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Fufina TY, Vasilieva LG. Role of hydrogen-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. Biophys Rev 2023; 15:921-937. [PMID: 37974998 PMCID: PMC10643783 DOI: 10.1007/s12551-023-01109-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 08/01/2023] [Indexed: 11/19/2023] Open
Abstract
For the last decades, significant progress has been made in studying the biological functions of H-bond networks in membrane proteins, proton transporters, receptors, and photosynthetic reaction centers. Increasing availability of the X-ray crystal and cryo-electron microscopy structures of photosynthetic complexes resolved with high atomic resolution provides a platform for their comparative analysis. It allows identifying structural factors that are ensuring the high quantum yield of the photochemical reactions and are responsible for the stability of the membrane complexes. The H-bond networks are known to be responsible for proton transport associated with electron transfer from the primary to the secondary quinone as well as in the processes of water oxidation in photosystem II. Participation of such networks in reactions proceeding on the periplasmic side of bacterial photosynthetic reaction centers is less studied. This review summarizes the current understanding of the role of H-bond networks on the donor side of photosynthetic reaction centers from purple bacteria. It is discussed that the networks may be involved in providing close association with mobile electron carriers, in light-induced proton transport, in regulation of the redox properties of bacteriochlorophyll cofactors, and in stabilization of the membrane protein structure at the interface of membrane and soluble phases.
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Affiliation(s)
- T. Yu. Fufina
- Federal Research Center Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Str, 2, 142290 Pushchino, Russia
| | - L. G. Vasilieva
- Federal Research Center Pushchino Scientific Center for Biological Research, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya Str, 2, 142290 Pushchino, Russia
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2
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Allen JP, Chamberlain KD, Williams JC. Identification of amino acid residues in a proton release pathway near the bacteriochlorophyll dimer in reaction centers from Rhodobacter sphaeroides. PHOTOSYNTHESIS RESEARCH 2023; 155:23-34. [PMID: 36197600 DOI: 10.1007/s11120-022-00968-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 09/21/2022] [Indexed: 06/16/2023]
Abstract
Insight into control of proton transfer, a crucial attribute of cellular functions, can be gained from investigations of bacterial reaction centers. While the uptake of protons associated with the reduction of the quinone is well characterized, the release of protons associated with the oxidized bacteriochlorophyll dimer has been poorly understood. Optical spectroscopy and proton release/uptake measurements were used to examine the proton release characteristics of twelve mutant reaction centers, each containing a change in an amino acid residue near the bacteriochlorophyll dimer. The mutant reaction centers had optical spectra similar to wild-type and were capable of transferring electrons to the quinones after light excitation of the bacteriochlorophyll dimer. They exhibited a large range in the extent of proton release and in the slow recovery of the optical signal for the oxidized dimer upon continuous illumination. Key roles were indicated for six amino acid residues, Thr L130, Asp L155, Ser L244, Arg M164, Ser M190, and His M193. Analysis of the results points to a hydrogen-bond network that contains these residues, with several additional residues and bound water molecules, forming a proton transfer pathway. In addition to proton transfer, the properties of the pathway are proposed to be responsible for the very slow charge recombination kinetics observed after continuous illumination. The characteristics of this pathway are compared to proton transfer pathways near the secondary quinone as well as those found in photosystem II and cytochrome c oxidase.
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Affiliation(s)
- J P Allen
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA.
| | - K D Chamberlain
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
| | - J C Williams
- School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287-1604, USA
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3
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Wei RJ, Zhang Y, Mao J, Kaur D, Khaniya U, Gunner MR. Comparison of proton transfer paths to the Q A and Q B sites of the Rb. sphaeroides photosynthetic reaction centers. PHOTOSYNTHESIS RESEARCH 2022; 152:153-165. [PMID: 35344134 DOI: 10.1007/s11120-022-00906-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 02/18/2022] [Indexed: 06/14/2023]
Abstract
The photosynthetic bacterial reaction centers from purple non-sulfur bacteria use light energy to drive the transfer of electrons from cytochrome c to ubiquinone. Ubiquinone bound in the QA site cycles between quinone, QA, and anionic semiquinone, QA·-, being reduced once and never binding protons. In the QB site, ubiquinone is reduced twice by QA·-, binds two protons and is released into the membrane as the quinol, QH2. The network of hydrogen bonds formed in a molecular dynamics trajectory was drawn to investigate proton transfer pathways from the cytoplasm to each quinone binding site. QA is isolated with no path for protons to enter from the surface. In contrast, there is a complex and tangled network requiring residues and waters that can bring protons to QB. There are three entries from clusters of surface residues centered around HisH126, GluH224, and HisH68. The network is in good agreement with earlier studies, Mutation of key nodes in the network, such as SerL223, were previously shown to slow proton delivery. Mutational studies had also shown that double mutations of residues such as AspM17 and AspL210 along multiple paths in the network presented here slow the reaction, while single mutations do not. Likewise, mutation of both HisH126 and HisH128, which are at the entry to two paths reduce the rate of proton uptake.
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Affiliation(s)
- Rongmei Judy Wei
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, NY, 10016, USA
- Department of Physics, City College of New York, New York, NY, 10031, USA
| | - Yingying Zhang
- Department of Physics, City College of New York, New York, NY, 10031, USA
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - Junjun Mao
- Department of Physics, City College of New York, New York, NY, 10031, USA
| | - Divya Kaur
- Department of Chemistry, Brock University, 500 Glenridge Avenue, St. Catharines, ON, L2S 3A1, Canada
| | - Umesh Khaniya
- Department of Physics, City College of New York, New York, NY, 10031, USA
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA
| | - M R Gunner
- Ph.D. Program in Chemistry, The Graduate Center, City University of New York, New York, NY, 10016, USA.
- Department of Physics, City College of New York, New York, NY, 10031, USA.
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, New York, NY, 10016, USA.
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4
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Gorka M, Cherepanov DA, Semenov AY, Golbeck JH. Control of electron transfer by protein dynamics in photosynthetic reaction centers. Crit Rev Biochem Mol Biol 2020; 55:425-468. [PMID: 32883115 DOI: 10.1080/10409238.2020.1810623] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Trehalose and glycerol are low molecular mass sugars/polyols that have found widespread use in the protection of native protein states, in both short- and long-term storage of biological materials, and as a means of understanding protein dynamics. These myriad uses are often attributed to their ability to form an amorphous glassy matrix. In glycerol, the glass is formed only at cryogenic temperatures, while in trehalose, the glass is formed at room temperature, but only upon dehydration of the sample. While much work has been carried out to elucidate a mechanistic view of how each of these matrices interact with proteins to provide stability, rarely have the effects of these two independent systems been directly compared to each other. This review aims to compile decades of research on how different glassy matrices affect two types of photosynthetic proteins: (i) the Type II bacterial reaction center from Rhodobacter sphaeroides and (ii) the Type I Photosystem I reaction center from cyanobacteria. By comparing aggregate data on electron transfer, protein structure, and protein dynamics, it appears that the effects of these two distinct matrices are remarkably similar. Both seem to cause a "tightening" of the solvation shell when in a glassy state, resulting in severely restricted conformational mobility of the protein and associated water molecules. Thus, trehalose appears to be able to mimic, at room temperature, nearly all of the effects on protein dynamics observed in low temperature glycerol glasses.
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Affiliation(s)
- Michael Gorka
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA
| | - Dmitry A Cherepanov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Alexey Yu Semenov
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.,Department of Chemistry, The Pennsylvania State University, University Park, PA, USA
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Espiritu E, Olson TL, Williams JC, Allen JP. Binding and Energetics of Electron Transfer between an Artificial Four-Helix Mn-Protein and Reaction Centers from Rhodobacter sphaeroides. Biochemistry 2017; 56:6460-6469. [PMID: 29131579 DOI: 10.1021/acs.biochem.7b00978] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability of an artificial four-helix bundle Mn-protein, P1, to bind and transfer an electron to photosynthetic reaction centers from the purple bacterium Rhodobacter sphaeroides was characterized using optical spectroscopy. Upon illumination of reaction centers, an electron is transferred from P, the bacteriochlorophyll dimer, to QA, the primary electron acceptor. The P1 Mn-protein can bind to the reaction center and reduce the oxidized bacteriochlorophyll dimer, P+, with a dissociation constant of 1.2 μM at pH 9.4, comparable to the binding constant of c-type cytochromes. Amino acid substitutions of surface residues on the Mn-protein resulted in increases in the dissociation constant to 8.3 μM. The extent of reduction of P+ by the P1 Mn-protein was dependent on the P/P+ midpoint potential and the pH. Analysis of the free energy difference yielded a midpoint potential of approximately 635 mV at pH 9.4 for the Mn cofactor of the P1 Mn-protein, a value similar to those found for other Mn cofactors in proteins. The linear dependence of -56 mV/pH is consistent with one proton being released upon Mn oxidation, allowing the complex to maintain overall charge neutrality. These outcomes demonstrate the feasibility of designing four-helix bundles and other artificial metalloproteins to bind and transfer electrons to bacterial reaction centers and establish the usefulness of this system as a platform for designing sites to bind novel metal cofactors capable of performing complex oxidation-reduction reactions.
