1
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Lockwood CWJ, Nash BW, Newton-Payne SE, van Wonderen JH, Whiting KPS, Connolly A, Sutton-Cook AL, Crook A, Aithal AR, Edwards MJ, Clarke TA, Sachdeva A, Butt JN. Genetic Code Expansion in Shewanella oneidensis MR-1 Allows Site-Specific Incorporation of Bioorthogonal Functional Groups into a c-Type Cytochrome. ACS Synth Biol 2024. [PMID: 39158169 DOI: 10.1021/acssynbio.4c00248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Genetic code expansion has enabled cellular synthesis of proteins containing unique chemical functional groups to allow the understanding and modulation of biological systems and engineer new biotechnology. Here, we report the development of efficient methods for site-specific incorporation of structurally diverse noncanonical amino acids (ncAAs) into proteins expressed in the electroactive bacterium Shewanella oneidensis MR-1. We demonstrate that the biosynthetic machinery for ncAA incorporation is compatible and orthogonal to the endogenous pathways of S. oneidensis MR-1 for protein synthesis, maturation of c-type cytochromes, and protein secretion. This allowed the efficient synthesis of a c-type cytochrome, MtrC, containing site-specifically incorporated ncAA in S. oneidensis MR-1 cells. We demonstrate that site-specific replacement of surface residues in MtrC with ncAAs does not influence its three-dimensional structure and redox properties. We also demonstrate that site-specifically incorporated bioorthogonal functional groups could be used for efficient site-selective labeling of MtrC with fluorophores. These synthetic biology developments pave the way to expand the chemical repertoire of designer proteins expressed in S. oneidensis MR-1.
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Affiliation(s)
- Colin W J Lockwood
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Benjamin W Nash
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Simone E Newton-Payne
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Jessica H van Wonderen
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Keir P S Whiting
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Abigail Connolly
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Alexander L Sutton-Cook
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Archie Crook
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Advait R Aithal
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Marcus J Edwards
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, U.K
| | - Thomas A Clarke
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Amit Sachdeva
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
| | - Julea N Butt
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K
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2
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Garg K, Futera Z, Wu X, Jeong Y, Chiu R, Pisharam VC, Ha TQ, Aragonès AC, van Wonderen JH, Butt JN, Blumberger J, Díez-Pérez I. Shallow conductance decay along the heme array of a single tetraheme protein wire. Chem Sci 2024; 15:12326-12335. [PMID: 39118640 PMCID: PMC11304805 DOI: 10.1039/d4sc01366b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/24/2024] [Indexed: 08/10/2024] Open
Abstract
Multiheme cytochromes (MHCs) are the building blocks of highly conductive micrometre-long supramolecular wires found in so-called electrical bacteria. Recent studies have revealed that these proteins possess a long supramolecular array of closely packed heme cofactors along the main molecular axis alternating between perpendicular and stacking configurations (TST = T-shaped, stacked, T-shaped). While TST arrays have been identified as the likely electron conduit, the mechanisms of outstanding long-range charge transport observed in these structures remain unknown. Here we study charge transport on individual small tetraheme cytochromes (STCs) containing a single TST heme array. Individual STCs are trapped in a controllable nanoscale tunnelling gap. By modulating the tunnelling gap separation, we are able to selectively probe four different electron pathways involving 1, 2, 3 and 4 heme cofactors, respectively, leading to the determination of the electron tunnelling decay constant along the TST heme motif. Conductance calculations of selected single-STC junctions are in excellent agreement with experiments and suggest a mechanism of electron tunnelling with shallow length decay constant through an individual STC. These results demonstrate that an individual TST motif supporting electron tunnelling might contribute to a tunnelling-assisted charge transport diffusion mechanism in larger TST associations.
