxylate interactions is thus important for realistic simulations of proteins. Acetates are the simplest carboxylates that are amphipathic, and experimental data for alkali acetate solutions are available and can be compared with observables obtained from simulations. We carried out molecular dynamics simulations of alkali acetate solutions using polarizable and non-polarizable forcefields and examined the ion-acetate interactions. In particular, activity coefficients and association constants were studied in a range of concentrations (0.03, 0.1, and 1M). In addition, quantum-mechanics (QM) based energy decomposition analysis was performed in order to estimate the contribution of polarization, electrostatics, dispersion, and QM (non-classical) effects on the cation-acetate and cation-water interactions. Simulations of Li-acetate solutions in general overestimated the binding of Li+ and acetates. In lower concentrations, the activity coefficients of alkali-acetate solutions were too high, which is suggested to be due to the simulation protocol and not the forcefields. Energy decomposition analysis suggested that improvement of the forcefield parameters to enable accurate simulations of Li-acetate solutions can be achieved but may require the use of a polarizable forcefield. Importantly, simulations with some ion parameters could not reproduce the correct ion-oxygen distances, which calls for caution in the choice of ion parameters when protein simulations are performed in electrolyte solutions.
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Affiliation(s)
- Emma Ahlstrand
- Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
| | - Julio Zukerman Schpector
- Universidade Federal de São Carlos, Departamento de Química, CP 676, 13565-905 São Carlos, SP, Brazil
| | - Ran Friedman
- Department of Chemistry and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
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4
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Ahlstrand E, Hermansson K, Friedman R. Interaction Energies in Complexes of Zn and Amino Acids: A Comparison of Ab Initio and Force Field Based Calculations. J Phys Chem A 2017; 121:2643-2654. [DOI: 10.1021/acs.jpca.6b12969] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Emma Ahlstrand
- Department of Chemistry
and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Linnæus University Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
| | - Kersti Hermansson
- Department of Chemistry, Ångström Laboratory, Uppsala University, Box 538, 751 21 Uppsala, Sweden
| | - Ran Friedman
- Department of Chemistry
and Biomedical Sciences, Linnæus University, 391 82 Kalmar, Sweden
- Linnæus University Centre for Biomaterials Chemistry, 391 82 Kalmar, Sweden
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5
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Mahnam K, Raisi F. A theoretical and experimental study of calcium, iron, zinc, cadmium, and sodium ions absorption by aspartame. J Biol Phys 2017; 43:87-103. [PMID: 28150114 DOI: 10.1007/s10867-016-9435-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 11/21/2016] [Indexed: 10/20/2022] Open
Abstract
Aspartame (L-Aspartyl-L-phenylalanine methyl ester) is a sweet dipeptide used in some foods and beverages. Experimental studies show that aspartame causes osteoporosis and some illnesses, which are similar to those of copper and calcium deficiency. This raises the issue that aspartame in food may interact with cations and excrete them from the body. This study aimed to study aspartame interaction with calcium, zinc, iron, sodium, and cadmium ions via molecular dynamics simulation (MD) and spectroscopy. Following a 480-ns molecular dynamics simulation, it became clear that the aspartame is able to sequester Fe2+, Ca2+, Cd2+, and Zn2+ ions for a long time. Complexation led to increasing UV-Vis absorption spectra and emission spectra of the complexes. This study suggests a potential risk of cationic absorption of aspartame. This study suggests that purification of cadmium-polluted water by aspartame needs a more general risk assessment.
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Affiliation(s)
- Karim Mahnam
- Biology Department, Faculty of Sciences, Shehrekord University, Shahrekord, Iran.
| | - Fatame Raisi
- Biology Department, Faculty of Sciences, Payam Nour University, Isfahan, Iran
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6
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Pineda De Castro LF, Dopson M, Friedman R. Biological Membranes in Extreme Conditions: Anionic Tetraether Lipid Membranes and Their Interactions with Sodium and Potassium. J Phys Chem B 2016; 120:10628-10634. [PMID: 27668511 DOI: 10.1021/acs.jpcb.6b06206] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Archaea such as Sulfolobus acidocaldarius tolerate extreme temperatures and high acidity and can grow in the presence of toxic metals and low concentrations of Na+ or K+. It is believed that their unique tetraether membranes protect them from harsh environments and allow their survival under such conditions. We used molecular dynamics simulations to study membranes comprising glycerol dialkylnonitol tetraether lipids, which are the main component of S. acidocaldarius membranes, in solutions containing different concentrations of NaCl and KCl or with Na+ or K+ counterions (trace cations, 0 M). Anionic binding sites on the membranes were almost 50% occupied in the presence of counterions. The free energy of cation-phosphate complexation and the residence times of ions near the membranes were found to be both ion- and concentration-dependent. Sodium ions had more favorable interactions with the membranes and a longer residence time, whereas higher cation concentrations led to shorter ion residence times. When only counterions were present in the solutions, large residence times suggested that the membrane may function as a cation-attracting reservoir. The results suggested that the ions can be easily transferred to the cytoplasm as needed, explaining the growth curves of S. acidocaldarius under different salinities and pH.