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Affiliation(s)
- Eduardo Espiritu
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - Tien L Olson
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - JoAnn C Williams
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
| | - James P Allen
- School of Molecular Sciences, Arizona State University , Tempe, Arizona 85287-1604, United States
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Electrostatics of the photosynthetic bacterial reaction center. Protonation of Glu L 212 and Asp L 213 — A new method of calculation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015. [DOI: 10.1016/j.bbabio.2015.07.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Maróti Á, Wraight CA, Maróti P. Protonated rhodosemiquinone at the Q(B) binding site of the M265IT mutant reaction center of photosynthetic bacterium Rhodobacter sphaeroides. Biochemistry 2015; 54:2095-103. [PMID: 25760888 DOI: 10.1021/bi501553t] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The second electron transfer from primary ubiquinone Q(A) to secondary ubiquinone Q(B) in the reaction center (RC) from Rhodobacter sphaeroides involves a protonated Q(B)(-) intermediate state whose low pK(a) makes direct observation impossible. Here, we replaced the native ubiquinone with low-potential rhodoquinone at the Q(B) binding site of the M265IT mutant RC. Because the in situ midpoint redox potential of Q(A) of this mutant was lowered approximately the same extent (≈100 mV) as that of Q(B) upon exchange of ubiquinone with low-potential rhodoquinone, the inter-quinone (Q(A) → Q(B)) electron transfer became energetically favorable. After subsequent saturating flash excitations, a period of two damped oscillations of the protonated rhodosemiquinone was observed. The Q(B)H(•) was identified by (1) the characteristic band at 420 nm of the absorption spectrum after the second flash and (2) weaker damping of the oscillation at 420 nm (due to the neutral form) than at 460 nm (attributed to the anionic form). The appearance of the neutral semiquinone was restricted to the acidic pH range, indicating a functional pK(a) of <5.5, slightly higher than that of the native ubisemiquinone (pK(a) < 4.5) at pH 7. The analysis of the pH and temperature dependencies of the rates of the second electron transfer supports the concept of the pH-dependent pK(a) of the semiquinone at the Q(B) binding site. The local electrostatic potential is severely modified by the strongly interacting neighboring acidic cluster, and the pK(a) of the semiquinone is in the middle of the pH range of the complex titration. The kinetic and thermodynamic data are discussed according to the proton-activated electron transfer mechanism combined with the pH-dependent functional pK(a) of the semiquinone at the Q(B) site of the RC.
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Affiliation(s)
| | - Colin A Wraight
- §Center for Biophysics and Computational Biology and Department of Plant Biology, University of Illinois, Urbana, Illinois 61801-3838, United States
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8
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Computer modeling of electron and proton transport in chloroplasts. Biosystems 2014; 121:1-21. [PMID: 24835748 DOI: 10.1016/j.biosystems.2014.04.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2014] [Revised: 04/27/2014] [Accepted: 04/28/2014] [Indexed: 11/21/2022]
Abstract
Photosynthesis is one of the most important biological processes in biosphere, which provides production of organic substances from atmospheric CO2 and water at expense of solar energy. In this review, we contemplate computer models of oxygenic photosynthesis in the context of feedback regulation of photosynthetic electron transport in chloroplasts, the energy-transducing organelles of the plant cell. We start with a brief overview of electron and proton transport processes in chloroplasts coupled to ATP synthesis and consider basic regulatory mechanisms of oxygenic photosynthesis. General approaches to computer simulation of photosynthetic processes are considered, including the random walk models of plastoquinone diffusion in thylakoid membranes and deterministic approach to modeling electron transport in chloroplasts based on the mass action law. Then we focus on a kinetic model of oxygenic photosynthesis that includes key stages of the linear electron transport, alternative pathways of electron transfer around photosystem I (PSI), transmembrane proton transport and ATP synthesis in chloroplasts. This model includes different regulatory processes: pH-dependent control of the intersystem electron transport, down-regulation of photosystem II (PSII) activity (non-photochemical quenching), the light-induced activation of the Bassham-Benson-Calvin (BBC) cycle. The model correctly describes pH-dependent feedback control of electron transport in chloroplasts and adequately reproduces a variety of experimental data on induction events observed under different experimental conditions in intact chloroplasts (variations of CO2 and O2 concentrations in atmosphere), including a complex kinetics of P700 (primary electron donor in PSI) photooxidation, CO2 consumption in the BBC cycle, and photorespiration. Finally, we describe diffusion-controlled photosynthetic processes in chloroplasts within the framework of the model that takes into account complex architecture of chloroplasts and lateral heterogeneity of lamellar system of thylakoids. The lateral profiles of pH in the thylakoid lumen and in the narrow gap between grana thylakoids have been calculated under different metabolic conditions. Analyzing topological aspects of diffusion-controlled stages of electron and proton transport in chloroplasts, we conclude that along with the NPQ mechanism of attenuation of PSII activity and deceleration of PQH2 oxidation by the cytochrome b6f complex caused by the lumen acidification, the intersystem electron transport may be down-regulated due to the light-induced alkalization of the narrow partition between adjacent thylakoids of grana. The computer models of electron and proton transport described in this article may be integrated as appropriate modules into a comprehensive model of oxygenic photosynthesis.
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Okamura M. George Feher: a pioneer in reaction center research. PHOTOSYNTHESIS RESEARCH 2014; 120:29-42. [PMID: 24104959 DOI: 10.1007/s11120-013-9927-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 09/16/2013] [Indexed: 06/02/2023]
Abstract
Our understanding of photosynthesis has been greatly advanced by the elucidation of the structure and function of the reaction center (RC), the membrane protein responsible for the initial light-induced charge separation in photosynthetic bacteria and green plants. Although today we know a great deal about the details of the primary processes in photosynthesis, little was known in the early days. George Feher made pioneering contributions to photosynthesis research in characterizing RCs from photosynthetic bacteria following the ground-breaking work of Lou Duysens and Rod Clayton (see articles in this issue by van Gorkom and Wraight). The work in his laboratory at the University of California, San Diego, started in the late 1960s and continued for over 30 years. He isolated a pure RC protein and used magnetic resonance spectroscopy to study the primary reactants. Following this pioneering work, Feher studied the detailed structure of the RC and the basic electron and proton transfer functions that it performs using a wide variety of biophysical and biochemical techniques. These studies, together with work from many other researchers, have led to our present detailed understanding of these proteins and their function in photosynthesis. The present article is a brief historical account of his pioneering contributions to photosynthesis research. A more detailed description of his work can be found in an earlier biographical paper (Feher in Photosynth Res 55:1-40, 1998a).
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Affiliation(s)
- Melvin Okamura
- Department of Physics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093-0354, USA,
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Proton Binding Is Part of Protein Relaxation of Flash-Excited Reaction Center from Photosynthetic BacteriaRhodobacter sphaeroides. Isr J Chem 2013. [DOI: 10.1002/ijch.199900050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Onidas D, Sipka G, Asztalos E, Maróti P. Mutational control of bioenergetics of bacterial reaction center probed by delayed fluorescence. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1191-9. [PMID: 23685111 DOI: 10.1016/j.bbabio.2013.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 05/01/2013] [Accepted: 05/09/2013] [Indexed: 10/26/2022]
Abstract
The free energy gap between the metastable charge separated state P(+)QA(-) and the excited bacteriochlorophyll dimer P* was measured by delayed fluorescence of the dimer in mutant reaction center proteins of the photosynthetic bacterium Rhodobacter sphaeroides. The mutations were engineered both at the donor (L131L, M160L, M197F and M202H) and acceptor (M265I and M234E) sides. While the donor side mutations changed systematically the number of H-bonds to P, the acceptor side mutations modified the energetics of QA by altering the van-der-Waals and electronic interactions (M265IT) and H-bond network to the acidic cluster around QB (M234EH, M234EL, M234EA and M234ER). All mutants decreased the free energy gap of the wild type RC (~890meV), i.e. destabilized the P(+)QA(-) charge pair by 60-110meV at pH8. Multiple modifications in the hydrogen bonding pattern to P resulted in systematic changes of the free energy gap. The destabilization showed no pH-dependence (M234 mutants) or slight increase (WT, donor-side mutants and M265IT above pH8) with average slope of 10-15meV/pH unit over the 6-10.5pH range. In wild type and donor-side mutants, the free energy change of the charge separation consisted of mainly enthalpic term but the acceptor side mutants showed increased entropic (even above that of enthalpic) contributions. This could include softening the structure of the iron ligand (M234EH) and the QA binding pocket (M265IT) and/or increase of the multiplicity of the electron transfer of charge separation in the acceptor side upon mutation.