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Affiliation(s)
- Kavita Garg
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, King's College London, Britannia House 7 Trinity Street London SE1 1DB UK
| | - Zdenek Futera
- Faculty of Science, University of South Bohemia Branisovska 1760 370 05 Ceske Budejovice Czech Republic
| | - Xiaojing Wu
- Department of Physics and Astronomy, Thomas Young Centre, University College London Gower Street London WC1E 6BT UK
| | - Yongchan Jeong
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, King's College London, Britannia House 7 Trinity Street London SE1 1DB UK
| | - Rachel Chiu
- School of Chemistry, School of Biological Sciences, University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Varun Chittari Pisharam
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, King's College London, Britannia House 7 Trinity Street London SE1 1DB UK
| | - Tracy Q Ha
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, King's College London, Britannia House 7 Trinity Street London SE1 1DB UK
| | - Albert C Aragonès
- Departament de Ciència de Materials i Química Física, Universitat de Barcelona, Institut de Química Teòrica i Computacional (IQTC) Marti i Franquès 1 08028 Barcelona Spain
| | - Jessica H van Wonderen
- School of Chemistry, School of Biological Sciences, University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Julea N Butt
- School of Chemistry, School of Biological Sciences, University of East Anglia Norwich Research Park Norwich NR4 7TJ UK
| | - Jochen Blumberger
- Department of Physics and Astronomy, Thomas Young Centre, University College London Gower Street London WC1E 6BT UK
| | - Ismael Díez-Pérez
- Department of Chemistry, Faculty of Natural, Mathematical & Engineering Sciences, King's College London, Britannia House 7 Trinity Street London SE1 1DB UK
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3
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Zhang Y, Liang H, Qi P, Xu Z, Fei H, Guo C. Deciphering the Roles of Interfacial Amino Acids in Inter-Protein Charge Transport. NANO LETTERS 2024; 24:4178-4185. [PMID: 38552164 DOI: 10.1021/acs.nanolett.4c00164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Elucidating charge transport (CT) through proteins is critical for gaining insights into ubiquitous CT chain reactions in biological systems and developing high-performance bioelectronic devices. While intra-protein CT has been extensively studied, crucial knowledge about inter-protein CT via interfacial amino acids is still absent due to the structural complexity. Herein, by loading cytochrome c (Cyt c) on well-defined peptide self-assembled monolayers to mimic the protein-protein interface, we provide a precisely controlled platform for identifying the roles of interfacial amino acids in solid-state CT via peptide-Cyt c junctions. The terminal amino acid of peptides serves as a fine-tuning factor for both the interfacial interaction between peptides and Cyt c and the immobilized Cyt c orientation, resulting in a nearly 10-fold difference in current through peptide-Cyt c junctions with varied asymmetry. This work provides a valuable platform for studying CT across proteins and contributes to the understanding of fundamental principles governing inter-protein CT.
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Affiliation(s)
- Yongkang Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
| | - Han Liang
- College of Chemistry and Molecular Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
| | - Pan Qi
- College of Chemistry and Molecular Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
| | - Zhongchen Xu
- College of Chemistry and Molecular Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
| | - Houguo Fei
- College of Chemistry and Molecular Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
| | - Cunlan Guo
- College of Chemistry and Molecular Sciences, Wuhan University, 299 Bayi Road, Wuhan, Hubei 430072, China
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4
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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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5
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Bera S, Fereiro JA, Saxena SK, Chryssikos D, Majhi K, Bendikov T, Sepunaru L, Ehre D, Tornow M, Pecht I, Vilan A, Sheves M, Cahen D. Near-Temperature-Independent Electron Transport Well beyond Expected Quantum Tunneling Range via Bacteriorhodopsin Multilayers. J Am Chem Soc 2023; 145. [PMID: 37933117 PMCID: PMC10655127 DOI: 10.1021/jacs.3c09120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/08/2023]
Abstract
A key conundrum of biomolecular electronics is efficient electron transport (ETp) through solid-state junctions up to 10 nm, often without temperature activation. Such behavior challenges known charge transport mechanisms, especially via nonconjugated molecules such as proteins. Single-step, coherent quantum-mechanical tunneling proposed for ETp across small protein, 2-3 nm wide junctions, but it is problematic for larger proteins. Here we exploit the ability of bacteriorhodopsin (bR), a well-studied, 4-5 nm long membrane protein, to assemble into well-defined single and multiple bilayers, from ∼9 to 60 nm thick, to investigate ETp limits as a function of junction width. To ensure sufficient signal/noise, we use large area (∼10-3 cm2) Au-protein-Si junctions. Photoemission spectra indicate a wide energy separation between electrode Fermi and the nearest protein-energy levels, as expected for a polymer of mostly saturated components. Junction currents decreased exponentially with increasing junction width, with uniquely low length-decay constants (0.05-0.5 nm-1). Remarkably, even for the widest junctions, currents are nearly temperature-independent, completely so below 160 K. While, among other things, the lack of temperature-dependence excludes, hopping as a plausible mechanism, coherent quantum-mechanical tunneling over 60 nm is physically implausible. The results may be understood if ETp is limited by injection into one of the contacts, followed by more efficient charge propagation across the protein. Still, the electrostatics of the protein films further limit the number of charge carriers injected into the protein film. How electron transport across dozens of nanometers of protein layers is more efficient than injection defines a riddle, requiring further study.