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Affiliation(s)
- Luis Felipe Pineda De Castro
- Computational Chemistry and Biochemistry Research Group (CCBG), Department of Chemistry and Biomedical Sciences, ‡Centre of Excellence "Biomaterials Chemistry", and §Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University , 391 82 Kalmar, Sweden
| | - Mark Dopson
- Computational Chemistry and Biochemistry Research Group (CCBG), Department of Chemistry and Biomedical Sciences, ‡Centre of Excellence "Biomaterials Chemistry", and §Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University , 391 82 Kalmar, Sweden
| | - Ran Friedman
- Computational Chemistry and Biochemistry Research Group (CCBG), Department of Chemistry and Biomedical Sciences, ‡Centre of Excellence "Biomaterials Chemistry", and §Linnaeus University Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnæus University , 391 82 Kalmar, Sweden
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7
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Scheiner S. Monitoring the Charge Distribution during Proton and Sodium Ion Conduction along Chains of Water Molecules and Protein Residues. Isr J Chem 2016. [DOI: 10.1002/ijch.201600062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry; Utah State University; Logan UT 84322-0300 USA
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8
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Sharma V, Ala-Vannesluoma P, Vattulainen I, Wikström M, Róg T. Role of subunit III and its lipids in the molecular mechanism of cytochrome c oxidase. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:690-7. [PMID: 25896562 DOI: 10.1016/j.bbabio.2015.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Revised: 04/07/2015] [Accepted: 04/12/2015] [Indexed: 12/31/2022]
Abstract
The terminal respiratory enzyme cytochrome c oxidase (CcO) reduces molecular oxygen to water, and pumps protons across the inner mitochondrial membrane, or the plasma membrane of bacteria. A two-subunit CcO harbors all the elements necessary for oxygen reduction and proton pumping. However, it rapidly undergoes turnover-induced irreversible damage, which is effectively prevented by the presence of subunit III and its tightly bound lipids. We have performed classical atomistic molecular dynamics (MD) simulations on a three-subunit CcO, which show the formation of water wires between the polar head groups of lipid molecules bound to subunit III and the proton uptake site Asp91 (Bos taurus enzyme numbering). Continuum electrostatic calculations suggest that these lipids directly influence the proton affinity of Asp91 by 1-2pK units. We surmise that lipids bound to subunit III influence the rate of proton uptake through the D-pathway, and therefore play a key role in preventing turnover-induced inactivation. Atomistic MD simulations show that subunit III is rapidly hydrated in the absence of internally bound lipids, which is likely to affect the rate of O2 diffusion into the active-site. The role of subunit III with its indigenous lipids in the molecular mechanism of CcO is discussed.
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Affiliation(s)
- Vivek Sharma
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland.
| | | | - Ilpo Vattulainen
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland; MEMPHYS, Center for Biomembrane Physics, Department of Physics, University of Southern Denmark, Odense, Denmark
| | - Mårten Wikström
- Helsinki Bioenergetics Group, Programme for Structural Biology and Biophysics, Institute of Biotechnology, University of Helsinki, FI-00014 Helsinki, Finland
| | - Tomasz Róg
- Department of Physics, Tampere University of Technology, FI-33101 Tampere, Finland
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9
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Herzog E, Gu W, Juhnke H, Haas A, Mäntele W, Simon J, Helms V, Lancaster C. Hydrogen-bonded networks along and bifurcation of the E-pathway in quinol:fumarate reductase. Biophys J 2012; 103:1305-14. [PMID: 22995503 PMCID: PMC3446689 DOI: 10.1016/j.bpj.2012.07.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Revised: 07/24/2012] [Accepted: 07/25/2012] [Indexed: 02/06/2023] Open
Abstract
The E-pathway of transmembrane proton transfer has been demonstrated previously to be essential for catalysis by the diheme-containing quinol:fumarate reductase (QFR) of Wolinella succinogenes. Two constituents of this pathway, Glu-C180 and heme b(D) ring C (b(D)-C-) propionate, have been validated experimentally. Here, we identify further constituents of the E-pathway by analysis of molecular dynamics simulations. The redox state of heme groups has a crucial effect on the connectivity patterns of mobile internal water molecules that can transiently support proton transfer from the b(D)-C-propionate to Glu-C180. The short H-bonding paths formed in the reduced states can lead to high proton conduction rates and thus provide a plausible explanation for the required opening of the E-pathway in reduced QFR. We found evidence that the b(D)-C-propionate group is the previously postulated branching point connecting proton transfer to the E-pathway from the quinol-oxidation site via interactions with the heme b(D) ligand His-C44. An essential functional role of His-C44 is supported experimentally by site-directed mutagenesis resulting in its replacement with Glu. Although the H44E variant enzyme retains both heme groups, it is unable to catalyze quinol oxidation. All results obtained are relevant to the QFR enzymes from the human pathogens Campylobacter jejuni and Helicobacter pylori.
