1
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Bueno PR. On the fundamentals of quantum rate theory and the long-range electron transport in respiratory chains. Chem Soc Rev 2024; 53:5348-5365. [PMID: 38651285 DOI: 10.1039/d3cs00662j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
It has been shown that both the electron-transfer rate constant of an electrochemical reaction and the conductance quantum are correlated with the concept of quantum capacitance. This simple association between the two separate concepts has an entirely quantum rate basis that encompasses the electron-transfer rate theory as originally proposed by Rudolph A. Marcus whether statistical mechanics is appropriately taken into account. I have prepared a concise review of the quantum mechanical rate theory principles focused on its quantum electrodynamics character to demonstrate that it can reconcile the conflicting views established on attempting to use the super-exchange (supported on electron transfer) or 'metallic-like' (supported on conductance quantum) mechanisms separately to explain the highly efficient long-range electron transport observed in the respiratory processes of living cells. The unresolved issues related to long-range electron transport are clarified in light of the quantum rate theory with a discussion focused on Geobacter sulfurreducens films as a reference standard of the respiration chain. Theoretical analyses supported by experimental data suggest that the efficiency of respiration within a long-range electron transport path is intrinsically a quantum mechanical event that follows relativistic quantum electrodynamics principles as addressed by quantum rate theory.
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Affiliation(s)
- Paulo Roberto Bueno
- Institute of Chemistry, Department of Engineering, Physics and Mathematics, Sao Paulo State University, Araraquara, Sao Paulo, Brazil.
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2
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Guberman-Pfeffer MJ. To be or not to be a cytochrome: electrical characterizations are inconsistent with Geobacter cytochrome 'nanowires'. Front Microbiol 2024; 15:1397124. [PMID: 38633696 PMCID: PMC11021709 DOI: 10.3389/fmicb.2024.1397124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 03/21/2024] [Indexed: 04/19/2024] Open
Abstract
Geobacter sulfurreducens profoundly shapes Earth's biogeochemistry by discharging respiratory electrons to minerals and other microbes through filaments of a two-decades-long debated identity. Cryogenic electron microscopy has revealed filaments of redox-active cytochromes, but the same filaments have exhibited hallmarks of organic metal-like conductivity under cytochrome denaturing/inhibiting conditions. Prior structure-based calculations and kinetic analyses on multi-heme proteins are synthesized herein to propose that a minimum of ~7 cytochrome 'nanowires' can carry the respiratory flux of a Geobacter cell, which is known to express somewhat more (≥20) filaments to increase the likelihood of productive contacts. By contrast, prior electrical and spectroscopic structural characterizations are argued to be physiologically irrelevant or physically implausible for the known cytochrome filaments because of experimental artifacts and sample impurities. This perspective clarifies our mechanistic understanding of physiological metal-microbe interactions and advances synthetic biology efforts to optimize those interactions for bioremediation and energy or chemical production.
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3
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Portela PC, Shipps CC, Shen C, Srikanth V, Salgueiro CA, Malvankar NS. Widespread extracellular electron transfer pathways for charging microbial cytochrome OmcS nanowires via periplasmic cytochromes PpcABCDE. Nat Commun 2024; 15:2434. [PMID: 38509081 PMCID: PMC10954620 DOI: 10.1038/s41467-024-46192-0] [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: 08/04/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Extracellular electron transfer (EET) via microbial nanowires drives globally-important environmental processes and biotechnological applications for bioenergy, bioremediation, and bioelectronics. Due to highly-redundant and complex EET pathways, it is unclear how microbes wire electrons rapidly (>106 s-1) from the inner-membrane through outer-surface nanowires directly to an external environment despite a crowded periplasm and slow (<105 s-1) electron diffusion among periplasmic cytochromes. Here, we show that Geobacter sulfurreducens periplasmic cytochromes PpcABCDE inject electrons directly into OmcS nanowires by binding transiently with differing efficiencies, with the least-abundant cytochrome (PpcC) showing the highest efficiency. Remarkably, this defined nanowire-charging pathway is evolutionarily conserved in phylogenetically-diverse bacteria capable of EET. OmcS heme reduction potentials are within 200 mV of each other, with a midpoint 82 mV-higher than reported previously. This could explain efficient EET over micrometres at ultrafast (<200 fs) rates with negligible energy loss. Engineering this minimal nanowire-charging pathway may yield microbial chassis with improved performance.