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Affiliation(s)
- Sudipta Bera
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jerry A. Fereiro
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
- School
of Chemistry, Indian Institute of Science
Education and Research, Thiruvananthapuram 695551, Kerala, India
| | - Shailendra K. Saxena
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
- Department
of Physics and Nanotechnology, College of Engineering and Technology, SRM Institute of Science and Technology, Kattankulathur, Chennai 603203, Tamil
Nadu, India
| | - Domenikos Chryssikos
- Molecular
Electronics, Technical University of Munich, 85748 Garching, Germany
- Fraunhofer
Institute for Electronic Microsystems and Solid State Technologies
(EMFT), 80686 München, Germany
| | - Koushik Majhi
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tatyana Bendikov
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot 7610001, Israel
| | - Lior Sepunaru
- Department
of Chemistry and Biochemistry, University
of California, Santa
Barbara, California 93106, United States
| | - David Ehre
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Marc Tornow
- Molecular
Electronics, Technical University of Munich, 85748 Garching, Germany
- Fraunhofer
Institute for Electronic Microsystems and Solid State Technologies
(EMFT), 80686 München, Germany
| | - Israel Pecht
- Department
of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Ayelet Vilan
- Department
of Chemical and Biological Physics Weizmann
Institute of Science, Rehovot 7610001, Israel
| | - Mordechai Sheves
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Cahen
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
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6
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López-Ortiz M, Zamora RA, Giannotti MI, Gorostiza P. The Protein Matrix of Plastocyanin Supports Long-Distance Charge Transport with Photosystem I and the Copper Ion Regulates Its Spatial Span and Conductance. ACS NANO 2023; 17:20334-20344. [PMID: 37797170 DOI: 10.1021/acsnano.3c06390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/07/2023]
Abstract
Charge exchange is the fundamental process that sustains cellular respiration and photosynthesis by shuttling electrons in a cascade of electron transfer (ET) steps between redox cofactors. While intraprotein charge exchange is well characterized in protein complexes bearing multiple redox sites, interprotein processes are less understood due to the lack of suitable experimental approaches and the dynamic nature of the interactions. Proteins constrained between electrodes are known to support electron transport (ETp) through the protein matrix even without redox cofactors, as the charges housed by the redox sites in ET are furnished by the electrodes. However, it is unknown whether protein ETp mechanisms apply to the interprotein medium present under physiological conditions. We study interprotein charge exchange between plant photosystem I (PSI) and its soluble redox partner plastocyanin (Pc) and address the role of the Pc copper center. Using electrochemical scanning tunneling spectroscopy (ECSTS) current-distance and blinking measurements, we quantify the spatial span of charge exchange between individual Pc/PSI pairs and ETp through transient Pc/PSI complexes. Pc devoid of the redox center (Pcapo) can exchange charge with PSI at longer distances than with the copper ion (Pcholo). Conductance bursts associated with Pcapo/PSI complex formation are higher than in Pcholo/PSI. Thus, copper ions are not required for long-distance Pc/PSI ETp but regulate its spatial span and conductance. Our results suggest that the redox center that carries the charge in Pc is not necessary to exchange it in interprotein ET through the aqueous solution and question the canonical view of tight complex binding between redox protein partners.