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Affiliation(s)
- Elena Herzog
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Department of Structural Biology, Center of Human and Molecular Biology, Institute of Biophysics, Faculty of Medicine, Saarland University, Homburg, Germany
| | - Wei Gu
- Center for Bioinformatics and Center of Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - Hanno D. Juhnke
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Alexander H. Haas
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Werner Mäntele
- Institute of Biophysics, J. W. Goethe University, Frankfurt am Main, Germany
| | - Jörg Simon
- Institute of Molecular Biosciences, J. W. Goethe University, Frankfurt am Main, Germany
| | - Volkhard Helms
- Center for Bioinformatics and Center of Human and Molecular Biology, Saarland University, Saarbrücken, Germany
| | - C. Roy D. Lancaster
- Department of Molecular Membrane Biology, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
- Department of Structural Biology, Center of Human and Molecular Biology, Institute of Biophysics, Faculty of Medicine, Saarland University, Homburg, Germany
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10
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Gaigeot MP, Cimas A, Seydou M, Kim JY, Lee S, Schermann JP. Proton Transfer from the Inactive Gas-Phase Nicotine Structure to the Bioactive Aqueous-Phase Structure. J Am Chem Soc 2010; 132:18067-77. [DOI: 10.1021/ja103759v] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marie-Pierre Gaigeot
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Alvaro Cimas
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Mahamadou Seydou
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Ju-Young Kim
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Sungyul Lee
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
| | - Jean-Pierre Schermann
- Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, LAMBE UMR8587 CNRS, Université d’Evry val d’Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Institut Universitaire de France IUF, 103 boulevard St Michel, 75005 Paris, France, Subatech, Ecole des Mines de Nantes, 4 rue Alfred Kastler, 44307 Nantes, France, Department of Applied Chemistry, Kyunghee University, Kyungki 446-701, South Korea, Department of Biophysics and Biochemical Chemistry, WCU, Seoul
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11
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Ojemyr L, Sandén T, Widengren J, Brzezinski P. Lateral proton transfer between the membrane and a membrane protein. Biochemistry 2009; 48:2173-9. [PMID: 19166299 DOI: 10.1021/bi8022152] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Proton transport across biological membranes is a key step of the energy conservation machinery in living organisms, and it has been proposed that the membrane itself plays an important role in this process. In the present study we have investigated the effect of incorporation of a proton transporter, cytochrome c oxidase, into a membrane on the protonation kinetics of a fluorescent pH-sensitive probe attached at the surface of the protein. The results show that proton transfer to the probe was slightly accelerated upon attachment at the protein surface (approximately 7 x 1010 s(-1) M(-1), compared to the expected value of (1-2) x 10(10) s(-1) M(-1)), which is presumably due to the presence of acidic/His groups in the vicinity. Upon incorporation of the protein into small unilamellar phospholipid vesicles the rate increased by more than a factor of 400 to approximately 3 x 10(13) s(-1) M(-1), which indicates that the protein-attached probe is in rapid protonic contact with the membrane surface. The results indicate that the membrane acts to accelerate proton uptake by the membrane-bound proton transporter.