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Affiliation(s)
- Delphine Onidas
- Laboratoire de Chimie Physique UMR 8000, Batiment 350, Orsay-Cedex, Université de Paris-Sud, 91405, France
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12
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Gibasiewicz K, Pajzderska M, Potter JA, Fyfe PK, Dobek A, Brettel K, Jones MR. Mechanism of recombination of the P+H(A)- radical pair in mutant Rhodobacter sphaeroides reaction centers with modified free energy gaps between P+B(A)- and P+H(A)-. J Phys Chem B 2011; 115:13037-50. [PMID: 21970763 DOI: 10.1021/jp206462g] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The kinetics of recombination of the P(+)H(A)(-) radical pair were compared in wild-type reaction centers from Rhodobacter sphaeroides and in seven mutants in which the free energy gap, ΔG, between the charge separated states P(+)B(A)(-) and P(+)H(A)(-) was either increased or decreased. Five of the mutant RCs had been described previously, and X-ray crystal structures of two newly constructed complexes were determined by X-ray crystallography. The charge recombination reaction was accelerated in all mutants with a smaller ΔG than in the wild-type, and was slowed in a mutant having a larger ΔG. The free energy difference between the state P(+)H(A)(-) and the PH(A) ground state was unaffected by most of these mutations. These observations were consistent with a model in which the P(+)H(A)(-) → PH(A) charge recombination is thermally activated and occurs via the intermediate state P(+)B(A)(-), with a mean rate related to the size of the ΔG between the states P(+)B(A)(-) and P(+)H(A)(-) and not the ΔG between P(+)H(A)(-) and the ground state. A more detailed analysis of charge recombination in the mutants showed that the kinetics of the reaction were multiexponential, and characterized by ~0.5, ~1-3, and 7-17 ns lifetimes, similar to those measured for wild-type reaction centers. The exact lifetimes and relative amplitudes of the three components were strongly modulated by the mutations. Two models were considered in order to explain the observed multiexponentiality and modulation, involving heterogeneity or relaxation of P(+)H(A)(-) states, with the latter model giving a better fit to the experimental results.
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Deshmukh SS, Akhavein H, Williams JC, Allen JP, Kálmán L. Light-Induced Conformational Changes in Photosynthetic Reaction Centers: Impact of Detergents and Lipids on the Electronic Structure of the Primary Electron Donor. Biochemistry 2011; 50:5249-62. [DOI: 10.1021/bi200595z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- S. S. Deshmukh
- Department of Physics, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - H. Akhavein
- Department of Physics, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - J. C. Williams
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, 85287-1604, United States
| | - J. P. Allen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona, 85287-1604, United States
| | - L. Kálmán
- Department of Physics, Concordia University, Montreal, Quebec H4B 1R6, Canada
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Deshmukh SS, Williams JC, Allen JP, Kálmán L. Light-Induced Conformational Changes in Photosynthetic Reaction Centers: Redox-Regulated Proton Pathway near the Dimer. Biochemistry 2011; 50:3321-31. [DOI: 10.1021/bi200169y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sasmit S. Deshmukh
- Department of Physics, Concordia University, Montreal, Quebec H4B 1R6, Canada
| | - JoAnn C. Williams
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - James P. Allen
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, Arizona 85287-1604, United States
| | - László Kálmán
- Department of Physics, Concordia University, Montreal, Quebec H4B 1R6, Canada
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The local electric field within phospholipid membranes modulates the charge transfer reactions in reaction centres. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1039-49. [DOI: 10.1016/j.bbabio.2009.03.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2009] [Revised: 03/03/2009] [Accepted: 03/05/2009] [Indexed: 11/19/2022]
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Cheap H, Bernad S, Derrien V, Gerencsér L, Tandori J, de Oliveira P, Hanson DK, Maróti P, Sebban P. M234Glu is a component of the proton sponge in the reaction center from photosynthetic bacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1505-15. [PMID: 19632193 DOI: 10.1016/j.bbabio.2009.07.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 07/13/2009] [Accepted: 07/15/2009] [Indexed: 10/20/2022]
Abstract
Bacterial reaction centers use light energy to couple the uptake of protons to the successive semi-reduction of two quinones, namely Q(A) and Q(B). These molecules are situated symmetrically in regard to a non-heme iron atom. Four histidines and one glutamic acid, M234Glu, constitute the five ligands of this atom. By flash-induced absorption spectroscopy and delayed fluorescence we have studied in the M234EH and M234EL variants the role played by this acidic residue on the energetic balance between the two quinones as well as in proton uptake. Delayed fluorescence from the P(+)Q(A)(-) state (P is the primary electron donor) and temperature dependence of the rate of P(+)Q(A)(-) charge recombination that are in good agreement show that in the two RC variants, both Q(A)(-) and Q(B)(-) are destabilized by about the same free energy amount: respectively approximately 100 +/- 5 meV and 90 +/- 5 meV for the M234EH and M234EL variants, as compared to the WT. Importantly, in the M234EH and M234EL variants we observe a collapse of the high pH band (present in the wild-type reaction center) of the proton uptake amplitudes associated with formation of Q(A)(-) and Q(B)(-). This band has recently been shown to be a signature of a collective behaviour of an extended, multi-entry, proton uptake network. M234Glu seems to play a central role in the proton sponge-like system formed by the RC protein.
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Affiliation(s)
- Hélène Cheap
- Laboratoire de Chimie Physique, UMR 8000, University of Paris-Sud 11/CNRS, 91405 cedex, France
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Iwata T, Paddock ML, Okamura MY, Kandori H. Identification of FTIR bands due to internal water molecules around the quinone binding sites in the reaction center from Rhodobacter sphaeroides. Biochemistry 2009; 48:1220-9. [PMID: 19161296 DOI: 10.1021/bi801990s] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial reaction center (RC) is a membrane protein complex that performs photosynthetic electron transfer from a bacteriochlorophyll dimer to quinone acceptors Q(A) and Q(B). Q(B) accepts electrons from the primary quinone, Q(A), in two sequential electron transfer reactions coupled to uptake of a proton from solution. It has been suggested that water molecules along the proton uptake pathway are protonated upon quinone reduction on the basis of FTIR difference spectra [Breton, J., and Nabedryk, E. (1998) Photosynth. Res. 55, 301-307]. We examined the possible involvement of water molecules in the photoreaction processes by studying (18)O water isotope effects on FTIR difference spectra resulting from formation of Q(A)(-) and Q(B)(-). Continuum bands in D(2)O due to Q(B)(-) formation in the 2300-1800 cm(-1) region did not show spectral shifts by (18)O water in the wild-type (WT) RC, suggesting that these bands do not originate from (protonated) water. In contrast, the Q(B)(-)/Q(B) spectrum of the EQ-L212 mutant RC showed a spectral shift of a band near 2100 cm(-1) due to (18)O water substitution, consistent with protonation of internal water. FTIR shifts due to (18)O water were also observed following formation of Q(A)(-) and Q(B)(-) in the spectral region of 3700-3500 cm(-1) characteristic of weakly hydrogen bonded water. The water responsible for the Q(B)(-) change was localized near Glu-L212 by spectral shifts in mutant RCs. The weakly hydrogen bonded water perturbed by quinone reduction may play a role in stabilizing the charge-separated state.
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Affiliation(s)
- Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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Krammer EM, Till MS, Sebban P, Ullmann GM. Proton-transfer pathways in photosynthetic reaction centers analyzed by profile hidden markov models and network calculations. J Mol Biol 2009; 388:631-43. [PMID: 19285988 DOI: 10.1016/j.jmb.2009.03.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 03/05/2009] [Accepted: 03/08/2009] [Indexed: 11/28/2022]
Abstract
In the bacterial reaction center (bRC) of Rhodobacter sphaeroides, the key residues of proton transfer to the secondary quinone (Q(B)) are known. Also, several possible proton entry points and proton-transfer pathways have been proposed. However, the mechanism of the proton transfer to Q(B) remains unclear. The proton transfer to Q(B) in the bRC of Blastochloris viridis is less explored. To analyze whether the bRCs of different species use the same key residues for proton transfer to Q(B), we determined the conservation of these residues. We performed a multiple-sequence alignment based on profile hidden Markov models. Residues involved in proton transfer but not located at the protein surface are conserved or are only exchanged to functionally similar amino acids, whereas potential proton entry points are not conserved to the same extent. The analysis of the hydrogen-bond network of the bRC from R. sphaeroides and that from B. viridis showed that a large network connects Q(B) with the cytoplasmic region in both bRCs. For both species, all non-surface key residues are part of the network. However, not all proton entry points proposed for the bRC of R. sphaeroides are included in the network in the bRC of B. viridis. From our analysis, we could identify possible proton entry points. These proton entry points differ between the two bRCs. Together, the results of the conservation analysis and the hydrogen-bond network analysis make it likely that the proton transfer to Q(B) is not mediated by distinct pathways but by a large hydrogen-bond network.