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Affiliation(s)
- Manuel López-Ortiz
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
| | - Ricardo A Zamora
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
| | - Marina I Giannotti
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
- Department of Materials Science and Physical Chemistry, University of Barcelona, Martí i Franquès 1-11, Barcelona 08028, Spain
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona 08028, Spain
- CIBER-BBN, ISCIII, Barcelona 08028, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona 08010, Spain
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7
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Vacek J, Zatloukalová M, Dorčák V, Cifra M, Futera Z, Ostatná V. Electrochemistry in sensing of molecular interactions of proteins and their behavior in an electric field. Mikrochim Acta 2023; 190:442. [PMID: 37847341 PMCID: PMC10582152 DOI: 10.1007/s00604-023-05999-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Electrochemical methods can be used not only for the sensitive analysis of proteins but also for deeper research into their structure, transport functions (transfer of electrons and protons), and sensing their interactions with soft and solid surfaces. Last but not least, electrochemical tools are useful for investigating the effect of an electric field on protein structure, the direct application of electrochemical methods for controlling protein function, or the micromanipulation of supramolecular protein structures. There are many experimental arrangements (modalities), from the classic configuration that works with an electrochemical cell to miniaturized electrochemical sensors and microchip platforms. The support of computational chemistry methods which appropriately complement the interpretation framework of experimental results is also important. This text describes recent directions in electrochemical methods for the determination of proteins and briefly summarizes available methodologies for the selective labeling of proteins using redox-active probes. Attention is also paid to the theoretical aspects of electron transport and the effect of an external electric field on the structure of selected proteins. Instead of providing a comprehensive overview, we aim to highlight areas of interest that have not been summarized recently, but, at the same time, represent current trends in the field.
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Affiliation(s)
- Jan Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic.
| | - Martina Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Vlastimil Dorčák
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacky University, Hnevotinska 3, 77515, Olomouc, Czech Republic
| | - Michal Cifra
- Institute of Photonics and Electronics of the Czech Academy of Sciences, Chaberska 1014/57, 18200, Prague, Czech Republic
| | - Zdeněk Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 37005, Ceske Budejovice, Czech Republic
| | - Veronika Ostatná
- Institute of Biophysics, The Czech Academy of Sciences, v.v.i., Kralovopolska 135, 61200, Brno, Czech Republic
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8
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Niman CM, Sukenik N, Dang T, Nwachukwu J, Thirumurthy MA, Jones AK, Naaman R, Santra K, Das TK, Paltiel Y, Baczewski LT, El-Naggar MY. Bacterial extracellular electron transfer components are spin selective. J Chem Phys 2023; 159:145101. [PMID: 37811828 DOI: 10.1063/5.0154211] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/01/2023] [Indexed: 10/10/2023] Open
Abstract
Metal-reducing bacteria have adapted the ability to respire extracellular solid surfaces instead of soluble oxidants. This process requires an electron transport pathway that spans from the inner membrane, across the periplasm, through the outer membrane, and to an external surface. Multiheme cytochromes are the primary machinery for moving electrons through this pathway. Recent studies show that the chiral-induced spin selectivity (CISS) effect is observable in some of these proteins extracted from the model metal-reducing bacteria, Shewanella oneidensis MR-1. It was hypothesized that the CISS effect facilitates efficient electron transport in these proteins by coupling electron velocity to spin, thus reducing the probability of backscattering. However, these studies focused exclusively on the cell surface electron conduits, and thus, CISS has not been investigated in upstream electron transfer components such as the membrane-associated MtrA, or periplasmic proteins such as small tetraheme cytochrome (STC). By using conductive probe atomic force microscopy measurements of protein monolayers adsorbed onto ferromagnetic substrates, we show that electron transport is spin selective in both MtrA and STC. Moreover, we have determined the spin polarization of MtrA to be ∼77% and STC to be ∼35%. This disparity in spin polarizations could indicate that spin selectivity is length dependent in heme proteins, given that MtrA is approximately two times longer than STC. Most significantly, our study indicates that spin-dependent interactions affect the entire extracellular electron transport pathway.