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Affiliation(s)
- Linda Ojemyr
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, Sweden
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12
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13
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Till MS, Essigke T, Becker T, Ullmann GM. Simulating the proton transfer in gramicidin A by a sequential dynamical Monte Carlo method. J Phys Chem B 2008; 112:13401-10. [PMID: 18826179 DOI: 10.1021/jp801477b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The large interest in long-range proton transfer in biomolecules is triggered by its importance for many biochemical processes such as biological energy transduction and drug detoxification. Since long-range proton transfer occurs on a microsecond time scale, simulating this process on a molecular level is still a challenging task and not possible with standard simulation methods. In general, the dynamics of a reactive system can be described by a master equation. A natural way to describe long-range charge transfer in biomolecules is to decompose the process into elementary steps which are transitions between microstates. Each microstate has a defined protonation pattern. Although such a master equation can in principle be solved analytically, it is often too demanding to solve this equation because of the large number of microstates. In this paper, we describe a new method which solves the master equation by a sequential dynamical Monte Carlo algorithm. Starting from one microstate, the evolution of the system is simulated as a stochastic process. The energetic parameters required for these simulations are determined by continuum electrostatic calculations. We apply this method to simulate the proton transfer through gramicidin A, a transmembrane proton channel, in dependence on the applied membrane potential and the pH value of the solution. As elementary steps in our reaction, we consider proton uptake and release, proton transfer along a hydrogen bond, and rotations of water molecules that constitute a proton wire through the channel. A simulation of 8 mus length took about 5 min on an Intel Pentium 4 CPU with 3.2 GHz. We obtained good agreement with experimental data for the proton flux through gramicidin A over a wide range of pH values and membrane potentials. We find that proton desolvation as well as water rotations are equally important for the proton transfer through gramicidin A at physiological membrane potentials. Our method allows to simulate long-range charge transfer in biological systems at time scales, which are not accessible by other methods.
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Affiliation(s)
- Mirco S Till
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstr. 30, BGI, 95447 Bayreuth, Germany
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14
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Roy A, Taraphder S. Identification of Proton-Transfer Pathways in Human Carbonic Anhydrase II. J Phys Chem B 2007; 111:10563-76. [PMID: 17691838 DOI: 10.1021/jp073499t] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the probable proton-transfer pathways from the surface of human carbonic anhydrase II into the active site cavity through His-64 that has been widely implicated as a key residue along the proton-transfer path. A recursive analysis of hydrogen-bonded clusters in the static crystallographic structure shows that there is no complete path through His-64 in either of its experimentally detected conformations. Side chain conformational fluctuation of His-64 from its outward conformation toward the active site is found to provide a crucial dynamic connectivity needed to complete the path coupled to local reorganization of the protein structure and hydration. The energy and free energy barriers along the detected pathway have been estimated to derive the mechanism of His-64 rotation toward the active site. We also investigate a dynamical connectivity map that highlights networks of disordered water molecules that may promote a direct (and probably transient) access of the solvent to the active site. Our studies reveal how such solvent access channels may be related to the putative proton shuttle mediated by His-64. The paths thus identified can be potentially used as reaction coordinates for further studies on the molecular mechanism of enzyme action.
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Affiliation(s)
- Arijit Roy
- Department of Chemistry, Indian Institute of Technology, Kharagpur 721302, India
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15
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Friedman R, Fischer S, Nachliel E, Scheiner S, Gutman M. Minimum Energy Pathways for Proton Transfer between Adjacent Sites Exposed to Water. J Phys Chem B 2007; 111:6059-70. [PMID: 17488114 DOI: 10.1021/jp070781r] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The capacity to transfer protons between surface groups is an innate property of many proteins. The transfer of a proton between donor and acceptor, located as far as 6-7 A apart, necessitates the participation of water molecules in the process. In a previous study we investigated the mechanism of proton transfer (PT) between bulk exposed sites, a few ångströms apart, using as a model the proton exchange between the proton-binding sites of the fluorescein molecule in dilute aqueous solution.1 The present study expands the understanding of PT reactions between adjacent sites exposed to water through the calculation the minimum energy pathways (MEPs) by the conjugate peak refinement algorithm2 and a quantum-mechanical potential. The PT reaction trajectories were calculated for the fluorescein system with an increasing number of water molecules. The MEP calculations reveal that the transition state is highly strained and involves a supramolecular structure in which fluorescein and the interconnecting water molecules are covalently bonded together and the protons are shared between neighboring oxygens. These findings are in accord with the high activation energy, as measured for the reaction, and indicate that PT reactions on the surface proceed by a semi- or fully concerted rather than stepwise mechanism. A similar mechanism is assumed to be operative on the surface of proteins and renders water-mediated PT reactions as highly efficient as they are.
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Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, Tel Aviv University, Ramat Aviv, Tel Aviv, Israel.
