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Maroudas-Sklare N, Goren N, Yochelis S, Jung G, Keren N, Paltiel Y. Probing the design principles of photosynthetic systems through fluorescence noise measurement. Sci Rep 2024; 14:13877. [PMID: 38880795 DOI: 10.1038/s41598-024-64068-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 06/05/2024] [Indexed: 06/18/2024] Open
Abstract
Elucidating the energetic processes which govern photosynthesis, the engine of life on earth, are an essential goal both for fundamental research and for cutting-edge biotechnological applications. Fluorescent signal of photosynthetic markers has long been utilised in this endeavour. In this research we demonstrate the use of fluorescent noise analysis to reveal further layers of intricacy in photosynthetic energy transfer. While noise is a common tool analysing dynamics in physics and engineering, its application in biology has thus far been limited. Here, a distinct behaviour in photosynthetic pigments across various chemical and biological environments is measured. These changes seem to elucidate quantum effects governing the generation of oxidative radicals. Although our method offers insights, it is important to note that the interpretation should be further validated expertly to support as conclusive theory. This innovative method is simple, non-invasive, and immediate, making it a promising tool to uncover further, more complex energetic events in photosynthesis, with potential uses in environmental monitoring, agriculture, and food-tech.
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Affiliation(s)
- Naama Maroudas-Sklare
- Department of Applied Physics, Hebrew University of Jerusalem, 91904, Jerusalem, Israel
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Naama Goren
- Department of Applied Physics, Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Shira Yochelis
- Department of Applied Physics, Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Grzegorz Jung
- Department of Physics, Ben Gurion University of the Negev, 84105, Beer Sheva, Israel
- Instytut Fizyki PAN, 02668, Warszawa, Poland
| | - Nir Keren
- Department of Plant & Environmental Sciences, The Alexander Silberman Institute of Life Sciences, Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yossi Paltiel
- Department of Applied Physics, Hebrew University of Jerusalem, 91904, Jerusalem, Israel.
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2
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Matarèse BFE, Rusin A, Seymour C, Mothersill C. Quantum Biology and the Potential Role of Entanglement and Tunneling in Non-Targeted Effects of Ionizing Radiation: A Review and Proposed Model. Int J Mol Sci 2023; 24:16464. [PMID: 38003655 PMCID: PMC10671017 DOI: 10.3390/ijms242216464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
It is well established that cells, tissues, and organisms exposed to low doses of ionizing radiation can induce effects in non-irradiated neighbors (non-targeted effects or NTE), but the mechanisms remain unclear. This is especially true of the initial steps leading to the release of signaling molecules contained in exosomes. Voltage-gated ion channels, photon emissions, and calcium fluxes are all involved but the precise sequence of events is not yet known. We identified what may be a quantum entanglement type of effect and this prompted us to consider whether aspects of quantum biology such as tunneling and entanglement may underlie the initial events leading to NTE. We review the field where it may be relevant to ionizing radiation processes. These include NTE, low-dose hyper-radiosensitivity, hormesis, and the adaptive response. Finally, we present a possible quantum biological-based model for NTE.
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Affiliation(s)
- Bruno F. E. Matarèse
- Department of Haematology, University of Cambridge, Cambridge CB2 1TN, UK;
- Department of Physics, University of Cambridge, Cambridge CB2 1TN, UK
| | - Andrej Rusin
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
| | - Colin Seymour
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
| | - Carmel Mothersill
- Department of Biology, McMaster University, Hamilton, ON L8S 4L8, Canada; (A.R.); (C.S.)
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3
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Zheltikov AM. Thermal and Quantum Barrier Passage as Potential-Driven Markovian Dynamics. J Phys Chem B 2023; 127:9413-9422. [PMID: 37905974 PMCID: PMC10863070 DOI: 10.1021/acs.jpcb.3c02744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 09/08/2023] [Indexed: 11/02/2023]
Abstract
Rapidly progressing laser technologies provide powerful tools to study potential barrier-passage dynamics in physical, chemical, and biological systems with unprecedented temporal and spatial resolution and a remarkable chemical and structural specificity. The available theories of barrier passage, however, operate with equations, potentials, and parameters that are best suited for a specific area of research and a specific class of systems and processes. Making connections among these theories is often anything but easy. Here, we address this problem by presenting a unified framework for the description of a vast variety of classical and quantum barrier-passage phenomena, revealing an innate connection between various types of barrier-passage dynamics and providing closed-form equations showing how the signature exponentials in classical and quantum barrier-passage rates relate to and translate into each other. In this framework, the Arrhenius-law kinetics, the emergence of the Gibbs distribution, Hund's molecular wave-packet well-to-well oscillatory dynamics, Keldysh photoionization, and Kramers' escape over a potential barrier are all understood as manifestations of a potential-driven Markovian dynamics whereby a system evolves from a state of local stability. Key to the irreducibility of quantum tunneling to thermally activated barrier passage is the difference in the ways the diffusion-driving potentials emerge in these two tunneling settings, giving rise to stationary states with a distinctly different structure.
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Affiliation(s)
- A. M. Zheltikov
- Institute for Quantum Science and Engineering,
Department of Physics and Astronomy, Texas
A&M University, College Station, Texas 77843, United States
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4
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Huang H, Xue L, Bu Y. Multifunctional Roles of Clathrate Hydrate Nanoreactors for CO 2 Reduction. Chemistry 2023; 29:e202302253. [PMID: 37580312 DOI: 10.1002/chem.202302253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/12/2023] [Accepted: 08/14/2023] [Indexed: 08/16/2023]
Abstract
In this study, we explore a possible platform for the CO2 reduction (CO2 R) in one of water's solid phases, namely clathrate hydrates (CHs), by ab initio molecular dynamics and well-tempered metadynamics simulations with periodic boundary conditions. We found that the stacked H2 O nanocages in CHs help to initialize CO2 R by increasing the electron-binding ability of CO2 . The substantial CO2 R processes are further influenced by the hydrogen bond networks in CHs. The first intermediate CO2 - in this process can be stabilized through cage structure reorganization into the H-bonded [CO2 - ⋅⋅⋅H-OHcage ] complex. Further cooperative structural dynamics enables the complex to convert into a vital transient [CO2 2- ⋅⋅⋅H-OHcage ] intermediate in a low-barrier disproportionation-like process. Such a highly reactive intermediate spontaneously triggers subsequent double proton transfer along its tethering H-bonds, finally converting it into HCOOH. These hydrogen-bonded nanoreactors feature multiple functions in facilitating CO2 R such as confining, tethering, H-bond catalyzing and proton pumping. Our findings have a general interest and extend the knowledge of CO2 R into porous aqueous systems.
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Affiliation(s)
- Haibei Huang
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Lijuan Xue
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
| | - Yuxiang Bu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, P. R. China
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5
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Bérczi A, Márton Z, Laskay K, Tóth A, Rákhely G, Duzs Á, Sebők-Nagy K, Páli T, Zimányi L. Spectral and Redox Properties of a Recombinant Mouse Cytochrome b561 Protein Suggest Transmembrane Electron Transfer Function. Molecules 2023; 28:molecules28052261. [PMID: 36903505 PMCID: PMC10005133 DOI: 10.3390/molecules28052261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 02/23/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Cytochrome b561 proteins (CYB561s) are integral membrane proteins with six trans-membrane domains, two heme-b redox centers, one on each side of the host membrane. The major characteristics of these proteins are their ascorbate reducibility and trans-membrane electron transferring capability. More than one CYB561 can be found in a wide range of animal and plant phyla and they are localized in membranes different from the membranes participating in bioenergization. Two homologous proteins, both in humans and rodents, are thought to participate-via yet unidentified way-in cancer pathology. The recombinant forms of the human tumor suppressor 101F6 protein (Hs_CYB561D2) and its mouse ortholog (Mm_CYB561D2) have already been studied in some detail. However, nothing has yet been published about the physical-chemical properties of their homologues (Hs_CYB561D1 in humans and Mm_CYB561D1 in mice). In this paper we present optical, redox and structural properties of the recombinant Mm_CYB561D1, obtained based on various spectroscopic methods and homology modeling. The results are discussed in comparison to similar properties of the other members of the CYB561 protein family.