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Affiliation(s)
- Pilar C Portela
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal
| | - Catharine C Shipps
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Carlos A Salgueiro
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
- UCIBIO - Applied Molecular Biosciences Unit, Department of Chemistry, NOVA School of Science and Technology, Universidade NOVA de Lisboa, Caparica, Portugal.
| | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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4
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Nguyen HTT, Le GTH, Park SG, Jadhav DA, Le TTQ, Kim H, Vinayak V, Lee G, Yoo K, Song YC, Chae KJ. Optimizing electrochemically active microorganisms as a key player in the bioelectrochemical system: Identification methods and pathways to large-scale implementation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 914:169766. [PMID: 38181955 DOI: 10.1016/j.scitotenv.2023.169766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/15/2023] [Accepted: 12/28/2023] [Indexed: 01/07/2024]
Abstract
The rapid global economic growth driven by industrialization and population expansion has resulted in significant issues, including reliance on fossil fuels, energy scarcity, water crises, and environmental emissions. To address these issues, bioelectrochemical systems (BES) have emerged as a dual-purpose solution, harnessing electrochemical processes and the capabilities of electrochemically active microorganisms (EAM) to simultaneously recover energy and treat wastewater. This review examines critical performance factors in BES, including inoculum selection, pretreatment methods, electrodes, and operational conditions. Further, authors explore innovative approaches to suppress methanogens and simultaneously enhance the EAM in mixed cultures. Additionally, advanced techniques for detecting EAM are discussed. The rapid detection of EAM facilitates the selection of suitable inoculum sources and optimization of enrichment strategies in BESs. This optimization is essential for facilitating the successful scaling up of BES applications, contributing substantially to the realization of clean energy and sustainable wastewater treatment. This analysis introduces a novel viewpoint by amalgamating contemporary research on the selective enrichment of EAM in mixed cultures. It encompasses identification and detection techniques, along with methodologies tailored for the selective enrichment of EAM, geared explicitly toward upscaling applications in BES.
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Affiliation(s)
- Ha T T Nguyen
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Department of Convergence Study on the Ocean Science and Technology, Ocean Science and Technology School (OST), Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea
| | - Giang T H Le
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea
| | - Sung-Gwan Park
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea
| | - Dipak A Jadhav
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea
| | - Trang T Q Le
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea
| | - Hyunsu Kim
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea
| | - Vandana Vinayak
- Diatom Nanoengineering and Metabolism Laboratory (DNM), School of Applied Science, Dr. Hari Singh Gour Central University, Sagar, MP 470003, India
| | - Gihan Lee
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea
| | - Keunje Yoo
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea
| | - Young-Chae Song
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea.
| | - Kyu-Jung Chae
- Department of Environmental Engineering, College of Ocean Science and Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea; Interdisciplinary Major of Ocean Renewable Energy Engineering, Korea Maritime and Ocean University, 727 Taejong-ro, Yeongdo-gu, Busan 49112, Republic of Korea.
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5
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Parson WW, Huang J, Kulke M, Vermaas JV, Kramer DM. Electron transfer in a crystalline cytochrome with four hemes. J Chem Phys 2024; 160:065101. [PMID: 38341797 DOI: 10.1063/5.0186958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 01/18/2024] [Indexed: 02/13/2024] Open
Abstract
Diffusion of electrons over distances on the order of 100 μm has been observed in crystals of a small tetraheme cytochrome (STC) from Shewanella oneidensis [J. Huang et al. J. Am. Chem. Soc. 142, 10459-10467 (2020)]. Electron transfer between hemes in adjacent subunits of the crystal is slower and more strongly dependent on temperature than had been expected based on semiclassical electron-transfer theory. We here explore explanations for these findings by molecular-dynamics simulations of crystalline and monomeric STC. New procedures are developed for including time-dependent quantum mechanical energy differences in the gap between the energies of the reactant and product states and for evaluating fluctuations of the electronic-interaction matrix element that couples the two hemes. Rate constants for electron transfer are calculated from the time- and temperature-dependent energy gaps, coupling factors, and Franck-Condon-weighted densities of states using an expression with no freely adjustable parameters. Back reactions are considered, as are the effects of various protonation states of the carboxyl groups on the heme side chains. Interactions with water are found to dominate the fluctuations of the energy gap between the reactant and product states. The calculated rate constant for electron transfer from heme IV to heme Ib in a neighboring subunit at 300 K agrees well with the measured value. However, the calculated activation energy of the reaction in the crystal is considerably smaller than observed. We suggest two possible explanations for this discrepancy. The calculated rate constant for transfer from heme I to II within the same subunit of the crystal is about one-third that for monomeric STC in solution.
