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Capone M, Romanelli M, Castaldo D, Parolin G, Bello A, Gil G, Vanzan M. A Vision for the Future of Multiscale Modeling. ACS PHYSICAL CHEMISTRY AU 2024; 4:202-225. [PMID: 38800726 PMCID: PMC11117712 DOI: 10.1021/acsphyschemau.3c00080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 05/29/2024]
Abstract
The rise of modern computer science enabled physical chemistry to make enormous progresses in understanding and harnessing natural and artificial phenomena. Nevertheless, despite the advances achieved over past decades, computational resources are still insufficient to thoroughly simulate extended systems from first principles. Indeed, countless biological, catalytic and photophysical processes require ab initio treatments to be properly described, but the breadth of length and time scales involved makes it practically unfeasible. A way to address these issues is to couple theories and algorithms working at different scales by dividing the system into domains treated at different levels of approximation, ranging from quantum mechanics to classical molecular dynamics, even including continuum electrodynamics. This approach is known as multiscale modeling and its use over the past 60 years has led to remarkable results. Considering the rapid advances in theory, algorithm design, and computing power, we believe multiscale modeling will massively grow into a dominant research methodology in the forthcoming years. Hereby we describe the main approaches developed within its realm, highlighting their achievements and current drawbacks, eventually proposing a plausible direction for future developments considering also the emergence of new computational techniques such as machine learning and quantum computing. We then discuss how advanced multiscale modeling methods could be exploited to address critical scientific challenges, focusing on the simulation of complex light-harvesting processes, such as natural photosynthesis. While doing so, we suggest a cutting-edge computational paradigm consisting in performing simultaneous multiscale calculations on a system allowing the various domains, treated with appropriate accuracy, to move and extend while they properly interact with each other. Although this vision is very ambitious, we believe the quick development of computer science will lead to both massive improvements and widespread use of these techniques, resulting in enormous progresses in physical chemistry and, eventually, in our society.
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Affiliation(s)
- Matteo Capone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, L’Aquila 67010, Italy
| | - Marco Romanelli
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Davide Castaldo
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Giovanni Parolin
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
| | - Alessandro Bello
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, Informatics and Mathematics, University of Modena and Reggio Emilia, Modena 41125, Italy
| | - Gabriel Gil
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Instituto
de Cibernética, Matemática y Física (ICIMAF), La Habana 10400, Cuba
| | - Mirko Vanzan
- Department
of Chemical Sciences, University of Padova, Padova 35131, Italy
- Department
of Physics, University of Milano, Milano 20133, Italy
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Walters KA, Redding KE, Golbeck JH. Identification and characterization of the low molecular mass ferredoxins involved in central metabolism in Heliomicrobium modesticaldum. PHOTOSYNTHESIS RESEARCH 2024:10.1007/s11120-023-01069-z. [PMID: 38306001 DOI: 10.1007/s11120-023-01069-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 12/11/2023] [Indexed: 02/03/2024]
Abstract
The homodimeric Type I reaction center (RC) from Heliomicrobium modesticaldum lacks the PsaC subunit found in Photosystem I and instead uses the interpolypeptide [4Fe-4S] cluster FX as the terminal electron acceptor. Our goal was to identify which of the small mobile dicluster ferredoxins encoded by the H. modesticaldum genome are capable of accepting electrons from the heliobacterial RC (HbRC) and pyruvate:ferredoxin oxidoreductase (PFOR), a key metabolic enzyme. Analysis of the genome revealed seven candidates: HM1_1462 (PshB1), HM1_1461 (PshB2), HM1_2505 (Fdx3), HM1_0869 (FdxB), HM1_1043, HM1_0357, and HM1_2767. Heterologous expression in Escherichia coli and studies using time-resolved optical spectroscopy revealed that only PshB1, PshB2, and Fdx3 are capable of accepting electrons from the HbRC and PFOR. Modeling studies using AlphaFold show that only PshB1, PshB2, and Fdx3 should be capable of docking on PFOR at a positively charged patch that overlays a surface-proximal [4Fe-4S] cluster. Proteomic analysis of wild-type and gene deletion strains ΔpshB1, ΔpshB2, ΔpshB1pshB2, and Δfdx3 grown under nitrogen-replete conditions revealed that Fdx3 is undetectable in the wild-type, ΔpshB1, and Δfdx3 strains, but it is present in the ΔpshB2 and ΔpshB1pshB2 strains, implying that Fdx3 may substitute for PshB2. When grown under nitrogen-deplete conditions, Fdx3 is present in the wild-type and all deletion strains except for Δfdx3. None of the knockout strains demonstrated significant impairment during chemotrophic dark growth on pyruvate, photoheterotrophic light growth on pyruvate, or phototrophic growth on acetate+CO2, indicating a high degree of redundancy among these three electron transfer proteins. Loss of both PshB1 and PshB2, but not FdxB, resulted in poor growth under N2-fixing conditions.