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Affiliation(s)
- Alajos Bérczi
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - Zsuzsanna Márton
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - Krisztina Laskay
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - András Tóth
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
| | - Gábor Rákhely
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
| | - Ágnes Duzs
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Department of Biotechnology, University of Szeged, H-6726 Szeged, Hungary
| | - Krisztina Sebők-Nagy
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - Tibor Páli
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre Szeged, H-6726 Szeged, Hungary
- Correspondence:
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6
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Cardiac Contractility Modulation Therapy in Patients with Amyloid Cardiomyopathy and Heart Failure, Case Report, Review of the Biophysics of CCM Function, and AMY-CCM Registry Presentation. J Clin Med 2023; 12:jcm12031184. [PMID: 36769832 PMCID: PMC9917884 DOI: 10.3390/jcm12031184] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Cardiac amyloidosis may result in an aggressive form of heart failure (HF). Cardiac contractility modulation (CCM) has been shown to be a concrete therapeutic option in patients with symptomatic HF, but there is no evidence of its application in patients with cardiac amyloidosis. We present the case of TTR amyloidosis, where CCM therapy proved to be effective. The patient had a history of multiple HF hospitalizations due to an established diagnosis of wild type TTR-Amyloidosis with significant cardiac involvement. Since he was highly symptomatic, except during continuous dobutamine and diuretic infusion, it was opted to pursue CCM therapy device implantation. At follow up, a significant improvement in clinical status was reported with an increase of EF, functional status (6 min walk test improved from zero meters at baseline, to 270 m at 1 month and to 460 m at 12 months), and a reduction in pulmonary pressures. One year after device implantation, no other HF hospital admission was needed. CCM therapy may be effective in this difficult clinical setting. The AMY-CCM Registry, which has just begun, will evaluate the efficacy of CCM in patients with HF and diagnosed TTR amyloidosis to bring new evidence on its potential impact as a therapeutic option.
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7
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Phenylene-linked tetrapyrrole arrays containing free base and diverse metal chelate forms – Versatile synthetic architectures for catalysis and artificial photosynthesis. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2021.214278] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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8
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Khoroshyy P, Tenger K, Chertkova RV, Bocharova OV, Kirpichnikov MP, Borovok N, Groma GI, Dolgikh DA, Kotlyar AB, Zimányi L. Kinetics and Energetics of Intramolecular Electron Transfer in Single-Point Labeled TUPS-Cytochrome c Derivatives. Molecules 2021; 26:molecules26226976. [PMID: 34834068 PMCID: PMC8621336 DOI: 10.3390/molecules26226976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 11/13/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
Electron transfer within and between proteins is a fundamental biological phenomenon, in which efficiency depends on several physical parameters. We have engineered a number of horse heart cytochrome c single-point mutants with cysteine substitutions at various positions of the protein surface. To these cysteines, as well as to several native lysine side chains, the photoinduced redox label 8-thiouredopyrene-1,3,6-trisulfonate (TUPS) was covalently attached. The long-lived, low potential triplet excited state of TUPS, generated with high quantum efficiency, serves as an electron donor to the oxidized heme c. The rates of the forward (from the label to the heme) and the reverse (from the reduced heme back to the oxidized label) electron transfer reactions were obtained from multichannel and single wavelength flash photolysis absorption kinetic experiments. The electronic coupling term and the reorganization energy for electron transfer in this system were estimated from temperature-dependent experiments and compared with calculated parameters using the crystal and the solution NMR structure of the protein. These results together with the observation of multiexponential kinetics strongly support earlier conclusions that the flexible arm connecting TUPS to the protein allows several shortcut routes for the electron involving through space jumps between the label and the protein surface.
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Affiliation(s)
- Petro Khoroshyy
- Institute of Biophysics, Biological Research Centre, Temesvári Körút 62, H-6726 Szeged, Hungary; (P.K.); (K.T.); (G.I.G.)
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Flemingovo Náměstí 542/2, 16000 Prague, Czech Republic
| | - Katalin Tenger
- Institute of Biophysics, Biological Research Centre, Temesvári Körút 62, H-6726 Szeged, Hungary; (P.K.); (K.T.); (G.I.G.)
| | - Rita V. Chertkova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.V.C.); (O.V.B.); (M.P.K.); (D.A.D.)
| | - Olga V. Bocharova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.V.C.); (O.V.B.); (M.P.K.); (D.A.D.)
| | - Mikhail P. Kirpichnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.V.C.); (O.V.B.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, Leninskie Gory 1/12, 119899 Moscow, Russia
| | - Natalia Borovok
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel; (N.B.); (A.B.K.)
| | - Géza I. Groma
- Institute of Biophysics, Biological Research Centre, Temesvári Körút 62, H-6726 Szeged, Hungary; (P.K.); (K.T.); (G.I.G.)
| | - Dmitry A. Dolgikh
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya 16/10, 117997 Moscow, Russia; (R.V.C.); (O.V.B.); (M.P.K.); (D.A.D.)
- Biology Department, Lomonosov Moscow State University, Leninskie Gory 1/12, 119899 Moscow, Russia
| | - Alexander B. Kotlyar
- Department of Biochemistry and Molecular Biology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel; (N.B.); (A.B.K.)
| | - László Zimányi
- Institute of Biophysics, Biological Research Centre, Temesvári Körút 62, H-6726 Szeged, Hungary; (P.K.); (K.T.); (G.I.G.)
- Correspondence:
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9
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Vershubskii AV, Tikhonov AN. Structural and Functional Aspects of Electron Transport Thermoregulation and ATP Synthesis in Chloroplasts. BIOCHEMISTRY (MOSCOW) 2021; 86:92-104. [PMID: 33705285 DOI: 10.1134/s0006297921010090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The review is focused on analysis of the mechanisms of temperature-dependent regulation of electron transport and ATP synthesis in chloroplasts of higher plants. Importance of photosynthesis thermoregulation is determined by the fact that plants are ectothermic organisms, whose own temperature depends on the ambient temperature. The review discusses the effects of temperature on the following processes in thylakoid membranes: (i) photosystem 2 activity and plastoquinone reduction; (ii) electron transfer from plastoquinol (via the cytochrome b6f complex and plastocyanin) to photosystem 1; (iii) transmembrane proton transfer; and (iv) ATP synthesis. The data on the relationship between the functional properties of chloroplasts (photosynthetic transfer of electrons and protons, functioning of ATP synthase) and structural characteristics of membrane lipids (fluidity) obtained by electron paramagnetic resonance studies are presented.