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Affiliation(s)
- William W Parson
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, USA
| | - Jingcheng Huang
- DOE-Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Martin Kulke
- DOE-Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Josh V Vermaas
- DOE-Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - David M Kramer
- DOE-Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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6
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Kulke M, Olson DM, Huang J, Kramer DM, Vermaas JV. Long-Range Electron Transport Rates Depend on Wire Dimensions in Cytochrome Nanowires. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2304013. [PMID: 37653599 DOI: 10.1002/smll.202304013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 08/18/2023] [Indexed: 09/02/2023]
Abstract
The ability to redirect electron transport to new reactions in living systems opens possibilities to store energy, generate new products, or probe physiological processes. Recent work by Huang et al. showed that 3D crystals of small tetraheme cytochromes (STC) can transport electrons over nanoscopic to mesoscopic distances by an electron hopping mechanism, making them promising materials for nanowires. However, fluctuations at room temperature may distort the nanostructure, hindering efficient electron transport. Classical molecular dynamics simulations of these fluctuations at the nano- and mesoscopic scales allowed us to develop a graph network representation to estimate maximum electron flow that can be driven through STC wires. In longer nanowires, transient structural fluctuations at protein-protein interfaces tended to obstruct efficient electron transfer, but these blockages are ameliorated in thicker crystals where alternative electron transfer pathways become more efficient. The model implies that more flexible proteinprotein interfaces limit the required minimum diameter to carry currents commensurate with conventional electronics.
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Affiliation(s)
- Martin Kulke
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
| | - Dayna M Olson
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
| | - Jingcheng Huang
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
| | - David M Kramer
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Rd, East Lansing, MI, 48824, United States of America
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7
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Afsari S, Mukherjee S, Halloran N, Ghirlanda G, Ryan E, Wang X, Lindsay S. Heavy Water Reduces the Electronic Conductance of Protein Wires via Deuteron Interactions with Aromatic Residues. NANO LETTERS 2023; 23:8907-8913. [PMID: 37772726 PMCID: PMC11177565 DOI: 10.1021/acs.nanolett.3c02263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/30/2023]
Abstract
Proteins are versatile, self-assembling nanoelectronic components, but their hopping conductivity is expected to be influenced by solvent fluctuations. The role of the solvent was investigated by measuring the single molecule conductance of several proteins in both H2O and D2O. The conductance of a homologous series of protein wires decreases more rapidly with length in D2O, indicating a 6-fold decrease in carrier diffusion constant relative to the same protein in H2O. The effect was found to depend on the specific aromatic amino acid composition. A tryptophan zipper protein showed a decrease in conductance similar to that of the protein wires, whereas a phenylalanine zipper protein was insensitive to solvent changes. Tryptophan contains an indole amine, whereas the phenylalanine aromatic ring has no exchangeable protons, so the effect of heavy water on conductance is a consequence of specific D- or H-interactions with the aromatic residues.
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Affiliation(s)
- Sepideh Afsari
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Sohini Mukherjee
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Nicholas Halloran
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | | | - Eathen Ryan
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85287
- Department of Physics, Arizona State University, Tempe, AZ 85287
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8
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Krishnan S, Aksimentiev A, Lindsay S, Matyushov D. Long-Range Conductivity in Proteins Mediated by Aromatic Residues. ACS PHYSICAL CHEMISTRY AU 2023; 3:444-455. [PMID: 37780537 PMCID: PMC10540285 DOI: 10.1021/acsphyschemau.3c00017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/18/2023] [Accepted: 05/19/2023] [Indexed: 09/30/2023]
Abstract
Single-molecule measurements show that many proteins, lacking any redox cofactors, nonetheless exhibit electrical conductance on the order of a nanosiemen over 10 nm distances, implying that electrons can transit an entire protein in less than a nanosecond when subject to a potential difference of less than 1 V. This is puzzling because, for fast transport (i.e., a free energy barrier of zero), the hopping rate is determined by the reorganization energy of approximately 0.8 eV, and this sets the time scale of a single hop to at least 1 μs. Furthermore, the Fermi energies of typical metal electrodes are far removed from the energies required for sequential oxidation and reduction of the aromatic residues of the protein, which should further reduce the hopping current. Here, we combine all-atom molecular dynamics (MD) simulations of non-redox-active proteins (consensus tetratricopeptide repeats) with an electron transfer theory to demonstrate a molecular mechanism that can account for the unexpectedly fast electron transport. According to our MD simulations, the reorganization energy produced by the energy shift on charging (the Stokes shift) is close to the conventional value of 0.8 eV. However, the non-ergodic sampling of molecular configurations by the protein results in reaction-reorganization energies, extracted directly from the distribution of the electrostatic energy fluctuations, that are only ∼0.2 eV, which is small enough to enable long-range conductivity, without invoking quantum coherent transport. Using the MD values of the reorganization energies, we calculate a current decay with distance that is in agreement with experiment.