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Affiliation(s)
- Christina M Niman
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Nir Sukenik
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
| | - Tram Dang
- Department of Biological Sciences, University of Southern California, Los Angeles, California 91030, USA
| | - Justus Nwachukwu
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Miyuki A Thirumurthy
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Anne K Jones
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, USA
| | - Ron Naaman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Kakali Santra
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Tapan K Das
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yossi Paltiel
- Institute of Applied Physics, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | | | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, California 91030, USA
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA
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9
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Li T, Bandari VK, Schmidt OG. Molecular Electronics: Creating and Bridging Molecular Junctions and Promoting Its Commercialization. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2209088. [PMID: 36512432 DOI: 10.1002/adma.202209088] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/28/2022] [Indexed: 06/02/2023]
Abstract
Molecular electronics is driven by the dream of expanding Moore's law to the molecular level for next-generation electronics through incorporating individual or ensemble molecules into electronic circuits. For nearly 50 years, numerous efforts have been made to explore the intrinsic properties of molecules and develop diverse fascinating molecular electronic devices with the desired functionalities. The flourishing of molecular electronics is inseparable from the development of various elegant methodologies for creating nanogap electrodes and bridging the nanogap with molecules. This review first focuses on the techniques for making lateral and vertical nanogap electrodes by breaking, narrowing, and fixed modes, and highlights their capabilities, applications, merits, and shortcomings. After summarizing the approaches of growing single molecules or molecular layers on the electrodes, the methods of constructing a complete molecular circuit are comprehensively grouped into three categories: 1) directly bridging one-molecule-electrode component with another electrode, 2) physically bridging two-molecule-electrode components, and 3) chemically bridging two-molecule-electrode components. Finally, the current state of molecular circuit integration and commercialization is discussed and perspectives are provided, hoping to encourage the community to accelerate the realization of fully scalable molecular electronics for a new era of integrated microsystems and applications.
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Affiliation(s)
- Tianming Li
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09111, Chemnitz, Germany
| | - Vineeth Kumar Bandari
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09111, Chemnitz, Germany
| | - Oliver G Schmidt
- Research Center for Materials, Architectures and Integration of Nanomembranes (MAIN), Chemnitz University of Technology, 09126, Chemnitz, Germany
- Material Systems for Nanoelectronics, Chemnitz University of Technology, 09111, Chemnitz, Germany
- Nanophysics, Dresden University of Technology, 01069, Dresden, Germany
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10
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Kontkanen OV, Biriukov D, Futera Z. Applicability of perturbed matrix method for charge transfer studies at bio/metallic interfaces: a case of azurin. Phys Chem Chem Phys 2023; 25:12479-12489. [PMID: 37097130 DOI: 10.1039/d3cp00197k] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2023]
Abstract
As the field of nanoelectronics based on biomolecules such as peptides and proteins rapidly grows, there is a need for robust computational methods able to reliably predict charge transfer properties at bio/metallic interfaces. Traditionally, hybrid quantum-mechanical/molecular-mechanical techniques are employed for systems where the electron hopping transfer mechanism is applicable to determine physical parameters controlling the thermodynamics and kinetics of charge transfer processes. However, these approaches are limited by a relatively high computational cost when extensive sampling of a configurational space is required, like in the case of soft biomatter. For these applications, semi-empirical approaches such as the perturbed matrix method (PMM) have been developed and successfully used to study charge-transfer processes in biomolecules. Here, we explore the performance of PMM on prototypical redox-active protein azurin in various environments, from solution to vacuum interfaces with gold surfaces and protein junction. We systematically benchmarked the robustness and convergence of the method with respect to the quantum-centre size, size of the Hamiltonian, number of samples, and level of theory. We show that PMM can adequately capture all the trends associated with the structural and electronic changes related to azurin oxidation at bio/metallic interfaces.
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Affiliation(s)
- Outi Vilhelmiina Kontkanen
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
| | - Denys Biriukov
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
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11
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Bera S, Govinda S, Fereiro JA, Pecht I, Sheves M, Cahen D. Biotin Binding Hardly Affects Electron Transport Efficiency across Streptavidin Solid-State Junctions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:1394-1403. [PMID: 36648410 PMCID: PMC9893813 DOI: 10.1021/acs.langmuir.2c02378] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 12/29/2022] [Indexed: 05/27/2023]
Abstract
The electron transport (ETp) efficiency of solid-state protein-mediated junctions is highly influenced by the presence of electron-rich organic cofactors or transition metal ions. Hence, we chose to investigate an interesting cofactor-free non-redox protein, streptavidin (STV), which has unmatched strong binding affinity for an organic small-molecule ligand, biotin, which lacks any electron-rich features. We describe for the first time meso-scale ETp via electrical junctions of STV monolayers and focus on the question of whether the rate of ETp across both native and thiolated STV monolayers is influenced by ligand binding, a process that we show to cause some structural conformation changes in the STV monolayers. Au nanowire-electrode-protein monolayer-microelectrode junctions, fabricated by modifying an earlier procedure to improve the yields of usable junctions, were employed for ETp measurements. Our results on compactly integrated, dense, uniform, ∼3 nm thick STV monolayers indicate that, notwithstanding the slight structural changes in the STV monolayers upon biotin binding, there is no statistically significant conductance change between the free STV and that bound to biotin. The ETp temperature (T) dependence over the 80-300 K range is very small but with an unusual, slightly negative (metallic-like) dependence toward room temperature. Such dependence can be accounted for by the reversible structural shrinkage of the STV at temperatures below 160 K.