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10
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Sahu N, Richardson JO, Berger R. Instanton calculations of tunneling splittings in chiral molecules. J Comput Chem 2021; 42:210-221. [PMID: 33259074 DOI: 10.1002/jcc.26447] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/20/2020] [Accepted: 08/27/2020] [Indexed: 11/11/2022]
Abstract
We report the ground state tunneling splittings (ΔE± ) of a number of axially chiral molecules using the ring-polymer instanton (RPI) method (J. Chem. Phys., 2011, 134, 054109). The list includes isotopomers of hydrogen dichalcogenides H2 X2 (X = O, S, Se, Te, and Po), hydrogen thioperoxide HSOH and dichlorodisulfane S2 Cl2 . Ab initio electronic-structure calculations have been performed on the level of second-order Møller-Plesset perturbation (MP2) theory either with split-valance basis sets or augmented correlation-consistent basis sets on H, O, S, and Cl atoms. Energy-consistent pseudopotential and corresponding triple zeta basis sets of the Stuttgart group are used on Se, Te, and Po atoms. The results are further improved using single point calculations performed at the coupled cluster level with iterative singles and doubles and perturbative triples amplitudes. When available for comparison, our computed values of ΔE± are found to lie within the same order of magnitude as values reported in the literature, although RPI also provides predictions for H2 Po2 and S2 Cl2 , which have not previously been directly calculated. Since RPI is a single-shot method which does not require detailed prior knowledge of the optimal tunneling path, it offers an effective way for estimating the tunneling dynamics of more complex chiral molecules, and especially those with small tunneling splittings.
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Affiliation(s)
- Nityananda Sahu
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
| | | | - Robert Berger
- Fachbereich Chemie, Theoretische Chemie, Philipps Universität Marburg, Marburg, Germany
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11
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Wang Z, Shaik S, Wang B. Conformational Motion of Ferredoxin Enables Efficient Electron Transfer to Heme in the Full-Length P450 TT. J Am Chem Soc 2021; 143:1005-1016. [PMID: 33426875 DOI: 10.1021/jacs.0c11279] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome P450 monooxygenases (P450s) are versatile biocatalysts used in natural products biosynthesis, xenobiotic metabolisms, and biotechnologies. In P450s, the electrons required for O2 activation are supplied by NAD(P)H through stepwise electron transfers (ETs) mediated by redox partners. While much is known about the machinery of the catalytic cycle of P450s, the mechanisms of long-range ET are largely unknown. Very recently, the first crystal structure of full-length P450TT was solved. This enables us to decipher the interdomain ET mechanism between the [2Fe-2S]-containing ferredoxin and the heme, by use of molecular dynamics simulations. In contrast to the "distal" conformation characterized in the crystal structure where the [2Fe-2S] cluster is ∼28 Å away from heme-Fe, our simulations demonstrated a "proximal" conformation of [2Fe-2S] that is ∼17 Å [and 13.7 Å edge-to-edge] away from heme-Fe, which may enable the interdomain ET. Key residues involved in ET pathways and interdomain complexation were identified, some of which have already been verified by recent mutation studies. The conformational transit of ferredoxin between "distal" and "proximal" was found to be controlled mostly by the long-range electrostatic interactions between the ferredoxin domain and the other two domains. Furthermore, our simulations show that the full-length P450TT utilizes a flexible ET pathway that resembles either P450Scc or P450cam. Thus, this study provides a uniform picture of the ET process between reductase domains and heme domain.
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Affiliation(s)
- Zhanfeng Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Sason Shaik
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Binju Wang
- State Key Laboratory of Structural Chemistry of Solid Surface and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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12
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Dunnett AJ, Chin AW. Simulating Quantum Vibronic Dynamics at Finite Temperatures With Many Body Wave Functions at 0 K. Front Chem 2021; 8:600731. [PMID: 33505954 PMCID: PMC7831969 DOI: 10.3389/fchem.2020.600731] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/24/2020] [Indexed: 11/16/2022] Open
Abstract
For complex molecules, nuclear degrees of freedom can act as an environment for the electronic “system” variables, allowing the theory and concepts of open quantum systems to be applied. However, when molecular system-environment interactions are non-perturbative and non-Markovian, numerical simulations of the complete system-environment wave function become necessary. These many body dynamics can be very expensive to simulate, and extracting finite-temperature results—which require running and averaging over many such simulations—becomes especially challenging. Here, we present numerical simulations that exploit a recent theoretical result that allows dissipative environmental effects at finite temperature to be extracted efficiently from a single, zero-temperature wave function simulation. Using numerically exact time-dependent variational matrix product states, we verify that this approach can be applied to vibronic tunneling systems and provide insight into the practical problems lurking behind the elegance of the theory, such as the rapidly growing numerical demands that can appear for high temperatures over the length of computations.
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Affiliation(s)
- Angus J Dunnett
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, Paris, France
| | - Alex W Chin
- Sorbonne Université, CNRS, Institut des NanoSciences de Paris, Paris, France
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13
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Abstract
Enzymology is concerned with the study of enzyme structure, function, regulation and kinetics. It is an interdisciplinary subject that can be treated as an exclusive sphere of exhaustive inquiry within mathematical, physico-chemical and biological sciences. Hence, teaching of enzymology, in general, and enzyme kinetics, in particular, should be undertaken in an interdisciplinary manner for a holistic appreciation of this subject. Further, analogous examples from everyday life should form an integral component of the teaching for an intuitive grasp of the subject matter. Furthermore, simulation-based appreciation of enzyme kinetics should be preferred over simplifying assumptions and approximations of traditional enzyme kinetics teaching. In this Words of Advice, I outline the domain depth of enzymology across the various disciplines and provide initial ideas on how appropriate analogies can provide firm insights into the subject. Further, I demonstrate how an intuitive feel for the subject can help not only in grasping abstract concepts but also extending it in experimental design and subsequent interpretation. Use of simulations in grasping complex concepts is also advocated given the advantages this medium offers over traditional approaches involving images and molecular models. Furthermore, I discuss the merits of incorporating the historical backdrop of major discoveries in enzymological teaching. We, at AstraZeneca, have experimented with this approach with the desired outcome of generating interest in the subject from people practising diverse disciplines.
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Affiliation(s)
- Bharath Srinivasan
- Mechanistic Biology and Profiling, Discovery Sciences, R&D, AstraZeneca, Cambridge, UK
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14
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Minnis H, Posserud MB, Thompson L, Gillberg C. Hypothesis: The highly folded brain surface might be structured and located so as to facilitate inter-brain synchronization. RESEARCH IDEAS AND OUTCOMES 2020. [DOI: 10.3897/rio.6.e48887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We integrate recent findings from neuro-anatomy, electroencephalography, quantum biology and social/neurodevelopment to propose that the brain surface might be specialised for communication with other brains.
Ground breaking, but still small-scale, research has demonstrated that human brains can act in synchrony and detect the brain activity of other human brains. Group aggregation, in all species, maximises community support and safety but does not depend on verbal or visual interaction. The morphology of the brain’s outermost layers, across a wide range of species, exhibits a highly folded fractal structure that is likely to maximise exchange at the surface: in humans, a reduced brain surface area is associated with disorders of social communication. The brain sits in a vulnerable exposed location where it is prone to damage, rather than being housed in a central location such as within the ribcage.
These observations have led us to the hypothesis that the brain surface might be specialised for interacting with other brains at its surface, allowing synchronous non-verbal interaction. To our knowledge, this has not previously been proposed or investigated.