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Affiliation(s)
- Siddharth Krishnan
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Aleksei Aksimentiev
- Department
of Physics and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Stuart Lindsay
- Department
of Physics, Arizona State University, Tempe, Arizona 85281, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
- Biodesign
Institute, Arizona State University, Tempe, Arizona 85281, United States
| | - Dmitry Matyushov
- Department
of Physics, Arizona State University, Tempe, Arizona 85281, United States
- School
of Molecular Sciences, Arizona State University, Tempe, Arizona 85281, United States
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9
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Guberman-Pfeffer MJ. Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires. J Phys Chem B 2023; 127:7148-7161. [PMID: 37552847 DOI: 10.1021/acs.jpcb.3c02912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2023]
Abstract
Structural determinants of a 103-fold variation in electrical conductivity for helical homopolymers of tetra-, hexa-, and octa-heme cytochromes (named Omc- E, S, and Z, respectively) from Geobacter sulfurreducens are investigated with the Pathways model for electron tunneling, classical molecular dynamics, and hybrid quantum/classical molecular mechanics. Thermally averaged electronic couplings for through-space heme-to-heme electron transfer in the "nanowires" computed with density functional theory are ≤0.015 eV. Pathways analyses also indicate that couplings match within a factor of 5 for all "nanowires", but some alternative tunneling routes are found involving covalent protein backbone bonds (Omc- S and Z) or propionic acid-ligating His H-bonds on adjacent hemes (OmcZ). Reorganization energies computed from electrostatic vertical energy gaps or a version of the Marcus continuum expression parameterized on the total (donor + acceptor) solvent-accessible surface area typically agree within 20% and fall within the range 0.48-0.98 eV. Reaction free energies in all three "nanowires" are ≤|0.28| eV, even though Coulombic interactions primarily tune the site redox energies by 0.7-1.2 eV. Given the conserved energetic parameters, redox conductivity differs by < 103-fold among the cytochrome "nanowires". Redox currents do not exceed 3.0 × 10-3 pA at a physiologically relevant 0.1 V bias, with the slowest electron transfers being on a (μs) timescale much faster than typical (ms) enzymatic turnovers. Thus, the "nanowires" are proposed to be functionally robust to variations in structure that provide a habitat-customized protein interface. The 30 pA to 30 nA variation in conductivity previously reported from atomic force microscopy experiments is not intrinsic to the structures and/or does not result from the physiologically relevant redox conduction mechanism.
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Affiliation(s)
- Matthew J Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar Street, New Haven, Connecticut 06510, United States
- Microbial Sciences Institute, Yale University, 840 West Campus Drive, West Haven, Connecticut 06516, United States
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10
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Mostajabi Sarhangi S, Matyushov DV. Electron Tunneling in Biology: When Does it Matter? ACS OMEGA 2023; 8:27355-27365. [PMID: 37546584 PMCID: PMC10399179 DOI: 10.1021/acsomega.3c02719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 07/11/2023] [Indexed: 08/08/2023]
Abstract
Electrons can tunnel between cofactor molecules positioned along biological electron transport chains up to a distance of ≃ 20 Å on the millisecond time scale of enzymatic turnover. This tunneling range determines the design of biological energy chains facilitating the cross-membrane transport of electrons. Tunneling distance and cofactors' redox potentials become the main physical parameters affecting the rate of electron transport. In addition, universal charge-transport properties are assigned to all proteins, making protein identity, flexibility, and dynamics insignificant. This paradigm is challenged by dynamical models of electron transfer, showing that the electron hopping rate is constant within the crossover distance R* ≃ 12 Å, followed with an exponential falloff at longer distances. If this hypothesis is fully confirmed, natural and man-made energy chains for electron transport should be best designed by placing redox cofactors near the crossover distance R*. Protein flexibility and dynamics affect the magnitude of the maximum hopping rate within the crossover distance. Changes in protein flexibility between forward and backward transitions contribute to vectorial charge transport. For biological energy chains, charge transport through proteins is not defined by universal parameters, and protein identity matters.
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11
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Baquero DP, Cvirkaite-Krupovic V, Hu SS, Fields JL, Liu X, Rensing C, Egelman EH, Krupovic M, Wang F. Extracellular cytochrome nanowires appear to be ubiquitous in prokaryotes. Cell 2023; 186:2853-2864.e8. [PMID: 37290436 PMCID: PMC10330847 DOI: 10.1016/j.cell.2023.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/04/2023] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Electrically conductive appendages from the anaerobic bacterium Geobacter sulfurreducens, recently identified as extracellular cytochrome nanowires (ECNs), have received wide attention due to numerous potential applications. However, whether other organisms employ similar ECNs for electron transfer remains unknown. Here, using cryoelectron microscopy, we describe the atomic structures of two ECNs from two major orders of hyperthermophilic archaea present in deep-sea hydrothermal vents and terrestrial hot springs. Homologs of Archaeoglobus veneficus ECN are widespread among mesophilic methane-oxidizing Methanoperedenaceae, alkane-degrading Syntrophoarchaeales archaea, and in the recently described megaplasmids called Borgs. The ECN protein subunits lack similarities in their folds; however, they share a common heme arrangement, suggesting an evolutionarily optimized heme packing for efficient electron transfer. The detection of ECNs in archaea suggests that filaments containing closely stacked hemes may be a common and widespread mechanism for long-range electron transfer in both prokaryotic domains of life.