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Affiliation(s)
- Karim A Walters
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Kevin E Redding
- School of Molecular Sciences, Arizona State University, 1711 S Rural Rd, Box 871604, Tempe, AZ, 85287-1604, USA.
- Center for Bioenergy & Photosynthesis, Arizona State University, Tempe, AZ, 85287, USA.
| | - John H Golbeck
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, 16802, USA.
- Department of Chemistry, The Pennsylvania State University, University Park, PA, 16802, USA.
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Liang Y, Plourde A, Bueler SA, Liu J, Brzezinski P, Vahidi S, Rubinstein JL. Structure of mycobacterial respiratory complex I. Proc Natl Acad Sci U S A 2023; 120:e2214949120. [PMID: 36952383 PMCID: PMC10068793 DOI: 10.1073/pnas.2214949120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023] Open
Abstract
Oxidative phosphorylation, the combined activity of the electron transport chain (ETC) and adenosine triphosphate synthase, has emerged as a valuable target for the treatment of infection by Mycobacterium tuberculosis and other mycobacteria. The mycobacterial ETC is highly branched with multiple dehydrogenases transferring electrons to a membrane-bound pool of menaquinone and multiple oxidases transferring electrons from the pool. The proton-pumping type I nicotinamide adenine dinucleotide (NADH) dehydrogenase (Complex I) is found in low abundance in the plasma membranes of mycobacteria in typical in vitro culture conditions and is often considered dispensable. We found that growth of Mycobacterium smegmatis in carbon-limited conditions greatly increased the abundance of Complex I and allowed isolation of a rotenone-sensitive preparation of the enzyme. Determination of the structure of the complex by cryoEM revealed the "orphan" two-component response regulator protein MSMEG_2064 as a subunit of the assembly. MSMEG_2064 in the complex occupies a site similar to the proposed redox-sensing subunit NDUFA9 in eukaryotic Complex I. An apparent purine nucleoside triphosphate within the NuoG subunit resembles the GTP-derived molybdenum cofactor in homologous formate dehydrogenase enzymes. The membrane region of the complex binds acyl phosphatidylinositol dimannoside, a characteristic three-tailed lipid from the mycobacterial membrane. The structure also shows menaquinone, which is preferentially used over ubiquinone by gram-positive bacteria, in two different positions along the quinone channel, comparable to ubiquinone in other structures and suggesting a conserved quinone binding mechanism.
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Affiliation(s)
- Yingke Liang
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
| | - Alicia Plourde
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - Stephanie A. Bueler
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
| | - Jun Liu
- Department of Molecular Genetics, University of Toronto, TorontoM5S 1A8, Canada
| | - Peter Brzezinski
- Department of Biochemistry and Biophysics, Stockholm University, SE-106 91Stockholm, Sweden
| | - Siavash Vahidi
- Department of Molecular and Cellular Biology, University of Guelph, TorontoN1G 2W1, Canada
| | - John L. Rubinstein
- Molecular Medicine Program, The Hospital for Sick Children, TorontoM5G 0A4, Canada
- Department of Biochemistry, University of Toronto, TorontoM5S 1A8, Canada
- Department of Medical Biophysics, University of Toronto, TorontoM5G 1L7, Canada
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Gardiner AT, Nguyen-Phan TC, Cogdell RJ. A comparative look at structural variation among RC-LH1 'Core' complexes present in anoxygenic phototrophic bacteria. PHOTOSYNTHESIS RESEARCH 2020; 145:83-96. [PMID: 32430765 PMCID: PMC7423801 DOI: 10.1007/s11120-020-00758-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 05/10/2020] [Indexed: 05/30/2023]
Abstract
All purple photosynthetic bacteria contain RC-LH1 'Core' complexes. The structure of this complex from Rhodobacter sphaeroides, Rhodopseudomonas palustris and Thermochromatium tepidum has been solved using X-ray crystallography. Recently, the application of single particle cryo-EM has revolutionised structural biology and the structure of the RC-LH1 'Core' complex from Blastochloris viridis has been solved using this technique, as well as the complex from the non-purple Chloroflexi species, Roseiflexus castenholzii. It is apparent that these structures are variations on a theme, although with a greater degree of structural diversity within them than previously thought. Furthermore, it has recently been discovered that the only phototrophic representative from the phylum Gemmatimonadetes, Gemmatimonas phototrophica, also contains a RC-LH1 'Core' complex. At present only a low-resolution EM-projection map exists but this shows that the Gemmatimonas phototrophica complex contains a double LH1 ring. This short review compares these different structures and looks at the functional significance of these variations from two main standpoints: energy transfer and quinone exchange.
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Affiliation(s)
- Alastair T Gardiner
- Institute of Molecular, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK.
- Laboratory of Anoxygenic Phototrophs, Centre Algatech, Institute of Microbiology of the Czech Academy of Sciences, Novohradska 237, 379 01, Třeboň, Czech Republic.