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15
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Understanding resonant charge transport through weakly coupled single-molecule junctions. Nat Commun 2019; 10:4628. [PMID: 31604934 PMCID: PMC6789103 DOI: 10.1038/s41467-019-12625-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 09/20/2019] [Indexed: 11/24/2022] Open
Abstract
Off-resonant charge transport through molecular junctions has been extensively studied since the advent of single-molecule electronics and is now well understood within the framework of the non-interacting Landauer approach. Conversely, gaining a qualitative and quantitative understanding of the resonant transport regime has proven more elusive. Here, we study resonant charge transport through graphene-based zinc-porphyrin junctions. We experimentally demonstrate an inadequacy of non-interacting Landauer theory as well as the conventional single-mode Franck–Condon model. Instead, we model overall charge transport as a sequence of non-adiabatic electron transfers, with rates depending on both outer and inner-sphere vibrational interactions. We show that the transport properties of our molecular junctions are determined by a combination of electron–electron and electron-vibrational coupling, and are sensitive to interactions with the wider local environment. Furthermore, we assess the importance of nuclear tunnelling and examine the suitability of semi-classical Marcus theory as a description of charge transport in molecular devices. The mechanism of nonadiabatic electron transfer in molecular systems is an important research topic for understanding various chemical reactions. Thomas et al. quantify resonant charge transport through single-molecule junctions as a model system for examining quantum and Marcus theories.
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16
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Santabarbara S, Casazza AP. Kinetics and Energetics of Phylloquinone Reduction in Photosystem I: Insight From Modeling of the Site Directed Mutants. FRONTIERS IN PLANT SCIENCE 2019; 10:852. [PMID: 31312208 PMCID: PMC6614487 DOI: 10.3389/fpls.2019.00852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/13/2019] [Indexed: 06/10/2023]
Abstract
Two phylloquinone molecules (A 1), one being predominantly coordinated by PsaA subunit residues (A 1A) the other by those of PsaB (A 1B), act as intermediates in the two parallel electron transfer chains of Photosystem I. The oxidation kinetics of the two phyllosemiquinones by the iron-sulfur cluster FX differ by approximately one order of magnitude, with A 1 A - being oxidized in about 200 ns and A 1 B - in about 20 ns. These differences are generally explained in terms of asymmetries in the driving force for FX reduction on the two electron transfer chains. Site directed mutations of conserved amino acids composing the A 1 binding site have been engineered on both reaction center subunits, and proved to affect selectively the oxidation lifetime of either A 1 A - , for PsaA mutants, or A 1 B - , for PsaB mutants. The mutation effects are here critically reviewed, also by novel modeling simulations employing the tunneling formalism to estimate the electron transfer rates. Three main classes of mutation effects are in particular addressed: (i) those leading to an acceleration, (ii) those leading to a moderated slowing (~5-folds), and (iii) those leading to a severe slowing (>20-folds) of the kinetics. The effect of specific amino acid perturbations contributing to the poising of the phylloquinones redox potential and, in turn, to PSI functionality, is discussed.
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Affiliation(s)
- Stefano Santabarbara
- Centre for Fundamental Research in Photosynthesis, Vergiate, Italy
- Photosynthesis Research Unit, Centro Studi sulla Biologia Cellulare e Molecolare delle Piante, Milan, Italy
| | - Anna Paola Casazza
- Istituto di Biologia e Biotecnologia Agraria, Consiglio Nazionale delle Ricerche, Milan, Italy
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17
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Ru X, Zhang P, Beratan DN. Assessing Possible Mechanisms of Micrometer-Scale Electron Transfer in Heme-Free Geobacter sulfurreducens Pili. J Phys Chem B 2019; 123:5035-5047. [PMID: 31095388 DOI: 10.1021/acs.jpcb.9b01086] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The electrically conductive pili of Geobacter sulfurreducens are of both fundamental and practical interest. They facilitate extracellular and interspecies electron transfer (ET) and also provide an electrical interface between living and nonliving systems. We examine the possible mechanisms of G. sulfurreducens electron transfer in regimes ranging from incoherent to coherent transport. For plausible ET parameters, electron transfer in G. sulfurreducens bacterial nanowires mediated only by the protein is predicted to be dominated by incoherent hopping between phenylalanine (Phe) and tyrosine (Tyr) residues that are 3 to 4 Å apart, where Phe residues in the hopping pathways may create delocalized "islands." This mechanism could be accessible in the presence of strong oxidants that are capable of oxidizing Phe and Tyr residues. We also examine the physical requirements needed to sustain biological respiration via nanowires. We find that the hopping regimes with ET rates on the order of 108 s-1 between Phe islands and Tyr residues, and conductivities on the order of mS/cm, can support ET fluxes that are compatible with cellular respiration rates, although sustaining this delocalization in the heterogeneous protein environment may be challenging. Computed values of fully coherent electron fluxes through the pili are orders of magnitude too low to support microbial respiration. We suggest experimental probes of the transport mechanism based on mutant studies to examine the roles of aromatic amino acids and yet to be identified redox cofactors.
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Affiliation(s)
- Xuyan Ru
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - Peng Zhang
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States
| | - David N Beratan
- Department of Chemistry , Duke University , Durham , North Carolina 27708 , United States.,Department of Biochemistry , Duke University , Durham , North Carolina 27710 , United States.,Department of Physics , Duke University , Durham , North Carolina 27708 , United States
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18
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Cvitaš MT. Quadratic String Method for Locating Instantons in Tunneling Splitting Calculations. J Chem Theory Comput 2018; 14:1487-1500. [DOI: 10.1021/acs.jctc.7b00881] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marko T. Cvitaš
- Department of Physical Chemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia
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19
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Hay ME, Hui Wong S, Mukherjee S, Boudouris BW. Controlling open‐shell loading in norbornene‐based radical polymers modulates the solid‐state charge transport exponentially. ACTA ACUST UNITED AC 2017. [DOI: 10.1002/polb.24406] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Martha E. Hay
- Charles D. Davidson School of Chemical Engineering, Purdue UniversityWest Lafayette Indiana47907 USA
| | - Si Hui Wong
- Charles D. Davidson School of Chemical Engineering, Purdue UniversityWest Lafayette Indiana47907 USA
| | - Sanjoy Mukherjee
- Charles D. Davidson School of Chemical Engineering, Purdue UniversityWest Lafayette Indiana47907 USA
| | - Bryan W. Boudouris
- Charles D. Davidson School of Chemical Engineering, Purdue UniversityWest Lafayette Indiana47907 USA
- Department of ChemistryPurdue UniversityWest Lafayette Indiana47907 USA
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20
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Gunner MR, Koder R. The design features cells use to build their transmembrane proton gradient. Phys Biol 2017; 14:013001. [DOI: 10.1088/1478-3975/14/1/013001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Kumpulainen T, Lang B, Rosspeintner A, Vauthey E. Ultrafast Elementary Photochemical Processes of Organic Molecules in Liquid Solution. Chem Rev 2016; 117:10826-10939. [DOI: 10.1021/acs.chemrev.6b00491] [Citation(s) in RCA: 249] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tatu Kumpulainen
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Bernhard Lang
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Arnulf Rosspeintner
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry,
Sciences II, University of Geneva, 30 Quai Ernest Ansermet, CH-1211 Geneva 4, Switzerland
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22
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Santabarbara S, Bullock B, Rappaport F, Redding KE. Controlling electron transfer between the two cofactor chains of photosystem I by the redox state of one of their components. Biophys J 2016; 108:1537-1547. [PMID: 25809266 DOI: 10.1016/j.bpj.2015.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 12/29/2014] [Accepted: 01/07/2015] [Indexed: 10/23/2022] Open
Abstract
Two functional electron transfer (ET) chains, related by a pseudo-C2 symmetry, are present in the reaction center of photosystem I (PSI). Due to slight differences in the environment around the cofactors of the two branches, there are differences in both the kinetics of ET and the proportion of ET that occurs on the two branches. The strongest evidence that this is indeed the case relied on the observation that the oxidation rates of the reduced phylloquinone (PhQ) cofactor differ by an order of magnitude. Site-directed mutagenesis of residues involved in the respective PhQ-binding sites resulted in a specific alteration of the rates of semiquinone oxidation. Here, we show that the PsaA-F689N mutation results in an ∼100-fold decrease in the observed rate of PhQA(-) oxidation. This is the largest change of PhQA(-) oxidation kinetics observed so far for a single-point mutation, resulting in a lifetime that exceeds that of the terminal electron donor, P700(+). This situation allows a second photochemical charge separation event to be initiated before PhQA(-) has decayed, thereby mimicking in PSI a situation that occurs in type II reaction centers. The results indicate that the presence of PhQA(-) does not impact the overall quantum yield and leads to an almost complete redistribution of the fractional utilization of the two functional ET chains, in favor of the one that does not bear the charged species. The evolutionary implications of these results are also briefly discussed.