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Affiliation(s)
- Eva-Maria Krammer
- Structural Biology/Bioinformatics, University of Bayreuth, Universitätsstrasse 30, BGI, Bayreuth, Germany
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Nabedryk E, Breton J. Coupling of electron transfer to proton uptake at the QB site of the bacterial reaction center: A perspective from FTIR difference spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1229-48. [DOI: 10.1016/j.bbabio.2008.06.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2008] [Revised: 06/26/2008] [Accepted: 06/27/2008] [Indexed: 01/09/2023]
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20
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The redox midpoint potential of the primary quinone of reaction centers in chromatophores of Rhodobacter sphaeroides is pH independent. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:1207-17. [DOI: 10.1007/s00249-008-0301-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2007] [Revised: 02/11/2008] [Accepted: 03/02/2008] [Indexed: 10/22/2022]
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21
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Gibasiewicz K, Pajzderska M. Primary Radical Pair P+H- Lifetime in Rhodobacter sphaeroides with Blocked Electron Transfer to QA. Effect of o-Phenanthroline. J Phys Chem B 2008; 112:1858-65. [DOI: 10.1021/jp075184j] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Krzysztof Gibasiewicz
- Department of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614 Poznań, Poland
| | - Maria Pajzderska
- Department of Physics, Adam Mickiewicz University, ul. Umultowska 85, 61-614 Poznań, Poland
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22
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Koepke J, Krammer EM, Klingen AR, Sebban P, Ullmann GM, Fritzsch G. pH modulates the quinone position in the photosynthetic reaction center from Rhodobacter sphaeroides in the neutral and charge separated states. J Mol Biol 2007; 371:396-409. [PMID: 17570397 DOI: 10.1016/j.jmb.2007.04.082] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Revised: 04/05/2007] [Accepted: 04/17/2007] [Indexed: 11/30/2022]
Abstract
The structure of the photosynthetic reaction-center from Rhodobacter sphaeroides has been determined at four different pH values (6.5, 8.0, 9.0, 10.0) in the neutral and in charge separated states. At pH 8.0, in the neutral state, we obtain a resolution of 1.87 A, which is the best ever reported for the bacterial reaction center protein. Our crystallographic data confirm the existence of two different binding positions of the secondary quinone (QB). We observe a new orientation of QB in its distal position, which shows no ring-flip compared to the orientation in the proximal position. Datasets collected for the different pH values show a pH-dependence of the population of the proximal position. The new orientation of QB in the distal position and the pH-dependence could be confirmed by continuum electrostatics calculations. Our calculations are in agreement with the experimentally observed proton uptake upon charge separation. The high resolution of our crystallographic data allows us to identify new water molecules and external residues being involved in two previously described hydrogen bond proton channels. These extended proton-transfer pathways, ending at either of the two oxo-groups of QB in its proximal position, provide additional evidence that ring-flipping is not required for complete protonation of QB upon reduction.
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Affiliation(s)
- Juergen Koepke
- Max Planck Institute of Biophysics, Department of Molecular Membrane Biology, Max-von-Laue Strasse 3, D-60438 Frankfurt/Main, Germany.
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23
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Tandori J, Miksovska J, Valerio-Lepiniec M, Schiffer M, Maróti P, Hanson DK, Sebban P. Proton Uptake of Rhodobacter capsulatus Reaction Center Mutants Modified in the Primary Quinone Environment ¶dagger;. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2002)0750126puorcr2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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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: 286] [Impact Index Per Article: 15.9] [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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25
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Maklashina E, Hellwig P, Rothery RA, Kotlyar V, Sher Y, Weiner JH, Cecchini G. Differences in protonation of ubiquinone and menaquinone in fumarate reductase from Escherichia coli. J Biol Chem 2006; 281:26655-64. [PMID: 16829675 DOI: 10.1074/jbc.m602938200] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Escherichia coli quinol-fumarate reductase operates with both natural quinones, ubiquinone (UQ) and menaquinone (MQ), at a single quinone binding site. We have utilized a combination of mutagenesis, kinetic, EPR, and Fourier transform infrared methods to study the role of two residues, Lys-B228 and Glu-C29, at the quinol-fumarate reductase quinone binding site in reactions with MQ and UQ. The data demonstrate that Lys-B228 provides a strong hydrogen bond to MQ and is essential for reactions with both quinone types. Substitution of Glu-C29 with Leu and Phe caused a dramatic decrease in enzymatic reactions with MQ in agreement with previous studies, however, the succinate-UQ reductase reaction remains unaffected. Elimination of a negative charge in Glu-C29 mutant enzymes resulted in significantly increased stabilization of both UQ-* and MQ-* semiquinones. The data presented here suggest similar hydrogen bonding of the C1 carbonyl of both MQ and UQ, whereas there is different hydrogen bonding for their C4 carbonyls. The differences are shown by a single point mutation of Glu-C29, which transforms the enzyme from one that is predominantly a menaquinol-fumarate reductase to one that is essentially only functional as a succinate-ubiquinone reductase. These findings represent an example of how enzymes that are designed to accommodate either UQ or MQ at a single Q binding site may nevertheless develop sufficient plasticity at the binding pocket to react differently with MQ and UQ.
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Affiliation(s)
- Elena Maklashina
- Molecular Biology Division, Veterans Affairs Medical Center, San Francisco, California, 94121, USA
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26
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Mulkidjanian AY, Cherepanov DA. Probing biological interfaces by tracing proton passage across them. Photochem Photobiol Sci 2006; 5:577-87. [PMID: 16761086 DOI: 10.1039/b516443e] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The properties of water at the surface, especially at an electrically charged one, differ essentially from those in the bulk phase. Here we survey the traits of surface water as inferred from proton pulse experiments with membrane enzymes. In such experiments, protons that are ejected (or captured) by light-triggered enzymes are traced on their way between the membrane surface and the bulk aqueous phase. In several laboratories it has been shown that proton exchange between the membrane surface and the bulk aqueous phase takes as much as about 1 ms, but could be accelerated by added mobile pH-buffers. Since the accelerating capacity of the latter decreased with increase in their electric charge, it was suggested that the membrane surface is separated from the bulk aqueous phase by a barrier of electrostatic nature. In terms of ordinary electrostatics, the barrier could be ascribed to dielectric saturation of water at a charged surface. In terms of nonlocal electrostatics, the barrier could result from the dielectric overscreening in the surface water layers. It is discussed how the interfacial potential barrier can affect the reactions at interface, especially those coupled with biological energy conversion and membrane transport.
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Affiliation(s)
- Armen Y Mulkidjanian
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119899, Russia.
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27
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Mulkidjanian AY, Heberle J, Cherepanov DA. Protons @ interfaces: implications for biological energy conversion. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:913-30. [PMID: 16624250 DOI: 10.1016/j.bbabio.2006.02.015] [Citation(s) in RCA: 143] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2005] [Revised: 02/09/2006] [Accepted: 02/16/2006] [Indexed: 12/01/2022]
Abstract
The review focuses on the anisotropy of proton transfer at the surface of biological membranes. We consider (i) the data from "pulsed" experiments, where light-triggered enzymes capture or eject protons at the membrane surface, (ii) the electrostatic properties of water at charged interfaces, and (iii) the specific structural attributes of proton-translocating enzymes. The pulsed experiments revealed that proton exchange between the membrane surface and the bulk aqueous phase takes as much as about 1 ms, but could be accelerated by added mobile pH-buffers. Since the accelerating capacity of the latter decreased with the increase in their electric charge, it was concluded that the membrane surface is separated from the bulk aqueous phase by a barrier of electrostatic nature. The barrier could arise owing to the water polarization at the negatively charged membrane surface. The barrier height depends linearly on the charge of penetrating ions; for protons, it has been estimated as about 0.12 eV. While the proton exchange between the surface and the bulk aqueous phase is retarded by the interfacial barrier, the proton diffusion along the membrane, between neighboring enzymes, takes only microseconds. The proton spreading over the membrane is facilitated by the hydrogen-bonded networks at the surface. The membrane-buried layers of these networks can eventually serve as a storage/buffer for protons (proton sponges). As the proton equilibration between the surface and the bulk aqueous phase is slower than the lateral proton diffusion between the "sources" and "sinks", the proton activity at the membrane surface, as sensed by the energy transducing enzymes at steady state, might deviate from that measured in the adjoining water phase. This trait should increase the driving force for ATP synthesis, especially in the case of alkaliphilic bacteria.