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Richard J Cogdell
- Institute of Molecular, Cellular and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
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Bostick CD, Mukhopadhyay S, Pecht I, Sheves M, Cahen D, Lederman D. Protein bioelectronics: a review of what we do and do not know. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:026601. [PMID: 29303117 DOI: 10.1088/1361-6633/aa85f2] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.
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Affiliation(s)
- Christopher D Bostick
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, United States of America. Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, United States of America
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Serdenko TV, Barabash YM, Knox PP, Seifullina NK. The kinetic model for slow photoinduced electron transport in the reaction centers of purple bacteria. NANOSCALE RESEARCH LETTERS 2016; 11:286. [PMID: 27271854 PMCID: PMC4896891 DOI: 10.1186/s11671-016-1502-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 05/27/2016] [Indexed: 06/06/2023]
Abstract
The present work is related to the investigation of slow kinetics of electron transport in the reaction centers (RCs) of Rhodobacter sphaeroides. Experimental data on the absorption kinetics of aqueous solutions of reaction centers at different modes of photoexcitation are given. It is shown that the kinetics of oxidation and reduction of RCs are well described by the sum of three exponential functions. This allows to suggest a two-level kinetic model for electron transport in the RC as a system of four electron-conformational states which correspond to three balance differential equations combined with state equation. The solution of inverse problem made it possible to obtain the rate constant values in kinetic equations for different times and intensities of exciting light. Analysis of rate constant values in different modes of RC excitation allowed to suggest that two mechanisms of structural changes are involved in RC photo-oxidation. One mechanism leads to the increment of the rate of electron return, another one-to its drop. Structural changes were found out to occur in the RCs under incident light. After light was turned off, the reduction of RCs was determined by the second mechanism.
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Affiliation(s)
- T V Serdenko
- Department of Physics of Biological Systems, Institute of Physics NAS Ukraine, Prospect Nauky, 46, 03028, Kyiv, Ukraine.
| | - Y M Barabash
- Department of Physics of Biological Systems, Institute of Physics NAS Ukraine, Prospect Nauky, 46, 03028, Kyiv, Ukraine
| | - P P Knox
- Department of Biophysics, Biology Faculty of the M.V. Lomonosov Moscow State University, Leninskie Gory, 1, 119991, Moscow, Russia
| | - N Kh Seifullina
- Department of Biophysics, Biology Faculty of the M.V. Lomonosov Moscow State University, Leninskie Gory, 1, 119991, Moscow, Russia
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7
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Song DY, Pizano AA, Holder PG, Stubbe J, Nocera DG. Direct Interfacial Y 731 Oxidation in α 2 by a Photoβ 2 Subunit of E. coli Class Ia Ribonucleotide Reductase. Chem Sci 2015; 6:4519-4524. [PMID: 26504513 PMCID: PMC4618407 DOI: 10.1039/c5sc01125f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2015] [Accepted: 06/06/2015] [Indexed: 11/21/2022] Open
Abstract
Proton-coupled electron transfer (PCET) is a fundamental mechanism important in a wide range of biological processes including the universal reaction catalysed by ribonucleotide reductases (RNRs) in making de novo, the building blocks required for DNA replication and repair. These enzymes catalyse the conversion of nucleoside diphosphates (NDPs) to deoxynucleoside diphosphates (dNDPs). In the class Ia RNRs, NDP reduction involves a tyrosyl radical mediated oxidation occurring over 35 Å across the interface of the two required subunits (β2 and α2) involving multiple PCET steps and the conserved tyrosine triad [Y356(β2)-Y731(α2)-Y730(α2)]. We report the synthesis of an active photochemical RNR (photoRNR) complex in which a Re(I)-tricarbonyl phenanthroline ([Re]) photooxidant is attached site-specifically to the Cys in the Y356C-(β2) subunit and an ionizable, 2,3,5-trifluorotyrosine (2,3,5-F3Y) is incorporated in place of Y731 in α2. This intersubunit PCET pathway is investigated by ns laser spectroscopy on [Re356]-β2:2,3,5-F3Y731-α2 in the presence of substrate, CDP, and effector, ATP. This experiment has allowed analysis of the photoinjection of a radical into α2 from β2 in the absence of the interfacial Y356 residue. The system is competent for light-dependent substrate turnover. Time-resolved emission experiments reveal an intimate dependence of the rate of radical injection on the protonation state at position Y731(α2), which in turn highlights the importance of a well-coordinated proton exit channel involving the key residues, Y356 and Y731, at the subunit interface.
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Affiliation(s)
- David Y. Song
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
| | - Arturo A. Pizano
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
| | - Patrick G. Holder
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
| | - JoAnne Stubbe
- Department of Chemistry , Massachusetts Institute of Technology , 77 Massachusetts Avenue , Cambridge , MA 02139-4307 , USA .
| | - Daniel G. Nocera
- Department of Chemistry and Chemical Biology , 12 Oxford Street , Cambridge , MA 02138-2902 , USA .