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Affiliation(s)
- Stefano Santabarbara
- Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona; Institut de Biologie Physico-Chimique, UMR7141 CNRS-UPMC, Paris, France; Istituto di Biofisica, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Bradford Bullock
- Department of Chemistry, University of Alabama, Tuscaloosa, Alabama
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimique, UMR7141 CNRS-UPMC, Paris, France.
| | - Kevin E Redding
- Department of Chemistry & Biochemistry, Arizona State University, Tempe, Arizona.
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23
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Song P, Li Y, Ma F, Pullerits T, Sun M. Photoinduced Electron Transfer in Organic Solar Cells. CHEM REC 2016; 16:734-53. [PMID: 26853631 DOI: 10.1002/tcr.201500244] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2012] [Indexed: 11/07/2022]
Abstract
Electron transfer (ET) is the key process in light-driven charge separation reactions in organic solar cells. The current review summarizes the progress in theoretical modelling of ET in these materials. First we give an account of ET, with a description originating from Marcus theory. We systematically go through all the relevant parameters and show how they depend on different material properties, and discuss the consequences such dependencies have for the performance of the devices. Finally, we present a set of visualization methods which have proven to be very useful in analyzing the elementary processes in absorption and charge separation events. Such visualization tools help us to understand the properties of the photochemical and photobiological systems in solar cells.
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Affiliation(s)
- Peng Song
- Department of Physics, Liaoning University, Shenyang, 110036, P. R. China.,Beijing National Laboratory for Condensed Matter Physics, Institute of Physics Chinese Academy of Science, Beijing, 100190, P. R. China.,State Key laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics Chinese Academy of Science, Dalian, 116023, P. R. China
| | - Yuanzuo Li
- Beijing National Laboratory for Condensed Matter Physics, Institute of Physics Chinese Academy of Science, Beijing, 100190, P. R. China.,College of Science, Northeast Forestry University, Harbin, 150040, P. R. China
| | - Fengcai Ma
- Department of Physics, Liaoning University, Shenyang, 110036, P. R. China
| | - Tõnu Pullerits
- Department of Chemical Physics, Lund University, Box 124, Lund, 22100, Sweden.,State Key laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics Chinese Academy of Science, Dalian, 116023, P. R. China
| | - Mengtao Sun
- Department of Physics, Liaoning University, Shenyang, 110036, P. R. China.,Beijing National Laboratory for Condensed Matter Physics, Institute of Physics Chinese Academy of Science, Beijing, 100190, P. R. China
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24
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Cvitaš MT, Althorpe SC. Locating Instantons in Calculations of Tunneling Splittings: The Test Case of Malonaldehyde. J Chem Theory Comput 2016; 12:787-803. [PMID: 26756608 DOI: 10.1021/acs.jctc.5b01073] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The recently developed ring-polymer instanton (RPI) method [J. Chem. Phys. 2011, 134, 054109] is an efficient technique for calculating approximate tunneling splittings in high-dimensional molecular systems. The key step is locating the instanton tunneling-path at zero temperature. Here, we show that techniques previously designed for locating instantons in finite-temperature rate calculations can be adapted to the RPI method, where they become extremely efficient, reducing the number of potential energy calls by 2 orders of magnitude. We investigate one technique that employs variable time steps to minimize the action integral, and two that employ equally spaced position steps to minimize the abbreviated (i.e., Jacobi) action integral, using respectively the nudged elastic band (NEB) and string methods. We recommend use of the latter because it is parameter-free, but all three methods give comparable efficiency savings. Having located the instanton pathway, we then interpolate the instanton path onto a fine grid of imaginary time points, allowing us to compute the fluctuation prefactor. The crucial modification needed to the original finite-temperature algorithms is to allow the end points of the zero-temperature instanton path to describe overall rotations, which is done using a standard quaternion algorithm. These approaches will allow the RPI method to be combined effectively with expensive potential energy surfaces or on-the-fly electronic structure methods.
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Affiliation(s)
- Marko T Cvitaš
- Department of Physical Chemistry, Ruđer Bošković Institute , Bijenička Cesta 54, 10000 Zagreb, Croatia
| | - Stuart C Althorpe
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
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25
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Sjulstok E, Olsen JMH, Solov'yov IA. Quantifying electron transfer reactions in biological systems: what interactions play the major role? Sci Rep 2015; 5:18446. [PMID: 26689792 PMCID: PMC4686879 DOI: 10.1038/srep18446] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022] Open
Abstract
Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.
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Affiliation(s)
- Emil Sjulstok
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.,Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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26
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Hagras MA, Hayashi T, Stuchebrukhov AA. Quantum Calculations of Electron Tunneling in Respiratory Complex III. J Phys Chem B 2015; 119:14637-51. [DOI: 10.1021/acs.jpcb.5b09424] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Muhammad A. Hagras
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Tomoyuki Hayashi
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
| | - Alexei A. Stuchebrukhov
- Department of Chemistry, University of California, One Shields
Avenue, Davis, California 95616, United States
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27
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Delor M, Sazanovich IV, Towrie M, Weinstein JA. Probing and Exploiting the Interplay between Nuclear and Electronic Motion in Charge Transfer Processes. Acc Chem Res 2015; 48:1131-9. [PMID: 25789559 DOI: 10.1021/ar500420c] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The Born-Oppenheimer approximation refers to the assumption that the nuclear and electronic wave functions describing a molecular system evolve and can be determined independently. It is now well-known that this approximation often breaks down and that nuclear-electronic (vibronic) coupling contributes greatly to the ultrafast photophysics and photochemistry observed in many systems ranging from simple molecules to biological organisms. In order to probe vibronic coupling in a time-dependent manner, one must use spectroscopic tools capable of correlating the motions of electrons and nuclei on an ultrafast time scale. Recent developments in nonlinear multidimensional electronic and vibrational spectroscopies allow monitoring both electronic and structural factors with unprecedented time and spatial resolution. In this Account, we present recent studies from our group that make use of different variants of frequency-domain transient two-dimensional infrared (T-2DIR) spectroscopy, a pulse sequence combining electronic and vibrational excitations in the form of a UV-visible pump, a narrowband (12 cm(-1)) IR pump, and a broadband (400 cm(-1)) IR probe. In the first example, T-2DIR is used to directly compare vibrational dynamics in the ground and relaxed electronic excited states of Re(Cl)(CO)3(4,4'-diethylester-2,2'-bipyridine) and Ru(4,4'-diethylester-2,2'-bipyridine)2(NCS)2, prototypical charge transfer complexes used in photocatalytic CO2 reduction and electron injection in dye-sensitized solar cells. The experiments show that intramolecular vibrational redistribution (IVR) and vibrational energy transfer (VET) are up to an order of magnitude faster in the triplet charge transfer excited state than in the ground state. These results show the influence of electronic arrangement on vibrational coupling patterns, with direct implications for vibronic coupling mechanisms in charge transfer excited states. In the second example, we show unambiguously that electronic and vibrational movement are coupled in a donor-bridge-acceptor complex based on a Pt(II) trans-acetylide design motif. Time-resolved IR (TRIR) spectroscopy reveals that the rate of electron transfer (ET) is highly dependent on the amount of excess energy localized on the bridge following electronic excitation. Using an adaptation of T-2DIR, we are able to selectively perturb bridge-localized vibrational modes during charge separation, resulting in the donor-acceptor charge separation pathway being completely switched off, with all excess energy redirected toward the formation of a long-lived intraligand triplet state. A series of control experiments reveal that this effect is mode specific: it is only when the high-frequency bridging C≡C stretching mode is pumped that radical changes in photoproduct yields are observed. These experiments therefore suggest that one may perturb electronic movement by stimulating structural motion along the reaction coordinate using IR light. These studies add to a growing body of evidence suggesting that controlling the pathways and efficiency of charge transfer may be achieved through synthetic and perturbative approaches aiming to modulate vibronic coupling. Achieving such control would represent a breakthrough for charge transfer-based applications such as solar energy conversion and molecular electronics.