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Affiliation(s)
- Armen Y Mulkidjanian
- AN Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow, Russia.
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28
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Takahashi E, Wraight CA. Small weak acids reactivate proton transfer in reaction centers from Rhodobacter sphaeroides mutated at AspL210 and AspM17. J Biol Chem 2005; 281:4413-22. [PMID: 16354664 DOI: 10.1074/jbc.m511359200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In reaction centers of Rhodobacter sphaeroides, site-directed mutagenesis has implicated several acidic residues in the delivery of protons to the secondary quinone (Q(B)) during reduction to quinol. In a double mutant (Asp(L210) --> Asn + Asp(M17) --> Asn) that is severely impaired in proton transfer capability over a wide pH range, proton transfer was "rescued" by added weak acids. For low pK(a) acids the total concentration of salt required near neutral pH was high. The ionic strength effect of added salts stimulated the rate of proton-coupled electron transfer at pH < 7, but decreased it at pH > 7.5, indicating an effective isoelectric point between these limits. In this region, a substantial rate enhancement by weak acids was clearly evident. A Brønsted plot of activity versus pK(a) of the rescuing acids was linear, with a slope of -1, and extrapolated to a diffusion-limited rate at pK(a)(app) approximately 1. However, the maximum rate at saturating concentrations of acid did not correlate with pK(a), indicating that the acid and anion species compete for binding, both with weak affinity. This model predicts that pK(a)(app) corresponds to a true pK(a) = 4-5, similar to that for a carboxylic acid or Q(B)(-), itself. Only rather small, neutral acids were active, indicating a need to access a small internal volume, suggested to be a proton channel to the Q(B) domain. However, the on-rates were near the diffusion limit. The implications for intraprotein proton transfer pathway design are discussed.
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Affiliation(s)
- Eiji Takahashi
- Department of Biochemistry and Center for Biophysics and Computational Biology, University of Illinois, Urbana-Champaign, 61801, USA
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29
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Mulkidjanian AY, Kozlova MA, Cherepanov DA. Ubiquinone reduction in the photosynthetic reaction centre of Rhodobacter sphaeroides: interplay between electron transfer, proton binding and flips of the quinone ring. Biochem Soc Trans 2005; 33:845-50. [PMID: 16042612 DOI: 10.1042/bst0330845] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This review is focused on reactions that gate (control) the electron transfer between the primary quinone QA and secondary quinone QB in the photosynthetic reaction centre of Rhodobacter sphaeroides. The results on electron and proton transfer are discussed in relation to structural information and to the steered molecular dynamics simulations of the QB ring flip in its binding pocket. Depending on the initial position of QB in the pocket and on certain conditions, the rate of electron transfer is suggested to be limited either by the quinone ring flip or by the charge-compensating proton equilibration between the surface and the buried QB site.
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Affiliation(s)
- A Y Mulkidjanian
- A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119899, Moscow, Russia.
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30
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Utschig LM, Astashkin AV, Raitsimring AM, Thurnauer MC, Poluektov OG. Pulsed EPR/ENDOR Characterization of the Cu2+ Surface Site in Photosynthetic Bacterial Reaction Centers. J Phys Chem B 2004. [DOI: 10.1021/jp037730o] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- L. M. Utschig
- Chemistry Division, Argonne National Laboratory, Argonne, Illinois 60439, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - A. V. Astashkin
- Chemistry Division, Argonne National Laboratory, Argonne, Illinois 60439, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - A. M. Raitsimring
- Chemistry Division, Argonne National Laboratory, Argonne, Illinois 60439, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - M. C. Thurnauer
- Chemistry Division, Argonne National Laboratory, Argonne, Illinois 60439, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
| | - O. G. Poluektov
- Chemistry Division, Argonne National Laboratory, Argonne, Illinois 60439, and Department of Chemistry, University of Arizona, Tucson, Arizona 85721
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31
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Moser CC, Page CC, Cogdell RJ, Barber J, Wraight CA, Dutton PL. Length, time, and energy scales of photosystems. ADVANCES IN PROTEIN CHEMISTRY 2003; 63:71-109. [PMID: 12629967 DOI: 10.1016/s0065-3233(03)63004-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The design of photosynthetic systems reflects the length scales of the fundamental physical processes. Energy transfer is rapid at the few angstrom scale and continues to be rapid even at the 50-A scale of the membrane thickness. Electron tunneling is nearly as rapid at the shortest distances, but becomes physiologically too slow well before 20 A. Diffusion, which starts out at a relatively slow nanosecond time scale, has the most modest slowing with distance and is physiologically competent at all biologically relevant distances. Proton transfer always operates on the shortest angstrom scale. The structural consequences of these distance dependencies are that energy transfer networks can extend over large, multisubunit and multicomplex distances and take leaps of 20 A before entering the domain of charge separating centers. Electron transfer systems are effectively limited to individual distances of 15 A or less and span the 50 A dimensions of the bioenergetic membrane by use of redox chains. Diffusion processes are generally used to cover the intercomplex electron transfer distances of 50 A and greater and tend to compensate for the lack of directionality by restricting the diffusional space to the membrane or the membrane surface, and by multiplying the diffusing species through the use of pools. Proton transfer reactions act over distances larger than a few angstroms through the use of clusters or relays, which sometimes rely on water molecules and which may only be dynamically assembled. Proteins appear to place a premium on robustness of design, which is relatively easily achieved in the long-distance physical processes of energy transfer and electron tunneling. By placing cofactors close enough, the physical process is relatively rapid compared to decay processes. Thus suboptimal conditions such as cofactor orientation, energy level, or redox potential level can be tolerated and generally do not have to be finely tuned. The most fragile regions of design tend to come in areas of complex formation and catalysis involving proton management, where relatively small changes in distance or mutations can lead to a dramatic decrease in turnover, which may already be limiting the overall speed of energy conversion in these proteins. Light-activated systems also face a challenge to robust function from the ever-present dangers of high redox potential chemistry. This can turn the protein matrix and wandering oxygen molecules into unintentional redox partners, which in the case of PSII requires the frequent, costly replacement of protein subunits.
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Affiliation(s)
- Christopher C Moser
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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32
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Kálmán L, Williams JC, Allen JP. Proton release upon oxidation of tyrosine in reaction centers from Rhodobacter sphaeroides. FEBS Lett 2003; 545:193-8. [PMID: 12804774 DOI: 10.1016/s0014-5793(03)00532-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Markedly different light-induced protonational changes were measured in two reaction center mutants of Rhodobacter sphaeroides. A quadruple mutant containing alterations, at residues L131, M160, M197, and M210, that elevate the midpoint potential of the bacteriochlorophyll dimer was compared to the Y(M) mutant, which contains these alterations plus a tyrosine at M164 serving as a secondary electron donor [Kálmán et al., Nature 402 (1999) 696]. In the quadruple mutant, a proton uptake of 0.1-0.3 H(+)/reaction center between pH 6 and 10 resulted from formation of the oxidized bacteriochlorophyll donor and reduced primary quinone. In the Y(M) mutant, a maximal proton release of -0.5 H(+)/reaction center at pH 8 was attributed to formation of the tyrosyl radical and modeled using electrostatic and direct proton-releasing mechanisms.
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Affiliation(s)
- L Kálmán
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287-1604, USA
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33
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Taly A, Sebban P, Smith JC, Ullmann GM. The position of QB in the photosynthetic reaction center depends on pH: a theoretical analysis of the proton uptake upon QB reduction. Biophys J 2003; 84:2090-8. [PMID: 12609910 PMCID: PMC1302777 DOI: 10.1016/s0006-3495(03)75016-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2002] [Accepted: 09/26/2002] [Indexed: 11/20/2022] Open
Abstract
Electrostatics-based calculations have been performed to examine the proton uptake upon reduction of the terminal electron acceptor Q(B) in the photosynthetic reaction center of Rhodobacter sphaeroides as a function of pH and the associated conformational equilibrium. Two crystal structures of the reaction center were considered: one structure was determined in the dark and the other under illumination. In the two structures, the Q(B) was found in two different positions, proximal or distal to the nonheme iron. Because Q(B) was found mainly in the distal position in the dark and only in the proximal position under illumination, the two positions have been attributed mostly to the oxidized and the reduced forms of Q(B), respectively. We calculated the proton uptake upon Q(B) reduction by four different models. In the first model, Q(B) is allowed to equilibrate between the two positions with either oxidation state. This equilibrium was allowed to vary with pH. In the other three models the distribution of Q(B) between the proximal position and the distal position was pH-independent, with Q(B) occupying only the distal position or only the proximal position or populating the two positions with a fixed ratio. Only the first model, which includes the pH-dependent conformational equilibrium, reproduces both the experimentally measured pH dependence of the proton uptake and the crystallographically observed conformational equilibrium at pH 8. From this model, we find that Q(B) occupies only the distal position below pH 6.5 and only the proximal position above pH 9.0 in both oxidation states. Between these pH values both positions are partially occupied. The reduced Q(B) has a higher occupancy in the proximal position than the oxidized Q(B). In summary, the present results indicate that the conformational equilibrium of Q(B) depends not only on the redox state of Q(B), but also on the pH value of the solution.