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8
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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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Cogdell RJ, Gardiner AT, Molina PI, Cronin L. The use and misuse of photosynthesis in the quest for novel methods to harness solar energy to make fuel. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2013; 371:20110603. [PMID: 23816912 DOI: 10.1098/rsta.2011.0603] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
This short review will illustrate that photosynthesis can provide a real contribution towards our sustain- able, green fuel requirements in the future. However, it is argued that the focus on biofuels is misplaced and that, in the longer term, investment in artificial photosynthesis will prove much more beneficial.
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Affiliation(s)
- Richard J Cogdell
- Glasgow Biomedical Research Centre, Institute of Molecular Cell and Systems Biology, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK.
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10
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Al-Attar S, de Vries S. Energy transduction by respiratory metallo-enzymes: From molecular mechanism to cell physiology. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.05.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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11
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Engineering of an alternative electron transfer path in photosystem II. Proc Natl Acad Sci U S A 2010; 107:9650-5. [PMID: 20457933 DOI: 10.1073/pnas.1000187107] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The initial steps of oxygenic photosynthetic electron transfer occur within photosystem II, an intricate pigment/protein transmembrane complex. Light-driven electron transfer occurs within a multistep pathway that is efficiently insulated from competing electron transfer pathways. The heart of the electron transfer system, composed of six linearly coupled redox active cofactors that enable electron transfer from water to the secondary quinone acceptor Q(B), is mainly embedded within two proteins called D1 and D2. We have identified a site in silico, poised in the vicinity of the Q(A) intermediate quinone acceptor, which could serve as a potential binding site for redox active proteins. Here we show that modification of Lysine 238 of the D1 protein to glutamic acid (Glu) in the cyanobacterium Synechocystis sp. PCC 6803, results in a strain that grows photautotrophically. The Glu thylakoid membranes are able to perform light-dependent reduction of exogenous cytochrome c with water as the electron donor. Cytochrome c photoreduction by the Glu mutant was also shown to significantly protect the D1 protein from photodamage when isolated thylakoid membranes were illuminated. We have therefore engineered a novel electron transfer pathway from water to a soluble protein electron carrier without harming the normal function of photosystem II.
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12
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Lubner CE, Grimme R, Bryant DA, Golbeck JH. Wiring photosystem I for direct solar hydrogen production. Biochemistry 2010; 49:404-14. [PMID: 19947649 DOI: 10.1021/bi901704v] [Citation(s) in RCA: 124] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The generation of H(2) by the use of solar energy is a promising way to supply humankind's energy needs while simultaneously mitigating environmental concerns that arise due to climate change. The challenge is to find a way to connect a photochemical module that harnesses the sun's energy to a catalytic module that generates H(2) with high quantum yields and rates. In this review, we describe a technology that employs a "molecular wire" to connect a terminal [4Fe-4S] cluster of Photosystem I directly to a catalyst, which can be either a Pt nanoparticle or the distal [4Fe-4S] cluster of an [FeFe]- or [NiFe]-hydrogenase enzyme. The keys to connecting these two moieties are surface-located cysteine residues, which serve as ligands to Fe-S clusters and which can be changed through site-specific mutagenesis to glycine residues, and the use of a molecular wire terminated in sulfhydryl groups to connect the two modules. The sulfhydryl groups at the end of the molecular wire form a direct chemical linkage to a suitable catalyst or can chemically rescue a [4Fe-4S] cluster, thereby generating a strong coordination bond. Specifically, the molecular wire can connect the F(B) iron-sulfur cluster of Photosystem I either to a Pt nanoparticle or, by using the same type of genetic modification, to the differentiated iron atom of the distal [4Fe-4S].(Cys)(3)(Gly) cluster of hydrogenase. When electrons are supplied by a sacrificial donor, this technology forms the cathode of a photochemical half-cell that evolves H(2) when illuminated. If such a device were connected to the anode of a photochemical half-cell that oxidizes water, an in vitro solar energy converter could be realized that generates only O(2) and H(2) in the light. A similar methodology can be used to connect Photosystem I to other redox proteins that have surface-located [4Fe-4S] clusters. The controlled light-driven production of strong reductants by such systems can be used to produce other biofuels or to provide mechanistic insights into enzymes catalyzing multielectron, proton-coupled reactions.