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Affiliation(s)
- Milan Delor
- Department
of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Igor V. Sazanovich
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, STFC, Chilton, Oxfordshire OX11 0QX, U.K
| | - Michael Towrie
- Central
Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, STFC, Chilton, Oxfordshire OX11 0QX, U.K
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28
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Delor M, Scattergood PA, Sazanovich IV, Parker AW, Greetham GM, Meijer AJHM, Towrie M, Weinstein JA. Toward control of electron transfer in donor-acceptor molecules by bond-specific infrared excitation. Science 2015; 346:1492-5. [PMID: 25525241 DOI: 10.1126/science.1259995] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Electron transfer (ET) from donor to acceptor is often mediated by nuclear-electronic (vibronic) interactions in molecular bridges. Using an ultrafast electronic-vibrational-vibrational pulse-sequence, we demonstrate how the outcome of light-induced ET can be radically altered by mode-specific infrared (IR) excitation of vibrations that are coupled to the ET pathway. Picosecond narrow-band IR excitation of high-frequency bridge vibrations in an electronically excited covalent trans-acetylide platinum(II) donor-bridge-acceptor system in solution alters both the dynamics and the yields of competing ET pathways, completely switching a charge separation pathway off. These results offer a step toward quantum control of chemical reactivity by IR excitation.
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Affiliation(s)
- Milan Delor
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK
| | | | - Igor V Sazanovich
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK. Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Science and Technology Facilities Council, Chilton, Oxfordshire OX11 0QX, UK
| | - Anthony W Parker
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Science and Technology Facilities Council, Chilton, Oxfordshire OX11 0QX, UK
| | - Gregory M Greetham
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Science and Technology Facilities Council, Chilton, Oxfordshire OX11 0QX, UK
| | | | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Science and Technology Facilities Council, Chilton, Oxfordshire OX11 0QX, UK.
| | - Julia A Weinstein
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, UK.
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29
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Krasilnikov PM. Problems of the theory of electron transfer in biological systems. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350914010059] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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30
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Moser CC, Alegria G, Gunner M, Leslie Dutton P. Interpretation of the Electric Field Sensitivity of the Primary Charge Separation in Photosynthetic Reaction Centers. Isr J Chem 2013. [DOI: 10.1002/ijch.198800023] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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31
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Crofts AR, Hong S, Wilson C, Burton R, Victoria D, Harrison C, Schulten K. The mechanism of ubihydroquinone oxidation at the Qo-site of the cytochrome bc1 complex. BIOCHIMICA ET BIOPHYSICA ACTA 2013; 1827:1362-77. [PMID: 23396004 PMCID: PMC3995752 DOI: 10.1016/j.bbabio.2013.01.009] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 12/12/2012] [Accepted: 01/18/2013] [Indexed: 01/04/2023]
Abstract
1. Recent results suggest that the major flux is carried by a monomeric function, not by an intermonomer electron flow. 2. The bifurcated reaction at the Qo-site involves sequential partial processes, - a rate limiting first electron transfer generating a semiquinone (SQ) intermediate, and a rapid second electron transfer in which the SQ is oxidized by the low potential chain. 3. The rate constant for the first step in a strongly endergonic, proton-first-then-electron mechanism, is given by a Marcus-Brønsted treatment in which a rapid electron transfer is convoluted with a weak occupancy of the proton configuration needed for electron transfer. 4. A rapid second electron transfer pulls the overall reaction over. Mutation of Glu-295 of cyt b shows it to be a key player. 5. In more crippled mutants, electron transfer is severely inhibited and the bell-shaped pH dependence of wildtype is replaced by a dependence on a single pK at ~8.5 favoring electron transfer. Loss of a pK ~6.5 is explained by a change in the rate limiting step from the first to the second electron transfer; the pK ~8.5 may reflect dissociation of QH. 6. A rate constant (<10(3)s(-1)) for oxidation of SQ in the distal domain by heme bL has been determined, which precludes mechanisms for normal flux in which SQ is constrained there. 7. Glu-295 catalyzes proton exit through H(+) transfer from QH, and rotational displacement to deliver the H(+) to exit channel(s). This opens a volume into which Q(-) can move closer to the heme to speed electron transfer. 8. A kinetic model accounts well for the observations, but leaves open the question of gating mechanisms. For the first step we suggest a molecular "escapement"; for the second a molecular ballet choreographed through coulombic interactions. This article is part of a Special Issue entitled: Respiratory complex III and related bc complexes.
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Affiliation(s)
- Antony R Crofts
- Center for Biophysics and Computational Biology, University of Illinois, Urbana, IL 61801, USA; Department of Biochemistry, University of Illinois, Urbana, IL 61801, USA.
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32
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Chen JM, Mou CY, Lin SH. Rate of Reaction of Electron Transfer over a Long Range and Mediated by a Solvent. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.199200086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Ermakova A, Pramanik G, Cai JM, Algara-Siller G, Kaiser U, Weil T, Tzeng YK, Chang HC, McGuinness LP, Plenio MB, Naydenov B, Jelezko F. Detection of a few metallo-protein molecules using color centers in nanodiamonds. NANO LETTERS 2013; 13:3305-9. [PMID: 23738579 DOI: 10.1021/nl4015233] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Nanometer-sized diamonds containing nitrogen-vacancy defect centers (NV) are promising nanosensors in biological environments due to their biocompatibility, bright fluorescence, and high magnetic sensitivity at ambient conditions. Here we report on the detection of ferritin molecules using magnetic noise induced by the inner paramagnetic iron as a contrast mechanism. We observe a significant reduction of both coherence and relaxation time due to the presence of ferritin on the surface of nanodiamonds. Our theoretical model is in excellent agreement with the experimental data and establishes this method as a novel sensing technology for proteins.