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Affiliation(s)
- Sudipta Bera
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sharada Govinda
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Jerry A. Fereiro
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
- The
School of Chemistry, Indian Institute of
Science Education and Research, Thiruvananthapuram, Maruthamala, Kerala 695551, India
| | - Israel Pecht
- Department
of Immunology and Regenerative Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mordechai Sheves
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - David Cahen
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, Rehovot 7610001, Israel
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12
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Futera Z, Wu X, Blumberger J. Tunneling-to-Hopping Transition in Multiheme Cytochrome Bioelectronic Junctions. J Phys Chem Lett 2023; 14:445-452. [PMID: 36622944 DOI: 10.1021/acs.jpclett.2c03361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Multiheme cytochromes (MHCs) have attracted much interest for use in nanobioelectronic junctions due to their high electronic conductances. Recent measurements on dry MHC junctions suggested that a coherent tunneling mechanism is operative over surprisingly long long distances (>3 nm), which challenges our understanding of coherent transport phenomena. Here we show that this is due to (i) a low exponential distance decay constant for coherent conduction in MHCs (β = 0.2 Å-1) and (ii) a large density of protein electronic states which prolongs the coherent tunneling regime to distances that exceed those in molecular wires made of small molecules. Incoherent hopping conduction is uncompetitive due to the large energy level offset at the protein-electrode interface. Removing this offset, e.g., by gating, we predict that the transport mechanism crosses over from coherent tunneling to incoherent hopping at a protein size of ∼7 nm, thus enabling transport on the micrometer scale with a shallow polynomial (∼1/r) distance decay.
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Affiliation(s)
- Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
| | - Xiaojing Wu
- University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, U.K
| | - Jochen Blumberger
- University College London, Department of Physics and Astronomy, Gower Street, London WC1E 6BT, U.K
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13
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Zinelli R, Soni S, Cornelissen JJLM, Michel-Souzy S, Nijhuis CA. Charge Transport across Proteins inside Proteins: Tunneling across Encapsulin Protein Cages and the Effect of Cargo Proteins. Biomolecules 2023; 13:174. [PMID: 36671559 PMCID: PMC9855946 DOI: 10.3390/biom13010174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Charge transport across proteins can be surprisingly efficient over long distances-so-called long-range tunneling-but it is still unclear as to why and under which conditions (e.g., presence of co-factors, type of cargo) the long-range tunneling regime can be accessed. This paper describes molecular tunneling junctions based on an encapsulin (Enc), which is a large protein cage with a diameter of 24 nm that can be loaded with various types of (small) proteins, also referred to as "cargo". We demonstrate with dynamic light scattering, transmission electron microscopy, and atomic force microscopy that Enc, with and without cargo, can be made stable in solution and immobilized on metal electrodes without aggregation. We investigated the electronic properties of Enc in EGaIn-based tunnel junctions (EGaIn = eutectic alloy of Ga and In that is widely used to contact (bio)molecular monolayers) by measuring the current density for a large range of applied bias of ±2.5 V. The encapsulated cargo has an important effect on the electrical properties of the junctions. The measured current densities are higher for junctions with Enc loaded with redox-active cargo (ferritin-like protein) than those junctions without cargo or redox-inactive cargo (green fluorescent protein). These findings open the door to charge transport studies across complex biomolecular hierarchical structures.