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Affiliation(s)
- Diana P Baquero
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris 75015, France
| | | | - Shengen Shawn Hu
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA
| | - Jessie Lynda Fields
- Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA
| | - Xing Liu
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, Fujian, China
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA.
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, Paris 75015, France.
| | - Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA 22903, USA; Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35233, USA; O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL 35233, USA.
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12
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Kubař T, Elstner M, Cui Q. Hybrid Quantum Mechanical/Molecular Mechanical Methods For Studying Energy Transduction in Biomolecular Machines. Annu Rev Biophys 2023; 52:525-551. [PMID: 36791746 PMCID: PMC10810093 DOI: 10.1146/annurev-biophys-111622-091140] [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] [Indexed: 02/17/2023]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) methods have become indispensable tools for the study of biomolecules. In this article, we briefly review the basic methodological details of QM/MM approaches and discuss their applications to various energy transduction problems in biomolecular machines, such as long-range proton transports, fast electron transfers, and mechanochemical coupling. We highlight the particular importance for these applications of balancing computational efficiency and accuracy. Using several recent examples, we illustrate the value and limitations of QM/MM methodologies for both ground and excited states, as well as strategies for calibrating them in specific applications. We conclude with brief comments on several areas that can benefit from further efforts to make QM/MM analyses more quantitative and applicable to increasingly complex biological problems.
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Affiliation(s)
- T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany;
- Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology, Karlsruhe, Germany;
| | - Q Cui
- Department of Chemistry, Boston University, Boston, Massachusetts, USA;
- Department of Physics, Boston University, Boston, Massachusetts, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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13
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Pauli B, Ajmera S, Kost C. Determinants of synergistic cell-cell interactions in bacteria. Biol Chem 2023; 404:521-534. [PMID: 36859766 DOI: 10.1515/hsz-2022-0303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/08/2023] [Indexed: 03/03/2023]
Abstract
Bacteria are ubiquitous and colonize virtually every conceivable habitat on earth. To achieve this, bacteria require different metabolites and biochemical capabilities. Rather than trying to produce all of the needed materials by themselves, bacteria have evolved a range of synergistic interactions, in which they exchange different commodities with other members of their local community. While it is widely acknowledged that synergistic interactions are key to the ecology of both individual bacteria and entire microbial communities, the factors determining their establishment remain poorly understood. Here we provide a comprehensive overview over our current knowledge on the determinants of positive cell-cell interactions among bacteria. Taking a holistic approach, we review the literature on the molecular mechanisms bacteria use to transfer commodities between bacterial cells and discuss to which extent these mechanisms favour or constrain the successful establishment of synergistic cell-cell interactions. In addition, we analyse how these different processes affect the specificity among interaction partners. By drawing together evidence from different disciplines that study the focal question on different levels of organisation, this work not only summarizes the state of the art in this exciting field of research, but also identifies new avenues for future research.
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Affiliation(s)
- Benedikt Pauli
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, D-49076 Osnabrück, Germany
| | - Shiksha Ajmera
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, D-49076 Osnabrück, Germany
| | - Christian Kost
- Department of Ecology, School of Biology/Chemistry, Osnabrück University, D-49076 Osnabrück, Germany.,Center of Cellular Nanoanalytics (CellNanOs), Osnabrück University, Barbarastrasse 11, D-49076 Osnabrück, Germany
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14
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Atkinson JT, Chavez MS, Niman CM, El-Naggar MY. Living electronics: A catalogue of engineered living electronic components. Microb Biotechnol 2023; 16:507-533. [PMID: 36519191 PMCID: PMC9948233 DOI: 10.1111/1751-7915.14171] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 09/26/2022] [Accepted: 11/01/2022] [Indexed: 12/23/2022] Open
Abstract
Biology leverages a range of electrical phenomena to extract and store energy, control molecular reactions and enable multicellular communication. Microbes, in particular, have evolved genetically encoded machinery enabling them to utilize the abundant redox-active molecules and minerals available on Earth, which in turn drive global-scale biogeochemical cycles. Recently, the microbial machinery enabling these redox reactions have been leveraged for interfacing cells and biomolecules with electrical circuits for biotechnological applications. Synthetic biology is allowing for the use of these machinery as components of engineered living materials with tuneable electrical properties. Herein, we review the state of such living electronic components including wires, capacitors, transistors, diodes, optoelectronic components, spin filters, sensors, logic processors, bioactuators, information storage media and methods for assembling these components into living electronic circuits.