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16
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Shutova T, Klimov VV, Andersson B, Samuelsson G. A cluster of carboxylic groups in PsbO protein is involved in proton transfer from the water oxidizing complex of Photosystem II. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2007; 1767:434-40. [PMID: 17336919 DOI: 10.1016/j.bbabio.2007.01.020] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2006] [Revised: 01/26/2007] [Accepted: 01/29/2007] [Indexed: 10/23/2022]
Abstract
The hypothesis presented here for proton transfer away from the water oxidation complex of Photosystem II (PSII) is supported by biochemical experiments on the isolated PsbO protein in solution, theoretical analyses of better understood proton transfer systems like bacteriorhodopsin and cytochrome oxidase, and the recently published 3D structure of PS II (Pdb entry 1S5L). We propose that a cluster of conserved glutamic and aspartic acid residues in the PsbO protein acts as a buffering network providing efficient acceptors of protons derived from substrate water molecules. The charge delocalization of the cluster ensures readiness to promptly accept the protons liberated from substrate water. Therefore protons generated at the catalytic centre of PSII need not be released into the thylakoid lumen as generally thought. The cluster is the beginning of a localized, fast proton transfer conduit on the lumenal side of the thylakoid membrane. Proton-dependent conformational changes of PsbO may play a role in the regulation of both supply of substrate water to the water oxidizing complex and the resultant proton transfer.
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Affiliation(s)
- Tatiana Shutova
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-90187 Umeå, Sweden.
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17
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Brändén M, Sandén T, Brzezinski P, Widengren J. Localized proton microcircuits at the biological membrane-water interface. Proc Natl Acad Sci U S A 2006; 103:19766-70. [PMID: 17172452 PMCID: PMC1750901 DOI: 10.1073/pnas.0605909103] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cellular processes such as nerve conduction, energy metabolism, and import of nutrients into cells all depend on transport of ions across biological membranes through specialized membrane-spanning proteins. Understanding these processes at a molecular level requires mechanistic insights into the interaction between these proteins and the membrane itself. To explore the role of the membrane in ion translocation we used an approach based on fluorescence correlation spectroscopy. Specifically, we investigated exchange of protons between the water phase and the membrane surface, as well as diffusion of protons along membrane surfaces, at a single-molecule level. We show that the lipid head groups collectively act as a proton-collecting antenna, dramatically accelerating proton uptake from water to a membrane-anchored proton acceptor. Furthermore, the results show that proton transfer along the surface can be significantly faster than that between the lipid head groups and the surrounding water phase. Thus, ion translocation across membranes and between the different membrane protein components is a complex interplay between the proteins and the membrane itself, where the membrane acts as a proton-conducting link between membrane-spanning proton transporters.
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Affiliation(s)
- Magnus Brändén
- *Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden; and
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Tor Sandén
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Peter Brzezinski
- *Department of Biochemistry and Biophysics, Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden; and
- To whom correspondence should be addressed. E-mail:
| | - Jerker Widengren
- Experimental Biomolecular Physics, Department of Applied Physics, Royal Institute of Technology, Albanova University Center, SE-106 91 Stockholm, Sweden
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Wraight CA. Chance and design—Proton transfer in water, channels and bioenergetic proteins. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:886-912. [PMID: 16934216 DOI: 10.1016/j.bbabio.2006.06.017] [Citation(s) in RCA: 285] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 06/07/2006] [Accepted: 06/13/2006] [Indexed: 12/17/2022]
Abstract
Proton transfer and transport in water, gramicidin and some selected channels and bioenergetic proteins are reviewed. An attempt is made to draw some conclusions about how Nature designs long distance, proton transport functionality. The prevalence of water rather than amino acid hydrogen bonded chains is noted, and the possible benefits of waters as the major component are discussed qualitatively.
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Affiliation(s)
- Colin A Wraight
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA.
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Bondar AN, Smith JC, Fischer S. Structural and energetic determinants of primary proton transfer in bacteriorhodopsin. Photochem Photobiol Sci 2006; 5:547-52. [PMID: 16761083 DOI: 10.1039/b516451f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the light-driven bacteriorhodopsin proton pump, the first proton transfer step is from the retinal Schiff base to a nearby carboxylate group. The mechanism of this transfer step is highly controversial, in particular whether a direct proton jump is allowed. Here, we review the structural and energetic determinants of the direct proton transfer path computed by using a combined quantum mechanical/molecular mechanical approach. Both protein flexibility and electrostatic interactions play an important role in shaping the proton transfer energy profile. Detailed analysis of the energetics of putative transitions in the first half of the photocycle focuses on two elements that determine the likelihood that a given configuration of the active site is populated during the proton-pumping cycle. First, the rate-limiting barrier for proton transfer must be consistent with the kinetics of the photocycle. Second, the active-site configuration must be compatible with a productive overall pumping cycle.
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Affiliation(s)
- Ana-Nicoleta Bondar
- Computational Molecular Biophysics, IWR, Heidelberg University, Im Neuenheimer Feld 368, Heidelberg, Germany
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