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Affiliation(s)
- Antoine Taly
- Biocomputing Group, IWR, INF 368, Universität Heidelberg, Germany
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Taly A, Baciou L, Sebban P. The DMPC lipid phase transition influences differently the first and the second electron transfer reactions in bacterial reaction centers. FEBS Lett 2002; 532:91-6. [PMID: 12459469 DOI: 10.1016/s0014-5793(02)03635-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Photosynthetic reaction centers (RCs) from Rhodobacter sphaeroides were incorporated in dimyristoylphosphatidylcholine (DMPC) liposomes. The first and second electron transfer rates (k(AB)(1) and k(AB)(2), respectively) between the first and the second quinone electron acceptors have been measured as a function of temperature, across the phase transition of DMPC (23 degrees C). The Eyring plots of k(AB)(1) display straight lines. In contrast, the Eyring plots for k(AB)(2) in proteoliposomes show a break at about 23.5 degrees C. This physical discrimination between the two electron transfer reactions demonstrates that the stiffness of the lipid environment of the RCs and/or the protein-protein interactions influence the parameters governing k(AB)(2), but not the gating process limiting k(AB)(1).
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Affiliation(s)
- Antoine Taly
- Centre de Génétique Moléculaire, Bâtiment 24, CNRS, 91198 Gif-sur-Yvette, France
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35
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Tandori J, Maroti P, Alexov E, Sebban P, Baciou L. Key role of proline L209 in connecting the distant quinone pockets in the reaction center of Rhodobacter sphaeroides. Proc Natl Acad Sci U S A 2002; 99:6702-6. [PMID: 11983861 PMCID: PMC124466 DOI: 10.1073/pnas.092327799] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2001] [Indexed: 11/18/2022] Open
Abstract
Photosynthetic bacterial reaction centers convert light excitation into chemical free energy. The initial electron transfer leads to the consecutive semireductions of the primary (Q(A)) and secondary (Q(B)) quinone acceptors. The Q(A)(-) and Q(B)(-) formations induce proton uptake from the bulk. Their magnitudes (H(+)/Q(A)(-) and H(+)/Q(B)(-), respectively) probe the electrostatic interactions within the complex. The pH dependence of H(+)/Q(A)(-) and H(+)/Q(B)(-) were studied in five single mutants modified at the L209 site (L209P-->F,Y,W,E,T). This residue is situated at the border of a continuous chain of water molecules connecting Q(B) to the bulk. In the wild type (WT), a proton uptake band is present at high pH in the H(+)/Q(A)(-) and H(+)/Q(B)(-) curves and is commonly attributed to a cluster of acidic groups situated nearby Q(B). In the H(+)/Q(A)(-) curves of the L209 variants, this band is systematically absent but remains in the H(+)/Q(B)(-) curves. Moreover, notable increase of H(+)/Q(B)(-) is observed in the L209 mutants at neutral pH as compared with the WT. The large effects observed in all L209 mutants are not associated with significant structural changes (Kuglstatter, A., Ermler, U., Michel, H., Baciou, L. & Fritzsch, G. Biochemistry (2001) 40, 4253-4260). Our data suggest that, in the L209 mutants, the Q(B) cluster does not respond to the Q(A)(-) formation as observed in the WT. We propose that, in the mutants, removal of the rigid proline L209 breaks a necessary hydrogen bonding connection between the quinone sites. These findings suggest an important role for structural rigidity in ensuring a functional interaction between quinone binding sites.
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Affiliation(s)
- J Tandori
- Centre de Génétique Moléculaire, Centre National de la Recherche Scientifique, 91198 Gif-sur-Yvette, France
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36
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Tandori J, Miksovska J, Valerio-Lepiniec M, Schiffer M, Maróti P, Hanson DK, Sebban P. Proton uptake of rhodobacter capsulatus reaction center mutants modified in the primary quinone environment. Photochem Photobiol 2002; 75:126-33. [PMID: 11883600 DOI: 10.1562/0031-8655(2002)075<0126:puorcr>2.0.co;2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Flash-induced absorbance spectroscopy was used to analyze the proton uptake and electron transfer properties of photosynthetic reaction centers (RC) of Rhodobacter capsulatus that have been genetically modified near the primary quinone electron acceptor (Q(A)). M246Ala and M247Ala, which are symmetry-related to the positions of two acidic groups, L212Glu and L213Asp, in the secondary quinone electron acceptor (QB) protein environment, have been mutated to Glu and Asp, respectively. The pH dependence of the stoichiometry of proton uptake upon formation of the P+Q(A)- (H+/P+Q(A)-) and PQ(A) (H+/Q(A)-) (P is the primary electron donor, a noncovalently linked bacteriochlorophyll dimer) states have been measured in the M246Ala --> Glu and the M247Ala --> Asp mutant RC, in the M246Ala-M247Ala --> Glu-Asp double mutant and in the wild type (WT). Our results show that the introduction of an acidic group (Glu or Asp) in the QA protein region induces notable additional proton uptake over a large pH region (approximately 6-9), which reflects a delocalized response of the protein to the formation of Q(A)-. This may indicate the existence of a widely spread proton reservoir in the cytoplasmic region of the protein. Interestingly, the pH titration curves of the proton release caused by the formation of P+ (H+/P+: difference between H+/P+Q(A)- and H+/PQ(A)- curves) are nearly superimposable in the WT and the M246Ala --> Glu mutant RC, but substantial additional proton release is detected between pH 7 and 9 in the M247Ala --> Asp mutant RC. This effect can be accounted for by an increased proton release by the P+ environment in the M247Ala --> Asp mutant. The M247Ala --> Asp mutation reveals the existence of an energetic and conformational coupling between donor and acceptor sides of the RC at a distance of nearly 30A.
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37
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Kundrotas PJ, Karshikoff A. Model for calculation of electrostatic interactions in unfolded proteins. PHYSICAL REVIEW E 2002; 65:011901. [PMID: 11800712 DOI: 10.1103/physreve.65.011901] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2001] [Indexed: 11/07/2022]
Abstract
An approach for the calculation of electrostatic interactions and titration properties of unfolded polypeptide chains (denatured proteins) is proposed. It is based on a simple representation of the denatured proteins as a state with titratable sites distributed on the surface of a sphere, radius of which is assumed to be equal to the radius of gyration, R(g), of an unfolded molecule. Distances between the charges, d, obey constraints arising from the protein sequence. Criteria for evaluation of the parameters R(g) and d were obtained from computer simulations on a polypeptide consisting of 20 identical amino acids (polylysine). The model was applied for calculation of titration curves of denatured barnase and staphylococcal nuclease. It was demonstrated that the approach proposed gives considerably better agreement with the experimental data than the commonly used null approximation. It was also found that titration properties of denatured proteins are slightly, but distinguishably influenced by the amino-acid sequence of the protein.
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Affiliation(s)
- P J Kundrotas
- Department of Biosciences at Novum Research Park, Karolinska Institutet, SE-141 57 Huddinge, Stockholm, Sweden
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Tandori J, Baciou L, Alexov E, Maroti P, Schiffer M, Hanson DK, Sebban P. Revealing the involvement of extended hydrogen bond networks in the cooperative function between distant sites in bacterial reaction centers. J Biol Chem 2001; 276:45513-5. [PMID: 11604387 DOI: 10.1074/jbc.c100537200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In reaction center proteins of photosynthetic bacteria, the amplitude of proton uptake induced by the one-electron reduction of either of the two quinone electron acceptors (Q(A) and Q(B)) is an intrinsic observable of the electrostatic interactions associated with the redox function of the complex. We report here that, in Rhodobacter capsulatus, complete restoration of proton uptake (upon formation of Q(A)(-) and Q(B)(-)) to the level found in the wild type is observed in a mutant reaction center in which a tyrosine substitution in the Q(A) environment (Ala(M274) --> Tyr) is coupled with mutations of acidic residues near Q(B) (Glu(L212) --> Ala/Asp(L213) --> Ala) that initially cancel the proton uptake above pH 8. This result demonstrates that proton uptake occurs by strong cooperation between structural motifs, such as hydrogen-bonded networks, that span the 18 A distance between the two quinone acceptors.