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Affiliation(s)
- Joshua T Atkinson
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Marko S Chavez
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California, USA.,Department of Biological Sciences, University of Southern California, Los Angeles, California, USA.,Department of Chemistry, University of Southern California, Los Angeles, California, USA
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15
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Gu Y, Guberman-Pfeffer MJ, Srikanth V, Shen C, Giska F, Gupta K, Londer Y, Samatey FA, Batista VS, Malvankar NS. Structure of Geobacter cytochrome OmcZ identifies mechanism of nanowire assembly and conductivity. Nat Microbiol 2023; 8:284-298. [PMID: 36732469 PMCID: PMC9999484 DOI: 10.1038/s41564-022-01315-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 12/20/2022] [Indexed: 02/04/2023]
Abstract
OmcZ nanowires produced by Geobacter species have high electron conductivity (>30 S cm-1). Of 111 cytochromes present in G. sulfurreducens, OmcZ is the only known nanowire-forming cytochrome essential for the formation of high-current-density biofilms that require long-distance (>10 µm) extracellular electron transport. However, the mechanisms underlying OmcZ nanowire assembly and high conductivity are unknown. Here we report a 3.5-Å-resolution cryogenic electron microscopy structure for OmcZ nanowires. Our structure reveals linear and closely stacked haems that may account for conductivity. Surface-exposed haems and charge interactions explain how OmcZ nanowires bind to diverse extracellular electron acceptors and how organization of nanowire network re-arranges in different biochemical environments. In vitro studies explain how G. sulfurreducens employ a serine protease to control the assembly of OmcZ monomers into nanowires. We find that both OmcZ and serine protease are widespread in environmentally important bacteria and archaea, thus establishing a prevalence of nanowire biogenesis across diverse species and environments.
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Affiliation(s)
- Yangqi Gu
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- PNAC division, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK.
| | - Matthew J Guberman-Pfeffer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Vishok Srikanth
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Cong Shen
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Microbiology, Yale University, New Haven, CT, USA
| | - Fabian Giska
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Kallol Gupta
- Department of Cell Biology, Yale University, New Haven, CT, USA
- Nanobiology Institute, Yale University, West Haven, CT, USA
| | - Yuri Londer
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Fadel A Samatey
- Microbial Sciences Institute, Yale University, West Haven, CT, USA
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | | | - Nikhil S Malvankar
- Microbial Sciences Institute, Yale University, West Haven, CT, USA.
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
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16
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Mostajabi Sarhangi S, Matyushov DV. Effect of Water Deuteration on Protein Electron Transfer. J Phys Chem Lett 2023; 14:723-729. [PMID: 36648391 DOI: 10.1021/acs.jpclett.2c03690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Traditional theories of long-range protein electron transfer describe the reaction rate in terms of the tunneling distance and the reaction free energy. They do not recognize two physical effects: (i) local wetting of the active site by hydration water and (ii) protein identity affecting the rate through dynamics and flexibility. We find, by molecular dynamics simulations, a significant, ∼25 times, slowing down of the rate of protein electron transfer upon deuteration. H/D substitution changes the rate constant pre-exponential factor in the regime of electron transfer controlled by medium dynamics. Switching from light to heavy water increases the effective medium relaxation time. The effect is caused by both a global change in the flexibility of the protein backbone and locally stronger hydrogen bonds to charged residues.
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Affiliation(s)
- Setare Mostajabi Sarhangi
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
| | - Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
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17
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Guberman-Pfeffer MJ. Structural Determinants of Redox Conduction Favor Robustness over Tunability in Microbial Cytochrome Nanowires. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.21.525004. [PMID: 36712098 PMCID: PMC9882360 DOI: 10.1101/2023.01.21.525004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Helical homopolymers of multiheme cytochromes catalyze biogeochemically significant electron transfers with a reported 10 3 -fold variation in conductivity. Herein, classical molecular dynamics and hybrid quantum/classical molecular mechanics are used to elucidate the structural determinants of the redox potentials and conductivities of the tetra-, hexa-, and octaheme outer-membrane cytochromes E, S, and Z, respectively, from Geobacter sulfurreducens . Second-sphere electrostatic interactions acting on minimally polarized heme centers are found to regulate redox potentials over a computed 0.5-V range. However, the energetics of redox conduction are largely robust to the structural diversity: Single-step electronic couplings (⟨H mn ⟩), reaction free energies , and reorganization energies (λ mn ) are always respectively <|0.026|, <|0.26|, and between 0.5 - 1.0 eV. With these conserved parameter ranges, redox conductivity differed by less than a factor of 10 among the 'nanowires' and is sufficient to meet the demands of cellular respiration if 10 2 - 10 3 'nanowires' are expressed. The 'nanowires' are proposed to be differentiated by the protein packaging to interface with a great variety of environments, and not by conductivity, because the rate-limiting electron transfers are elsewhere in the respiratory process. Conducting-probe atomic force microscopy measurements that find conductivities 10 3 -10 6 -fold more than cellular demands are suggested to report on functionality that is either not used or not accessible under physiological conditions. The experimentally measured difference in conductivity between Omc- S and Z is suggested to not be an intrinsic feature of the CryoEM-resolved structures.