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Affiliation(s)
- Carolyn E Lubner
- Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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13
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Srinivasan N, Golbeck JH. Protein–cofactor interactions in bioenergetic complexes: The role of the A1A and A1B phylloquinones in Photosystem I. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:1057-88. [DOI: 10.1016/j.bbabio.2009.04.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2009] [Revised: 04/14/2009] [Accepted: 04/22/2009] [Indexed: 10/20/2022]
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14
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Wraight CA, Gunner MR. The Acceptor Quinones of Purple Photosynthetic Bacteria — Structure and Spectroscopy. THE PURPLE PHOTOTROPHIC BACTERIA 2009. [DOI: 10.1007/978-1-4020-8815-5_20] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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15
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Gunner MR, Madeo J, Zhu Z. Modification of quinone electrochemistry by the proteins in the biological electron transfer chains: examples from photosynthetic reaction centers. J Bioenerg Biomembr 2008; 40:509-19. [PMID: 18979192 DOI: 10.1007/s10863-008-9179-1] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2008] [Accepted: 08/31/2008] [Indexed: 11/29/2022]
Abstract
Quinones such as ubiquinone are the lipid soluble electron and proton carriers in the membranes of mitochondria, chloroplasts and oxygenic bacteria. Quinones undergo controlled redox reactions bound to specific sites in integral membrane proteins such as the cytochrome bc(1) oxidoreductase. The quinone reactions in bacterial photosynthesis are amongst the best characterized, presenting a model to understand how proteins modulate cofactor chemistry. The free energy of ubiquinone redox reactions in aqueous solution and in the Q(A) and Q(B) sites of the bacterial photosynthetic reaction centers (RCs) are compared. In the primary Q(A) site ubiquinone is reduced only to the anionic semiquinone (Q(*-)) while in the secondary Q(B) site the product is the doubly reduced, doubly protonated quinol (QH(2)). The ways in which the protein modifies the relative energy of each reduced and protonated intermediate are described. For example, the protein stabilizes Q(*-) while destabilizing Q(=) relative to aqueous solution through electrostatic interactions. In addition, kinetic and thermodynamic mechanisms for stabilizing the intermediate semiquinones are compared. Evidence for the protein sequestering anionic compounds by slowing both on and off rates as well as by binding the anion more tightly is reviewed.
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Affiliation(s)
- M R Gunner
- Physics Department, The City College of New York, New York, NY 10031, USA.
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16
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Cogdell RJ, Gardiner AT, Hashimoto H, Brotosudarmo THP. A comparative look at the first few milliseconds of the light reactions of photosynthesis. Photochem Photobiol Sci 2008; 7:1150-8. [PMID: 18846278 DOI: 10.1039/b807201a] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This mini-review describes the current state of our understanding of the structure and function of the photosynthetic light-harvesting and reaction centres. A comparative approach is used in order to highlight the underlying principles that must be satisfied for efficient energy-transfer (light-harvesting) and electron transfer (charge separation in the reaction centres).
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Affiliation(s)
- Richard John Cogdell
- Division of Biochemistry and Molecular Biology, IBLS, Glasgow Biomedical Research Centre, University of Glasgow, 120 University Place, Glasgow, G12 8TA, Scotland, UK.
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17
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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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18
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Noy D. Natural photosystems from an engineer's perspective: length, time, and energy scales of charge and energy transfer. PHOTOSYNTHESIS RESEARCH 2008; 95:23-35. [PMID: 17968671 DOI: 10.1007/s11120-007-9269-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Accepted: 10/03/2007] [Indexed: 05/25/2023]
Abstract
The vast structural and functional information database of photosynthetic enzymes includes, in addition to detailed kinetic records from decades of research on physical processes and chemical reaction-pathways, a variety of high and medium resolution crystal structures of key photosynthetic enzymes. Here, it is examined from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in novel biological and non-biological solar-energy conversion systems. This survey reveals that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Furthermore, the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. This underlines a critical challenge for projected de novo designed constructions, that is, the control of spatial organization of cofactor molecules within dense array of different cofactors, some well within 1 nm from each other.
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Affiliation(s)
- Dror Noy
- Plant Sciences Department, Weizmann Institute of Science, Rehovot, 76100, Israel.