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Affiliation(s)
- J Tandori
- Centre de Génétique Moléculaire, CNRS, Gif 91198, France
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39
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Drachev L, Mamedov M, Mulkidjanian A, Semenov A, Shinkarev V, Verkhovsky M. Electrogenesis associated with proton transfer in the reaction center protein of the purple bacterium Rhodobacter sphaeroides. FEBS Lett 2001. [DOI: 10.1016/0014-5793(90)80038-k] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Influence of pigment substitution on the electrochemical properties ofRhodobacter sphaeroides 601 reaction centers. ACTA ACUST UNITED AC 2001; 44:524-32. [DOI: 10.1007/bf02882395] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2001] [Indexed: 11/30/2022]
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41
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Osváth S, Larson JW, Wraight CA. Site specific labeling of Rhodobacter sphaeroides reaction centers with dye probes for surface pH measurements. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1505:238-47. [PMID: 11334788 DOI: 10.1016/s0005-2728(01)00173-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Covalently bound pH sensitive dyes are an important tool for characterizing the proteolytic reactions of protein complexes that play key roles in biological energy transduction. Here we demonstrate the feasibility of this method for photosynthetic reaction centers (RCs) for the first time, by the highly selective attachment of two thiol reactive derivatives of fluorescein to the two H subunit cysteines of the photosynthetic RC from Rhodobacter sphaeroides R-26 The pK(a) shifts of the dyes upon binding to the protein and in response to high salt were measured, and interpreted based on the structure of the RC. 2-[(5-fluoresceinyl)aminocarbonyl]ethyl-methanethiosulfonate was attached to Cys H156 and fluorescein-5-maleimide to Cys H234. By following the absorption changes of bound fluorescein (500 nm), and those of the hydrophilic pH indicator 8-hydroxypyrene-1,3,6-tris-sulfonic acid (468 nm), the surface and bulk pH were monitored separately with less than 5% crosstalk. Flash-induced proton uptake and external calibrations by mixing with aliquots of acid were measured in different redox states of the RCs. The results indicate that the charge in the quinone acceptor complex after flash activation (primary quinone acceptor (Q(A))- or secondary quinone acceptor (Q(B))-) has no effect on the surface pH and potential in the vicinity of these two attachment sites, between pH 6.5 and 9. Application of the method to other surface locations is discussed.
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Affiliation(s)
- S Osváth
- Department of Biochemistry/MC-712, 419 Roger Adams Laboratory, 600 South Mathews Avenue, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
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42
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Cherepanov DA, Krishtalik LI, Mulkidjanian AY. Photosynthetic electron transfer controlled by protein relaxation: analysis by Langevin stochastic approach. Biophys J 2001; 80:1033-49. [PMID: 11222272 PMCID: PMC1301303 DOI: 10.1016/s0006-3495(01)76084-5] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
Relaxation processes in proteins range in time from picoseconds to seconds. Correspondingly, biological electron transfer (ET) could be controlled by slow protein relaxation. We used the Langevin stochastic approach to describe this type of ET dynamics. Two different types of kinetic behavior were revealed, namely: oscillating ET (that could occur at picoseconds) and monotonically relaxing ET. On a longer time scale, the ET dynamics can include two different kinetic components. The faster one reflects the initial, nonadiabatic ET, whereas the slower one is governed by the medium relaxation. We derived a simple relation between the relative extents of these components, the change in the free energy (DeltaG), and the energy of the slow reorganization Lambda. The rate of ET was found to be determined by slow relaxation at -DeltaG < or = Lambda. The application of the developed approach to experimental data on ET in the bacterial photosynthetic reaction centers allowed a quantitative description of the oscillating features in the primary charge separation and yielded values of Lambda for the slower low-exothermic ET reactions. In all cases but one, the obtained estimates of Lambda varied in the range of 70-100 meV. Because the vast majority of the biological ET reactions are only slightly exothermic (DeltaG > or = -100 meV), the relaxationally controlled ET is likely to prevail in proteins.
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Affiliation(s)
- D A Cherepanov
- Division of Biophysics, Faculty of Biology/Chemistry, University of Osnabrück, D-49069 Osnabrück, Germany
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43
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Adelroth P, Paddock ML, Sagle LB, Feher G, Okamura MY. Identification of the proton pathway in bacterial reaction centers: both protons associated with reduction of QB to QBH2 share a common entry point. Proc Natl Acad Sci U S A 2000; 97:13086-91. [PMID: 11078513 PMCID: PMC27182 DOI: 10.1073/pnas.230439597] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2000] [Indexed: 11/18/2022] Open
Abstract
The reaction center from Rhodobacter sphaeroides uses light energy for the reduction and protonation of a quinone molecule, Q(B). This process involves the transfer of two protons from the aqueous solution to the protein-bound Q(B) molecule. The second proton, H(+)(2), is supplied to Q(B) by Glu-L212, an internal residue protonated in response to formation of Q(A)(-) and Q(B)(-). In this work, the pathway for H(+)(2) to Glu-L212 was studied by measuring the effects of divalent metal ion binding on the protonation of Glu-L212, which was assayed by two types of processes. One was proton uptake from solution after the one-electron reduction of Q(A) (DQ(A)-->D(+)Q(A)(-)) and Q(B) (DQ(B)-->D(+)Q(B)(-)), studied by using pH-sensitive dyes. The other was the electron transfer k(AB)((1)) (Q(A)(-)Q(B)-->Q(A)Q(B)(-)). At pH 8.5, binding of Zn(2+), Cd(2+), or Ni(2+) reduced the rates of proton uptake upon Q(A)(-) and Q(B)(-) formation as well as k(AB)((1)) by approximately an order of magnitude, resulting in similar final values, indicating that there is a common rate-limiting step. Because D(+)Q(A)(-) is formed 10(5)-fold faster than the induced proton uptake, the observed rate decrease must be caused by an inhibition of the proton transfer. The Glu-L212-->Gln mutant reaction centers displayed greatly reduced amplitudes of proton uptake and exhibited no changes in rates of proton uptake or electron transfer upon Zn(2+) binding. Therefore, metal binding specifically decreased the rate of proton transfer to Glu-L212, because the observed rates were decreased only when proton uptake by Glu-L212 was required. The entry point for the second proton H(+)(2) was thus identified to be the same as for the first proton H(+)(1), close to the metal binding region Asp-H124, His-H126, and His-H128.
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Affiliation(s)
- P Adelroth
- Department of Physics 0319, 9500 Gilman Drive, University of California at San Diego, La Jolla, CA 92093, USA
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44
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Rabenstein B, Ullmann GM, Knapp EW. Electron transfer between the quinones in the photosynthetic reaction center and its coupling to conformational changes. Biochemistry 2000; 39:10487-96. [PMID: 10956039 DOI: 10.1021/bi000413c] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The electron transfer between the two quinones Q(A) and Q(B) in the bacterial photosynthetic reaction center (bRC) is coupled to a conformational rearrangement. Recently, the X-ray structures of the dark-adapted and light-exposed bRC from Rhodobacter sphaeroides were solved, and the conformational changes were characterized structurally. We computed the reaction free energy for the electron transfer from to Q(B) in the X-ray structures of the dark-adapted and light-exposed bRC from Rb. sphaeroides. The computation was done by applying an electrostatic model using the Poisson-Boltzmann equation and Monte Carlo sampling. We accounted for possible protonation changes of titratable groups upon electron transfer. According to our calculations, the reaction energy of the electron transfer from to Q(B) is +157 meV for the dark-adapted and -56 meV for the light-exposed X-ray structure; i.e., the electron transfer is energetically uphill for the dark-adapted structure and downhill for the light-exposed structure. A common interpretation of experimental results is that the electron transfer between and Q(B) is either gated or at least influenced by a conformational rearrangement: A conformation in which the electron transfer from to Q(B) is inactive, identified with the dark-adapted X-ray structure, changes into an electron-transfer active conformation, identified with the light-exposed X-ray structure. This interpretation agrees with our computational results if one assumes that the positive reaction energy for the dark-adapted X-ray structure effectively prevents the electron transfer. We found that the strongly coupled pair of titratable groups Glu-L212 and Asp-L213 binds about one proton in the dark-adapted X-ray structure, where the electron is mainly localized at Q(A), and about two protons in the light-exposed structure, where the electron is mainly localized at Q(B). This finding agrees with recent experimental and theoretical studies. We compare the present results for the bRC from Rb. sphaeroides to our recent studies on the bRC from Rhodopseudomonas viridis. We discuss possible mechanisms for the gated electron transfer from to Q(B) and relate them to theoretical and experimental results.