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Affiliation(s)
- Matthew J. Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, CT, 06510
- Microbial Sciences Institute, Yale University, 840 West Campus Drive, West Haven, CT, 06516
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18
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Sarhangi SM, Matyushov DV. Theory of Protein Charge Transfer: Electron Transfer between Tryptophan Residue and Active Site of Azurin. J Phys Chem B 2022; 126:10360-10373. [PMID: 36459590 DOI: 10.1021/acs.jpcb.2c05258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
One reaction step in the conductivity relay of azurin, electron transfer between the Cu-based active site and the tryptophan residue, is studied theoretically and by classical molecular dynamics simulations. Oxidation of tryptophan results in electrowetting of this residue. This structural change makes the free energy surfaces of electron transfer nonparabolic as described by the Q-model of electron transfer. We analyze the medium dynamical effect on protein electron transfer produced by coupled Stokes-shift dynamics and the dynamics of the donor-acceptor distance modulating electron tunneling. The equilibrium donor-acceptor distance falls in the plateau region of the rate constant, where it is determined by the protein-water dynamics, and the probability of electron tunneling does not affect the rate. The crossover distance found here puts most intraprotein electron-transfer reactions under the umbrella of dynamical control. The crossover between the medium-controlled and tunneling-controlled kinetics is combined with the effect of the protein-water medium on the activation barrier to formulate principles of tunability of protein-based charge-transfer chains. The main principle in optimizing the activation barrier is the departure from the Gaussian-Gibbsian statistics of fluctuations promoting activated transitions. This is achieved either by incomplete (nonergodic) sampling, breaking the link between the Stokes-shift and variance reorganization energies, or through wetting-induced structural changes of the enzyme's active site.
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Affiliation(s)
- Setare Mostajabi Sarhangi
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
| | - Dmitry V Matyushov
- School of Molecular Sciences and Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona85287-1504, United States
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19
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Guberman-Pfeffer MJ. Assessing Thermal Response of Redox Conduction for Anti-Arrhenius Kinetics in a Microbial Cytochrome Nanowire. J Phys Chem B 2022; 126:10083-10097. [PMID: 36417757 PMCID: PMC9743091 DOI: 10.1021/acs.jpcb.2c06822] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
A micrometers-long helical homopolymer of the outer-membrane cytochrome type S (OmcS) from Geobacter sulfurreducens is proposed to transport electrons to extracellular acceptors in an ancient respiratory strategy of biogeochemical and technological significance. OmcS surprisingly exhibits higher conductivity upon cooling (anti-Arrhenius kinetics), an effect previously attributed to H-bond restructuring and heme redox potential shifts. Herein, the temperature sensitivity of redox conductivity is more thoroughly examined with conventional and constant-redox and -pH molecular dynamics and quantum mechanics/molecular mechanics. A 30 K drop in temperature constituted a weak perturbation to electron transfer energetics, changing electronic couplings (⟨Hmn⟩), reaction free energies (ΔGmn), reorganization energies (λmn), and activation energies (Ea) by at most |0.002|, |0.050|, |0.120|, and |0.045| eV, respectively. Changes in ΔGmn reflected -0.07 ± 0.03 V shifts in redox potentials that were caused in roughly equal measure by altered electrostatic interactions with the solvent and protein. Changes in intraprotein H-bonding reproduced the earlier observations. Single-particle diffusion and multiparticle steady-state flux models, parametrized with Marcus theory rates, showed that biologically relevant incoherent hopping cannot qualitatively or quantitatively describe electrical conductivity measured by atomic force microscopy in filamentous OmcS. The discrepancy is attributed to differences between solution-phase simulations and solid-state measurements and the need to model intra- and intermolecular vibrations explicitly.