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19
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Finikova OS, Troxler T, Senes A, DeGrado WF, Hochstrasser RM, Vinogradov SA. Energy and electron transfer in enhanced two-photon-absorbing systems with triplet cores. J Phys Chem A 2007; 111:6977-90. [PMID: 17608457 PMCID: PMC2441487 DOI: 10.1021/jp071586f] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Enhanced two-photon-absorbing (2PA) systems with triplet cores are currently under scrutiny for several biomedical applications, including photodynamic therapy (PDT) and two-photon microscopy of oxygen. The performance of so far developed molecules, however, is substantially below expected. In this study we take a detailed look at the processes occurring in these systems and propose ways to improve their performance. We focus on the interchromophore distance tuning as a means for optimization of two-photon sensors for oxygen. In these constructs, energy transfer from several 2PA chromophores is used to enhance the effective 2PA cross section of phosphorescent metalloporphyrins. Previous studies have indicated that intramolecular electron transfer (ET) can act as an effective quencher of phosphorescence, decreasing the overall sensor efficiency. We studied the interplay between 2PA, energy transfer, electron transfer, and phosphorescence emission using Rhodamine B-Pt tetrabenzoporphyrin (RhB-PtTBP) adducts as model compounds. 2PA cross sections (sigma2) of tetrabenzoporphyrins (TBPs) are in the range of several tens of GM units (near 800 nm), making TBPs superior 2PA chromophores compared to regular porphyrins (sigma2 values typically 1-2 GM). Relatively large 2PA cross sections of rhodamines (about 200 GM in 800-850 nm range) and their high photostabilities make them good candidates as 2PA antennae. Fluorescence of Rhodamine B (lambda(fl) = 590 nm, phi(fl) = 0.5 in EtOH) overlaps with the Q-band of phosphorescent PtTBP (lambda(abs) = 615 nm, epsilon = 98 000 M(-1) cm(-1), phi(p) approximately 0.1), suggesting that a significant amplification of the 2PA-induced phosphorescence via fluorescence resonance energy transfer (FRET) might occur. However, most of the excitation energy in RhB-PtTBP assemblies is consumed in several intramolecular ET processes. By installing rigid nonconducting decaproline spacers (Pro10) between RhB and PtTBP, the intramolecular ETs were suppressed, while the chromophores were kept within the Förster r0 distance in order to maintain high FRET efficiency. The resulting assemblies exhibit linear amplification of their 2PA-induced phosphorescence upon increase in the number of 2PA antenna chromophores and show high oxygen sensitivity. We also have found that PtTBPs possess unexpectedly strong forbidden S0 --> T1 bands (lambda(max) = 762 nm, epsilon = 120 M-1 cm-1). The latter may overlap with the laser spectrum and lead to unwanted linear excitation.
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Affiliation(s)
- Olga S Finikova
- Departments of Biochemistry and Biophysics and Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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20
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LeMaster DM, Anderson JS, Hernández G. Spatial distribution of dielectric shielding in the interior of Pyrococcus furiosus rubredoxin as sampled in the subnanosecond timeframe by hydrogen exchange. Biophys Chem 2007; 129:43-8. [PMID: 17544203 PMCID: PMC2063458 DOI: 10.1016/j.bpc.2007.05.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2007] [Revised: 05/08/2007] [Accepted: 05/10/2007] [Indexed: 11/23/2022]
Abstract
Experimental pK values of ionizable sidechains provide the most direct test for models representing dielectric shielding within the interior of a protein. However, only the strongly shifted pK values are particularly useful for discriminating among models. NMR titration studies have usually found only one or two such shifted pK values in each protein, so that the fitting of the experimental data to a uniform internal dielectric (epsilon(int)) model is not well constrained. The observed variation among proteins for such epsilon(int) estimates may reflect nonuniformity of dielectric shielding within each protein interior or qualitative differences between individual proteins. The differential amide kinetic acidities for a series of metal-substituted rubredoxins are shown to be consistent with Poisson-Boltzmann predictions of dielectric shielding that is relatively uniform for all of the amides that are sensitive to the metal charge, a region which corresponds to roughly 1/3 of the internal volume. The effective epsilon(int) values near 6 that are found in this study are significantly lower than many such estimates derived from sidechain pK measurements. The differing timeframes in which dielectric relaxation can respond to the highly transient peptide anion as compared to the longer lived states of the charged sidechains offers an explanation for the lower apparent dielectric constant deduced from these measurements.
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Affiliation(s)
- David M. LeMaster
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York, 12201 USA
| | - Janet S. Anderson
- Department of Chemistry, Union College, Schenectady, New York, 12308 USA
| | - Griselda Hernández
- Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, School of Public Health, University at Albany - SUNY, Empire State Plaza, Albany, New York, 12201 USA
- * Corresponding author Tel: (+1)518-474-4673, Fax: (+1)518-473-2900, E-mail:
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21
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Shinkarev VP, Wraight CA. Intermonomer electron transfer in the bc1 complex dimer is controlled by the energized state and by impaired electron transfer between low and high potential hemes. FEBS Lett 2007; 581:1535-41. [PMID: 17399709 PMCID: PMC1997310 DOI: 10.1016/j.febslet.2007.03.037] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 03/08/2007] [Accepted: 03/09/2007] [Indexed: 11/17/2022]
Abstract
The cytochrome bc(1) complex (commonly called Complex III) is the central enzyme of respiratory and photosynthetic electron transfer chains. X-ray structures have revealed the bc(1) complex to be a dimer, and show that the distance between low potential (b(L)) and high potential (b(H)) hemes, is similar to the distance between low potential hemes in different monomers. This suggests that electron transfer between monomers should occur at the level of the b(L) hemes. Here, we show that although the rate constant for b(L)-->b(L) electron transfer is substantial, it is slow compared to the forward rate from b(L) to b(H), and the intermonomer transfer only occurs after equilibration within the first monomer. The effective rate of intermonomer transfer is about 2-orders of magnitude slower than the direct intermonomer electron transfer.
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Affiliation(s)
- Vladimir P Shinkarev
- Department of Biochemistry, University of Illinois at Urbana Champaign, 156 Davenport Hall, 607 South Mathews Avenue, Urbana, IL 6l801, United States.