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Affiliation(s)
- B Rabenstein
- Institut für Chemie, Fachbereich Biologie, Chemie, Pharmazie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany
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45
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Peluso A, Di Donato M, Saracino GAA. An alternative way of thinking about electron transfer in proteins: Proton assisted electron transfer between the primary and the secondary quinones in photosynthetic reaction centers. J Chem Phys 2000. [DOI: 10.1063/1.1286918] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Cherepanov DA, Bibikov SI, Bibikova MV, Bloch DA, Drachev LA, Gopta OA, Oesterhelt D, Semenov AY, Mulkidjanian AY. Reduction and protonation of the secondary quinone acceptor of Rhodobacter sphaeroides photosynthetic reaction center: kinetic model based on a comparison of wild-type chromatophores with mutants carrying Arg-->Ile substitution at sites 207 and 217 in the L-subunit. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1459:10-34. [PMID: 10924896 DOI: 10.1016/s0005-2728(00)00110-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
After the light-induced charge separation in the photosynthetic reaction center (RC) of Rhodobacter sphaeroides, the electron reaches, via the tightly bound ubiquinone QA, the loosely bound ubiquinone Q(B) After two subsequent flashes of light, Q(B) is reduced to ubiquinol Q(B)H2, with a semiquinone anion Q-(B) formed as an intermediate after the first flash. We studied Q(B)H2 formation in chromatophores from Rb. sphaeroides mutants that carried Arg-->Ile substitution at sites 207 and 217 in the L-subunit. While Arg-L207 is 17 A away from Q(B), Arg-L217 is closer (9 A) and contacts the Q(B)-binding pocket. From the pH dependence of the charge recombination in the RC after the first flash, we estimated deltaG(AB), the free energy difference between the Q-(A)Q(B) and Q(A)Q-(B) states, and pK212, the apparent pK of Glu-L212, a residue that is only 4 A away from Q(B). As expected, the replacement of positively charged arginines by neutral isoleucines destabilized the Q-(B) state in the L217RI mutant to a larger extent than in the L207RI one. Also as expected, pK212 increased by approximately 0.4 pH units in the L207RI mutant. The value of pK212 in the L217RI mutant decreased by 0.3 pH units, contrary to expectations. The rate of the Q-(A)Q-(B)-->Q(A)Q(B)H2 transition upon the second flash, as monitored by electrometry via the accompanying changes in the membrane potential, was two times faster in the L207RI mutant than in the wild-type, but remained essentially unchanged in the L217RI mutant. To rationalize these findings, we developed and analyzed a kinetic model of the Q-(A)Q-(B)-->Q(A)Q(B)H2 transition. The model properly described the available experimental data and provided a set of quantitative kinetic and thermodynamic parameters of the Q(B) turnover. The non-electrostatic, 'chemical' affinity of the QB site to protons proved to be as important for the attracting protons from the bulk, as the appropriate electrostatic potential. The mutation-caused changes in the chemical proton affinity could be estimated from the difference between the experimentally established pK2J2 shifts and the expected changes in the electrostatic potential at Glu-L212, calculable from the X-ray structure of the RC. Based on functional studies, structural data and kinetic modeling, we suggest a mechanistic scheme of the QB turnover. The detachment of the formed ubiquinol from its proximal position next to Glu-L212 is considered as the rate-limiting step of the reaction cycle.
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Affiliation(s)
- D A Cherepanov
- Institute of Electrochemistry, Russian Academy of Sciences, Moscow
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47
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Knox PP, Churbanova IY, Lukashev EP, Zakharova NI, Rubin AB, Borissevitc GP. Dipyridamole and its derivatives modify the kinetics of the electron transport in reaction centers from Rhodobacter sphaeroides. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2000; 56:68-77. [PMID: 11073318 DOI: 10.1016/s1011-1344(00)00062-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A well known vasodilator dipyridamole (DIP), 2,6-bis(diethanolamino)-4,8-dipiperidinopyrimido[5,4-d]pyrim idine, and its derivatives have recently been shown as potential co-activators (modulators) in the phenomenon of multidrug resistance (MDR) in cancer therapy. They inhibit the specific function of a transmembrane P-glycoprotein responsible for the ex-flux of anti-cancer drugs from tumor cells. To clarify molecular mechanisms of the anti-MDR activity of DIP and its two derivatives, RA25 and RA47, we have studied their effects on electron transport in reaction centers (RC) from purple photosynthetic bacteria Rb. sphaeroides, using RC as a model system. Increasing concentrations of DIP and RA47 progressively accelerate the back electron transfer from the primary quinone acceptor QA to the bacteriochlorophyll dimer Bchl2 (Bchl2+ -QA- recombination). In the absence of o-phenantroline, when both quinone acceptors QA and QB are involved in the electron transport, RA47 is more effective than DIP. DIP stabilizes the electron on the secondary quinone acceptor QB, the effect manifested as the retardation of Bchl2+ -QB- recombination. Effects of RA25 are negligible in all cases. The drugs are proposed to change the electron transport affecting the RC structural dynamics and the stabilization of the electron on quinone acceptors through modification of H-bonds in the system.
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Affiliation(s)
- P P Knox
- Biophysics Department, Biology Faculty, M.V. Lomonosov State University, Moscow, Russia
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48
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Brandsburg-Zabary S, Fried O, Marantz Y, Nachliel E, Gutman M. Biophysical aspects of intra-protein proton transfer. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1458:120-34. [PMID: 10812028 DOI: 10.1016/s0005-2728(00)00063-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The passage of proton trough proteins is common to all membranal energy conserving enzymes. While the routes differ among the various proteins, the mechanism of proton propagation is based on the same chemical-physical principles. The proton progresses through a sequence of dissociation association steps where the protein and water molecules function as a solvent that lowers the energy penalty associated with the generation of ions in the protein. The propagation of the proton in the protein is a random walk, between the temporary proton binding sites that make the conducting path, that is biased by the intra-protein electrostatic potential. Kinetic measurements of proton transfer reactions, in the sub-ns up to micros time frame, allow to monitor the dynamics of the partial reactions of an overall proton transfer through a protein.
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Affiliation(s)
- S Brandsburg-Zabary
- Laser Laboratory for Fast reactions in Biology, Biochemistry, Tel Aviv University, Tel Aviv, Israel
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49
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Gunner MR, Alexov E. A pragmatic approach to structure based calculation of coupled proton and electron transfer in proteins. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1458:63-87. [PMID: 10812025 DOI: 10.1016/s0005-2728(00)00060-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The coupled motion of electrons and protons occurs in many proteins. Using appropriate tools for calculation, the three-dimensional protein structure can show how each protein modulates the observed electron and proton transfer reactions. Some of the assumptions and limitations involved in calculations that rely on continuum electrostatics to calculate the energy of charges in proteins are outlined. Approaches that mix molecular mechanics and continuum electrostatics are described. Three examples of the analysis of reactions in photosynthetic reaction centers are given: comparison of the electrochemistry of hemes in different sites; analysis of the role of the protein in stabilizing the early charge separated state in photosynthesis; and calculation of the proton uptake and protein motion coupled to the electron transfer from the primary (Q(A)) to secondary (Q(B)) quinone. Different mechanisms for stabilizing intra-protein charged cofactors are highlighted in each reaction.
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Affiliation(s)
- M R Gunner
- Physics Department City College of New York, New York, NY 10031, USA
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50
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Okamura MY, Paddock ML, Graige MS, Feher G. Proton and electron transfer in bacterial reaction centers. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1458:148-63. [PMID: 10812030 DOI: 10.1016/s0005-2728(00)00065-7] [Citation(s) in RCA: 252] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The bacterial reaction center couples light-induced electron transfer to proton pumping across the membrane by reactions of a quinone molecule Q(B) that binds two electrons and two protons at the active site. This article reviews recent experimental work on the mechanism of the proton-coupled electron transfer and the pathways for proton transfer to the Q(B) site. The mechanism of the first electron transfer, k((1))(AB), Q(-)(A)Q(B)-->Q(A)Q(-)(B), was shown to be rate limited by conformational gating. The mechanism of the second electron transfer, k((2))(AB), was shown to involve rapid reversible proton transfer to the semiquinone followed by rate-limiting electron transfer, H(+)+Q(-)(A)Q(-)(B) ifQ(-)(A)Q(B)H-->Q(A)(Q(B)H)(-). The pathways for transfer of the first and second protons were elucidated by high-resolution X-ray crystallography as well as kinetic studies showing changes in the rate of proton transfer due to site directed mutations and metal ion binding.
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Affiliation(s)
- M Y Okamura
- University of California, San Diego, La Jolla, CA 92093-0319, USA
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