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Affiliation(s)
- Matthew J. Guberman-Pfeffer
- Department
of Molecular Biophysics and Biochemistry, Yale University, 333 Cedar St., New Haven, Connecticut06510, United States,Microbial
Sciences Institute, Yale University, 840 West Campus Drive, West Haven, Connecticut06516, United States,
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20
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Neu J, Shipps CC, Guberman-Pfeffer MJ, Shen C, Srikanth V, Spies JA, Kirchhofer ND, Yalcin SE, Brudvig GW, Batista VS, Malvankar NS. Microbial biofilms as living photoconductors due to ultrafast electron transfer in cytochrome OmcS nanowires. Nat Commun 2022; 13:5150. [PMID: 36071037 PMCID: PMC9452534 DOI: 10.1038/s41467-022-32659-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 08/09/2022] [Indexed: 11/09/2022] Open
Abstract
Light-induced microbial electron transfer has potential for efficient production of value-added chemicals, biofuels and biodegradable materials owing to diversified metabolic pathways. However, most microbes lack photoactive proteins and require synthetic photosensitizers that suffer from photocorrosion, photodegradation, cytotoxicity, and generation of photoexcited radicals that are harmful to cells, thus severely limiting the catalytic performance. Therefore, there is a pressing need for biocompatible photoconductive materials for efficient electronic interface between microbes and electrodes. Here we show that living biofilms of Geobacter sulfurreducens use nanowires of cytochrome OmcS as intrinsic photoconductors. Photoconductive atomic force microscopy shows up to 100-fold increase in photocurrent in purified individual nanowires. Photocurrents respond rapidly (<100 ms) to the excitation and persist reversibly for hours. Femtosecond transient absorption spectroscopy and quantum dynamics simulations reveal ultrafast (~200 fs) electron transfer between nanowire hemes upon photoexcitation, enhancing carrier density and mobility. Our work reveals a new class of natural photoconductors for whole-cell catalysis. Despite enormous potential of solar-driven biocatalysis, most living systems lack photoactive proteins and require toxic and expensive synthetic materials limiting the performance. Here, a class of natural photoconductors is demonstrated through sub-picosecond heme-to-heme electron transfer in bacteria-produced protein nanowires.
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Affiliation(s)
- Jens Neu
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. .,Microbial Sciences Institute, Yale University, West Haven, CT, USA.
| | - Catharine C Shipps
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Matthew J Guberman-Pfeffer
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Cong Shen
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Vishok Srikanth
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Jacob A Spies
- Department of Chemistry, Yale University, New Haven, CT, USA
| | | | - Sibel Ebru Yalcin
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Microbial Sciences Institute, Yale University, West Haven, CT, USA
| | - Gary W Brudvig
- Department of Chemistry, Yale University, New Haven, CT, USA
| | | | - Nikhil S Malvankar
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. .,Microbial Sciences Institute, Yale University, West Haven, CT, USA.
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21
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Wang F, Chan CH, Suciu V, Mustafa K, Ammend M, Si D, Hochbaum AI, Egelman EH, Bond DR. Structure of Geobacter OmcZ filaments suggests extracellular cytochrome polymers evolved independently multiple times. eLife 2022; 11:81551. [PMID: 36062910 PMCID: PMC9473688 DOI: 10.7554/elife.81551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/03/2022] [Indexed: 11/26/2022] Open
Abstract
While early genetic and low-resolution structural observations suggested that extracellular conductive filaments on metal-reducing organisms such as Geobacter were composed of type IV pili, it has now been established that bacterial c-type cytochromes can polymerize to form extracellular filaments capable of long-range electron transport. Atomic structures exist for two such cytochrome filaments, formed from the hexaheme cytochrome OmcS and the tetraheme cytochrome OmcE. Due to the highly conserved heme packing within the central OmcS and OmcE cores, and shared pattern of heme coordination between subunits, it has been suggested that these polymers have a common origin. We have now used cryo-electron microscopy (cryo-EM) to determine the structure of a third extracellular filament, formed from the Geobacter sulfurreducens octaheme cytochrome, OmcZ. In contrast to the linear heme chains in OmcS and OmcE from the same organism, the packing of hemes, heme:heme angles, and between-subunit heme coordination is quite different in OmcZ. A branched heme arrangement within OmcZ leads to a highly surface exposed heme in every subunit, which may account for the formation of conductive biofilm networks, and explain the higher measured conductivity of OmcZ filaments. This new structural evidence suggests that conductive cytochrome polymers arose independently on more than one occasion from different ancestral multiheme proteins.
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Affiliation(s)
- Fengbin Wang
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, United States
| | - Chi Ho Chan
- Department of Plant and MIcrobial Biology, University of Minnesota, St. Paul, United States
| | - Victor Suciu
- Division of Computing and Software Systems, University of Washington Bothell, Bothell, United States
| | - Khawla Mustafa
- Department of Chemistry, University of California, Irvine, Irvine, United States
| | - Madeline Ammend
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, United States
| | - Dong Si
- Division of Computing and Software Systems, University of Washington Bothell, Bothell, United States
| | - Allon I Hochbaum
- Department of Chemistry, University of California, Irvine, Irvine, United States
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, United States
| | - Daniel R Bond
- Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, United States
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