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Affiliation(s)
- A Ermakova
- Institut für Quantenoptik and IQST, ‡Institut für Organische Chemie III and IQST, §Institut für Theoretische Physik and IQST, and ∥Materialwissenschaftliche Elektronenmikroskopie and IQST, Albert-Einstein Allee 11, Universität Ulm , 89069 Ulm, Germany
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34
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Borrelli R, Peluso A. Elementary electron transfer reactions: from basic concepts to recent computational advances. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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35
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George C, Szleifer I, Ratner M. Multiple-time-scale motion in molecularly linked nanoparticle arrays. ACS NANO 2013. [PMID: 23199199 DOI: 10.1021/nn303320w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
We explore the transport of electrons between electrodes that encase a two-dimensional array of metallic quantum dots linked by molecular bridges (such as α,ω alkaline dithiols). Because the molecules can move at finite temperatures, the entire transport structure comprising the quantum dots and the molecules is in dynamical motion while the charge is being transported. There are then several physical processes (physical excursions of molecules and quantum dots, electronic migration, ordinary vibrations), all of which influence electronic transport. Each can occur on a different time scale. It is therefore not appropriate to use standard approaches to this sort of electron transfer problem. Instead, we present a treatment in which three different theoretical approaches-kinetic Monte Carlo, classical molecular dynamics, and quantum transport-are all employed. In certain limits, some of the dynamical effects are unimportant. But in general, the transport seems to follow a sort of dynamic bond percolation picture, an approach originally introduced as formal models and later applied to polymer electrolytes. Different rate-determining steps occur in different limits. This approach offers a powerful scheme for dealing with multiple time scale transport problems, as will exist in many situations with several pathways through molecular arrays or even individual molecules that are dynamically disordered.
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Affiliation(s)
- Christopher George
- Department of Chemistry, Chemistry of Life Processes Institute, Northwestern University, Evanston, Illinois 60208, USA
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36
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Protein photo-folding and quantum folding theory. SCIENCE CHINA. LIFE SCIENCES 2012; 55:533-41. [PMID: 22744184 DOI: 10.1007/s11427-012-4316-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2011] [Accepted: 03/28/2012] [Indexed: 10/28/2022]
Abstract
The rates of protein folding with photon absorption or emission and the cross section of photon -protein inelastic scattering are calculated from quantum folding theory by use of a field-theoretical method. All protein photo-folding processes are compared with common protein folding without the interaction of photons (non-radiative folding). It is demonstrated that there exists a common factor (thermo-averaged overlap integral of the vibration wave function, TAOI) for protein folding and protein photo-folding. Based on this finding it is predicted that (i) the stimulated photo-folding rates and the photon-protein resonance Raman scattering sections show the same temperature dependence as protein folding; (ii) the spectral line of the electronic transition is broadened to a band that includes an abundant vibration spectrum without and with conformational transitions, and the width of each vibration spectral line is largely reduced. The particular form of the folding rate-temperature relation and the abundant spectral structure imply the existence of quantum tunneling between protein conformations in folding and photo-folding that demonstrates the quantum nature of the motion of the conformational-electronic system.
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37
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Hong S, Victoria D, Crofts AR. Inter-monomer electron transfer is too slow to compete with monomeric turnover in bc(1) complex. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1053-62. [PMID: 22465023 DOI: 10.1016/j.bbabio.2012.03.012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2011] [Revised: 03/08/2012] [Accepted: 03/11/2012] [Indexed: 11/30/2022]
Abstract
The homodimeric bc(1) complexes are membrane proteins essential in respiration and photosynthesis. The ~11Å distance between the two b(L)-hemes of the dimer opens the possibility of electron transfer between them, but contradictory reports make such inter-monomer electron transfer controversial. We have constructed in Rhodobacter sphaeroides a heterodimeric expression system similar to those used before, in which the bc(1) complex can be mutated differentially in the two copies of cyt b to test for inter-monomer electron transfer, but found that genetic recombination by cross-over then occurs to produce wild-type homodimer. Selection pressure under photosynthetic growth always favored the homodimer over heterodimeric variants enforcing inter-monomer electron transfer, showing that the latter are not competitive. These results, together with kinetic analysis of myxothiazol titrations, demonstrate that inter-monomer electron transfer does not occur at rates competitive with monomeric turnover. We examine the results from other groups interpreted as demonstrating rapid inter-monomer electron transfer, conclude that similar mechanisms are likely to be in play, and suggest that such claims might need to be re-examined.
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Affiliation(s)
- Sangjin Hong
- Departments of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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38
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Polizzi NF, Skourtis SS, Beratan DN. Physical constraints on charge transport through bacterial nanowires. Faraday Discuss 2012; 155:43-62; discussion 103-14. [PMID: 22470966 PMCID: PMC3392031 DOI: 10.1039/c1fd00098e] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extracellular appendages of the dissimilatory metal-reducing bacterium Shewanella oneidensis MR-1 were recently shown to sustain currents of 10(10) electrons per second over distances of 0.5 microns [El-Naggar et al., Proc. Natl. Acad. Sci. U. S. A., 2010, 107, 18127]. However, the identity of the charge localizing sites and their organization along the "nanowire" remain unknown. We use theory to predict redox cofactor separation distances that would permit charge flow at rates of 10(10) electrons per second over 0.5 microns for voltage biases of < or = IV, using a steady-state analysis governed by a non-adiabatic electron transport mechanism. We find the observed currents necessitate a multi-step hopping transport mechanism, with charge localizing sites separated by less than 1 nm and reorganization energies that rival the lowest known in biology.
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Affiliation(s)
| | | | - David N. Beratan
- Departments of Chemistry, Biochemistry and Physics, Duke University, Durham, NC, USA; Fax: (+919) 660-1605; Tel: (+919) 660-1526
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39
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Verhoeven JW, Koomen GJ, van der Kerk SM. Resonant tunnelling as a possible source of catalysis by energy-matched enzymes. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/recl.19861050920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Goldstein RF, Bearden A. Tunneling in Chromatium chromatophores: Detection of a Hopfield charge-transfer band. Proc Natl Acad Sci U S A 2010; 81:135-9. [PMID: 16593405 PMCID: PMC344625 DOI: 10.1073/pnas.81.1.135] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have observed a weak charge-transfer band in the cytochrome c-P(870) electron-transfer reaction in Chromatium vinosum chromatophores at 10 K and at 85 K. First, the intermediate acceptor, I, was trapped in the reduced state by lowering the redox potential at room temperature, then illuminating with white light at low temperature for 20 min. Next, illumination by broadband infrared (1-3 mum, 6.5 kW/m(2)) for 4 hr at 10 K decreased the I(-) electron spin resonance signal by 30%. One-hour infrared illumination at 85 K decreased the cytochrome c Soret band shift by 10%. The effect of infrared was to promote the system from the ground vibrational state with the electron on P(870) to an excited vibrational state with the electron on cytochrome c. The absorption band peak is near 2 mum, and the integrated cross section is approximately 6 x 10(-3) eV.M(-1).cm(-1). These values are consistent with small (0.02 nm) nuclear motion and with electron-transfer rates measured in the dark.
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Affiliation(s)
- R F Goldstein
- Department of Biophysics and Medical Physics and Division of Biology and Medicine, Lawrence Berkeley Laboratory, University of California, Berkeley, CA 94720
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41
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Li Z, Bruce A, Galley WC. Temperature dependence of the disulfide perturbation to the triplet state of tryptophan. Biophys J 2010; 61:1364-71. [PMID: 19431831 DOI: 10.1016/s0006-3495(92)81943-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Variability in the temperature dependence of disulfide quenching of the tryptophan phosphorescence of globular proteins in rigid glasses is illustrated with lysozyme and alpha-bungarotoxin. A laser-pulsed phosphorescence study of this short-range interaction with a model indole-disulfide system is described. The perturbation of secondary dibutyl disulfide on the triplet state of the indole moiety in 2-(3-indolyl)ethyl phenyl ketone in rigid media is found to display a bimodal temperature dependence. The quenching rate constant at contact between chromophore and perturber is observed to be temperature independent below 30 K, but to increase with temperature between 30 and 100 K with an activation energy of approximately 200 cm(-1). The results suggest that the underlying quenching interaction involves a photo-induced one-electron transfer from the excited state of indole to the disulfide.