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22
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Hong J, Kharenko OA, Ogawa MY. Incorporating electron-transfer functionality into synthetic metalloproteins from the bottom-up. Inorg Chem 2007; 45:9974-84. [PMID: 17140193 PMCID: PMC2566827 DOI: 10.1021/ic060222j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The alpha-helical coiled-coil motif serves as a robust scaffold for incorporating electron-transfer (ET) functionality into synthetic metalloproteins. These structures consist of a supercoiling of two or more aplha helices that are formed by the self-assembly of individual polypeptide chains whose sequences contain a repeating pattern of hydrophobic and hydrophilic residues. Early work from our group attached abiotic Ru-based redox sites to the most surface-exposed positions of two stranded coiled-coils and used electron-pulse radiolysis to study both intra- and intermolecular ET reactions in these systems. Later work used smaller metallopeptides to investigate the effects of conformational gating within electrostatic peptide-protein complexes. We have recently designed the C16C19-GGY peptide, which contains Cys residues located at both the "a" and "d" positions of its third heptad repeat in order to construct a nativelike metal-binding domain within its hydrophobic core. It was shown that the binding of both Cd(II) and Cu(I) ions induces the peptide to undergo a conformational change from a disordered random coil to a metal-bridged coiled-coil. However, whereas the Cd(II)-protein exists as a two-stranded coiled-coil, the Cu(I) derivative exists as a four-stranded coiled-coil. Upon the incorporation of other metal ions, metal-bridged peptide dimers, tetramers, and hexamers are formed. The Cu(I)-protein is of particular interest because it exhibits a long-lived (microsecond) room-temperature luminescence at 600 nm. The luminophore in this protein is thought to be a multinuclear CuI4Cys4(N/O)4 cage complex, which can be quenched by exogenous electron acceptors in solution, as shown by emission-lifetime and transient-absorption experiments. It is anticipated that further investigation into these systems will contribute to the expanding effort of bioinorganic chemists to prepare new kinds of functionally active synthetic metalloproteins.
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23
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Moser CC, Page CC, Dutton PL. Darwin at the molecular scale: selection and variance in electron tunnelling proteins including cytochrome c oxidase. Philos Trans R Soc Lond B Biol Sci 2006; 361:1295-305. [PMID: 16873117 PMCID: PMC1647310 DOI: 10.1098/rstb.2006.1868] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Biological electron transfer is designed to connect catalytic clusters by chains of redox cofactors. A review of the characterized natural redox proteins with a critical eye for molecular scale measurement of variation and selection related to physiological function shows no statistically significant differences in the protein medium lying between cofactors engaged in physiologically beneficial or detrimental electron transfer. Instead, control of electron tunnelling over long distances relies overwhelmingly on less than 14 A spacing between the cofactors in a chain. Near catalytic clusters, shorter distances (commonly less than 7 A) appear to be selected to generate tunnelling frequencies sufficiently high to scale the barriers of multi-electron, bond-forming/-breaking catalysis at physiological rates. We illustrate this behaviour in a tunnelling network analysis of cytochrome c oxidase. In order to surmount the large, thermally activated, adiabatic barriers in the 5-10 kcal mol-1 range expected for H+ motion and O2 reduction at the binuclear centre of oxidase on the 10(3)-10(5) s-1 time-scale of respiration, electron access with a tunnelling frequency of 10(9) or 10(10) s-1 is required. This is provided by selecting closely placed redox centres, such as haem a (6.9 A) or tyrosine (4.9 A). A corollary is that more distantly placed redox centres, such as CuA, cannot rapidly scale the catalytic site barrier, but must send their electrons through more closely placed centres, avoiding direct short circuits that might circumvent proton pumping coupled to haems a to a3 electron transfer. The selection of distances and energetic barriers directs electron transfer from CuA to haem a rather than a3, without any need for delicate engineering of the protein medium to 'hard wire' electron transfer. Indeed, an examination of a large number of oxidoreductases provides no evidence of such naturally selected wiring of electron tunnelling pathways.
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Affiliation(s)
| | | | - P. Leslie Dutton
- Author and address for correspondence: 1005 Stellar-Chance Laboratories, 422 Curie Boulevard, Philadelphia, PA 19104-6059, USA ()
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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: 285] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2006] [Revised: 06/07/2006] [Accepted: 06/13/2006] [Indexed: 12/17/2022]
Abstract
Proton transfer and transport in water, gramicidin and some selected channels and bioenergetic proteins are reviewed. An attempt is made to draw some conclusions about how Nature designs long distance, proton transport functionality. The prevalence of water rather than amino acid hydrogen bonded chains is noted, and the possible benefits of waters as the major component are discussed qualitatively.
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Affiliation(s)
- Colin A Wraight
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA.