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Affiliation(s)
- Z Li
- Department of Chemistry, McGill University, Montreal, PQ, Canada H3A 2K6
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42
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Moser CC, Anderson JLR, Dutton PL. Guidelines for tunneling in enzymes. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2010; 1797:1573-86. [PMID: 20460101 DOI: 10.1016/j.bbabio.2010.04.441] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2009] [Revised: 04/26/2010] [Accepted: 04/28/2010] [Indexed: 11/17/2022]
Abstract
Here we extend the engineering descriptions of simple, single-electron-tunneling chains common in oxidoreductases to quantify sequential oxidation-reduction rates of two-or-more electron cofactors and substrates. We identify when nicotinamides may be vulnerable to radical mediated oxidation-reduction and merge electron-tunneling expressions with the chemical rate expressions of Eyring. The work provides guidelines for the construction of new artificial oxidoreductases inspired by Nature but adopting independent design and redox engineering.
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Affiliation(s)
- Christopher C Moser
- Dept. Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Gomes PJS, Serpa C, Nunes RMD, Arnaut LG, Formosinho SJ. Exothermic Rate Restrictions in Long-Range Photoinduced Charge Separations in Rigid Media. J Phys Chem A 2010; 114:2778-87. [DOI: 10.1021/jp9108255] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Paulo J. S. Gomes
- Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Carlos Serpa
- Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Rui M. D. Nunes
- Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Luis G. Arnaut
- Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
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Murdock D, Burns LA, Vaccaro PH. Vibrational specificity of proton-transfer dynamics in ground-state tropolone. Phys Chem Chem Phys 2010; 12:8285-99. [DOI: 10.1039/c003140b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Santabarbara S, Redding KE, Rappaport F. Temperature Dependence of the Reduction of P700+ by Tightly Bound Plastocyanin in Vivo. Biochemistry 2009; 48:10457-66. [DOI: 10.1021/bi901052c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Stefano Santabarbara
- Department of Chemistry and Biochemistry, Arizona State University, 1711 South Rural Road, Tempe, Arizona 85287
- Institut de Biologie Physico-Chimique, UMR7141 CNRS-Universite Paris 6, 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - Kevin E. Redding
- Department of Chemistry and Biochemistry, Arizona State University, 1711 South Rural Road, Tempe, Arizona 85287
| | - Fabrice Rappaport
- Institut de Biologie Physico-Chimique, UMR7141 CNRS-Universite Paris 6, 13 Rue Pierre et Marie Curie, 75005 Paris, France
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46
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Liu W, Rumbley JN, Englander SW, Wand AJ. Fast structural dynamics in reduced and oxidized cytochrome c. Protein Sci 2009; 18:670-4. [PMID: 19241377 DOI: 10.1002/pro.72] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The sub-nanosecond structural dynamics of reduced and oxidized cytochrome c were characterized. Dynamic properties of the protein backbone measured by amide (15)N relaxation and side chains measured by the deuterium relaxation of methyl groups change little upon change in the redox state. These results imply that the solvent reorganization energy associated with electron transfer is small, consistent with previous theoretical analyses. The relative rigidity of both redox states also implies that dynamic relief of destructive electron transfer pathway interference is not operational in free cytochrome c.
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Affiliation(s)
- Weixia Liu
- Department of Biochemistry and Biophysics, Johnson Research Foundation, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6059, USA
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Floyd RA. Serendipitous findings while researching oxygen free radicals. Free Radic Biol Med 2009; 46:1004-13. [PMID: 19439210 PMCID: PMC2683184 DOI: 10.1016/j.freeradbiomed.2009.02.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2009] [Revised: 02/05/2009] [Accepted: 02/05/2009] [Indexed: 11/13/2022]
Abstract
This review is based on the honor of receiving the Discovery Award from the Society of Free Radical Biology and Medicine. The review is reflective and presents our thinking that led to experiments that yielded novel observations. Critical questioning of our understanding of oxygen free radicals in biomedical problems led us to use and develop more direct and extremely sensitive methods. This included nitrone free radical spin trapping and HPLC-electrochemical detection. This technology led to the pioneering use of salicylate to trap hydroxyl free radicals and show increased flux in ischemia/reperfused brain regions and also to first sensitively detect 8-hydroxyl-2-deoxyguanosine in oxidatively damaged DNA and help assess its role in cancer development. We demonstrated that methylene blue (MB) photoinduces formation of 8-hydroxyguanine in DNA and RNA and discovered that MB sensitively photoinactivates RNA viruses, including HIV and the West Nile virus. Studies in experimental stroke led us serendipitously to discover that alpha-phenyl-tert-butylnitrone (PBN) was neuroprotective if given after the stroke. This led to extensive commercial development of NXY-059, a PBN derivative, for the treatment of stroke. More recently we discovered that PBN nitrones have potent anti-cancer activity and are active in preventing hearing loss caused by acute acoustical trauma.
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Affiliation(s)
- Robert A Floyd
- Experimental Therapeutics Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73170, USA.
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Abstract
Abstract
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49
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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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50
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The Q-cycle reviewed: How well does a monomeric mechanism of the bc(1) complex account for the function of a dimeric complex? BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2008; 1777:1001-19. [PMID: 18501698 DOI: 10.1016/j.bbabio.2008.04.037] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2008] [Revised: 03/26/2008] [Accepted: 04/23/2008] [Indexed: 11/20/2022]
Abstract
Recent progress in understanding the Q-cycle mechanism of the bc(1) complex is reviewed. The data strongly support a mechanism in which the Q(o)-site operates through a reaction in which the first electron transfer from ubiquinol to the oxidized iron-sulfur protein is the rate-determining step for the overall process. The reaction involves a proton-coupled electron transfer down a hydrogen bond between the ubiquinol and a histidine ligand of the [2Fe-2S] cluster, in which the unfavorable protonic configuration contributes a substantial part of the activation barrier. The reaction is endergonic, and the products are an unstable ubisemiquinone at the Q(o)-site, and the reduced iron-sulfur protein, the extrinsic mobile domain of which is now free to dissociate and move away from the site to deliver an electron to cyt c(1) and liberate the H(+). When oxidation of the semiquinone is prevented, it participates in bypass reactions, including superoxide generation if O(2) is available. When the b-heme chain is available as an acceptor, the semiquinone is oxidized in a process in which the proton is passed to the glutamate of the conserved -PEWY- sequence, and the semiquinone anion passes its electron to heme b(L) to form the product ubiquinone. The rate is rapid compared to the limiting reaction, and would require movement of the semiquinone closer to heme b(L) to enhance the rate constant. The acceptor reactions at the Q(i)-site are still controversial, but likely involve a "two-electron gate" in which a stable semiquinone stores an electron. Possible mechanisms to explain the cyt b(150) phenomenon are discussed, and the information from pulsed-EPR studies about the structure of the intermediate state is reviewed. The mechanism discussed is applicable to a monomeric bc(1) complex. We discuss evidence in the literature that has been interpreted as shown that the dimeric structure participates in a more complicated mechanism involving electron transfer across the dimer interface. We show from myxothiazol titrations and mutational analysis of Tyr-199, which is at the interface between monomers, that no such inter-monomer electron transfer is detected at the level of the b(L) hemes. We show from analysis of strains with mutations at Asn-221 that there are coulombic interactions between the b-hemes in a monomer. The data can also be interpreted as showing similar coulombic interaction across the dimer interface, and we discuss mechanistic implications.
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