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25
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Noy D, Moser CC, Dutton PL. Design and engineering of photosynthetic light-harvesting and electron transfer using length, time, and energy scales. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2006; 1757:90-105. [PMID: 16457774 DOI: 10.1016/j.bbabio.2005.11.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2005] [Revised: 11/16/2005] [Accepted: 11/21/2005] [Indexed: 11/20/2022]
Abstract
Decades of research on the physical processes and chemical reaction-pathways in photosynthetic enzymes have resulted in an extensive database of kinetic information. Recently, this database has been augmented by a variety of high and medium resolution crystal structures of key photosynthetic enzymes that now include the two photosystems (PSI and PSII) of oxygenic photosynthetic organisms. Here, we examine the currently available structural and functional information from an engineer's point of view with the long-term goal of reproducing the key features of natural photosystems in de novo designed and custom-built molecular solar energy conversion devices. We find that the basic physics of the transfer processes, namely, the time constraints imposed by the rates of incoming photon flux and the various decay processes allow for a large degree of tolerance in the engineering parameters. Moreover, we find that the requirements to guarantee energy and electron transfer rates that yield high efficiency in natural photosystems are largely met by control of distance between chromophores and redox cofactors. Thus, for projected de novo designed constructions, the control of spatial organization of cofactor molecules within a dense array is initially given priority. Nevertheless, constructions accommodating dense arrays of different cofactors, some well within 1 nm from each other, still presents a significant challenge for protein design.
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Affiliation(s)
- Dror Noy
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
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26
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Matyushov DV. A phenomenological model of dynamical arrest of electron transfer in solvents in the glass-transition region. J Chem Phys 2005; 122:84507. [PMID: 15836063 DOI: 10.1063/1.1851981] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A phenomenological model of electron transfer reactions in solvents undergoing glass transition is discussed. The reaction constant cuts off slow polarization modes from the spectrum of nuclear thermal motions active on the observation time scale. The arrest of nuclear solvation in turn affects the reaction activation barrier making it dependent on the rate. The resultant rate constant is sought from a self-consistent equation. The model describes well the sharp change in the solvent Stokes shift of optical lines in the glass-transition region. It is also applied to describe the temperature dependence of primary charge separation and reduction of primary pair in photosynthetic reaction centers. The model shows that a weak dependence of the primary charge separation rate on temperature can be explained by dynamical arrest of nuclear solvation on the picosecond time scale of electron transfer. For reduction of primary pair by cytochrome, the model yields a sharp turnover of the reaction kinetics at the transition temperature when nuclear solvation freezes in.
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Affiliation(s)
- Dmitry V Matyushov
- Department of Chemistry and Biochemistry and the Center for the Early Events in Photosynthesis, Arizona State University, Tempe, AZ 85287-1604, USA.
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27
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Osyczka A, Moser CC, Dutton PL. Novel cyanide inhibition at cytochrome c1 of Rhodobacter capsulatus cytochrome bc1. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2004; 1655:71-6. [PMID: 15100019 DOI: 10.1016/j.bbabio.2003.07.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2003] [Revised: 07/14/2003] [Accepted: 07/14/2003] [Indexed: 11/18/2022]
Abstract
Oxidized cytochrome c(1) in photosynthetic bacterium Rhodobacter capsulatus cytochrome bc(1) reversibly binds cyanide with surprisingly high, micromolar affinity. The binding dramatically lowers the redox midpoint potential of heme c(1) and inhibits steady-state turnover activity of the enzyme. As cytochrome c(1), an auxiliary redox center of the high-potential chain of cytochrome bc(1), does not interact directly with the catalytic quinone/quinol binding sites Q(o) and Q(i), cyanide introduces a novel, Q-site independent locus of inhibition. This is the first report of a reversible inhibitor that manipulates the energetics and electron transfers of the high-potential redox chain of cytochrome bc(1), while maintaining quinone substrate catalytic sites in an intact form.
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Affiliation(s)
- Artur Osyczka
- The Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, 1004 Stellar-Chance Building, 422 Curie Boulevard, Philadelphia, PA 19104, USA.
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28
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Roszak AW, Howard TD, Southall J, Gardiner AT, Law CJ, Isaacs NW, Cogdell RJ. Crystal structure of the RC-LH1 core complex from Rhodopseudomonas palustris. Science 2003; 302:1969-72. [PMID: 14671305 DOI: 10.1126/science.1088892] [Citation(s) in RCA: 453] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The crystal structure at 4.8 angstrom resolution of the reaction center-light harvesting 1 (RC-LH1) core complex from Rhodopseudomonas palustris shows the reaction center surrounded by an oval LH1 complex that consists of 15 pairs of transmembrane helical alpha- and beta-apoproteins and their coordinated bacteriochlorophylls. Complete closure of the RC by the LH1 is prevented by a single transmembrane helix, out of register with the array of inner LH1 alpha-apoproteins. This break, located next to the binding site in the reaction center for the secondary electron acceptor ubiquinone (UQB), may provide a portal through which UQB can transfer electrons to cytochrome b/c1.
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Affiliation(s)
- Aleksander W Roszak
- Department of Chemistry, Institute of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
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