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Affiliation(s)
- Riccardo Zinelli
- Hybrid Materials for Opto-Electronics Group, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
- Biomolecular NanoTechnology, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
| | - Saurabh Soni
- Hybrid Materials for Opto-Electronics Group, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
| | - Jeroen J. L. M. Cornelissen
- Biomolecular NanoTechnology, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
| | - Sandra Michel-Souzy
- Biomolecular NanoTechnology, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
| | - Christian A. Nijhuis
- Hybrid Materials for Opto-Electronics Group, Department of Molecules and Materials, MESA+ Institute for Nanotechnology, Molecules Center and Center for Brain-Inspired Nano Systems, Faculty of Science and Technology, University of Twente, P.O. Box 2017, 7500 AE Enschede, The Netherlands
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14
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Gupta NK, Okamoto N, Karuppannan SK, Pasula RR, Ziyu Z, Qi DC, Lim S, Nakamura M, Nijhuis CA. The Role of Structural Order in the Mechanism of Charge Transport across Tunnel Junctions with Various Iron-Storing Proteins. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2203338. [PMID: 36103613 DOI: 10.1002/smll.202203338] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/19/2022] [Indexed: 06/15/2023]
Abstract
In biomolecular electronics, the role of structural order in charge transport (CT) is poorly understood. It has been reported that the metal oxide cores of protein cages (e.g., iron oxide and ferrihydrite nanoparticles (NPs) present in ferritin and E2-LFtn, which is E2 protein engineered with an iron-binding sequence) play an important role in the mechanism of CT. At the same time, the NP core also plays a major role in the structural integrity of the proteins. This paper describes the role of structural order in CT across tunnel junctions by comparing three iron-storing proteins. They are (1) DNA binding protein from starved cells (Dps, diameter (∅) = 9 nm); (2) engineered archaeal ferritin (AfFtn-AA, ∅ = 12 nm); and (3) engineered E2 of pyruvate dehydrogenase enzyme complex (E2-LFtn, ∅ = 25 nm). Both holo-Dps and apo-Dps proteins undergo CT by coherent tunneling because their globular architecture and relative structural stability provide a coherent conduction pathway. In contrast, apo-AfFtn-AA forms a disordered structure across which charges have to tunnel incoherently, but holo-AfFtn-AA retains its globular structure and supports coherent tunneling. The large E2-LFtn always forms disordered structures across which charges incoherently tunnel regardless of the presence of the NP core. These findings highlight the importance of structural order in the mechanism of CT across biomolecular tunnel junctions.
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Affiliation(s)
- Nipun Kumar Gupta
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore
| | - Naofumi Okamoto
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Senthil Kumar Karuppannan
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
- National Quantum Fabless Foundry (NQFF), Institute of Materials Research and Engineering, 2 Fusionopolis Way, Innovis Building, Singapore, 138634, Singapore
| | - Rupali Reddy Pasula
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
| | - Zhang Ziyu
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
| | - Dong-Chen Qi
- Centre for Materials Science, School of Chemistry and Physics, Queensland University of Technology, Brisbane, Queensland, 4001, Australia
| | - Sierin Lim
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, 70 Nanyang Drive, Singapore, 637457, Singapore
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, 59 Nanyang Drive, Experimental Medicine Building, Singapore, 636921, Singapore
| | - Masakazu Nakamura
- Division of Materials Science, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Christian A Nijhuis
- Department of Chemistry, National University of Singapore, 3 Science Drive, Singapore, 117543, Singapore
- Centre for Advanced 2D Materials, National University of Singapore, 6 Science Drive 2, Singapore, 117546, Singapore
- Department of Molecules and Materials, MESA+ Institute for Nanotechnology, and Center for Brain-Inspired Nano Systems (BRAINS), Faculty of Science and Technology, University of Twente, P.O. Box 217, Enschede, 7500 AE, The Netherlands
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15
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16
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Qiu X, Chiechi RC. Printable logic circuits comprising self-assembled protein complexes. Nat Commun 2022; 13:2312. [PMID: 35484124 PMCID: PMC9050843 DOI: 10.1038/s41467-022-30038-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 04/08/2022] [Indexed: 11/09/2022] Open
Abstract
This paper describes the fabrication of digital logic circuits comprising resistors and diodes made from protein complexes and wired together using printed liquid metal electrodes. These resistors and diodes exhibit temperature-independent charge-transport over a distance of approximately 10 nm and require no encapsulation or special handling. The function of the protein complexes is determined entirely by self-assembly. When induced to self-assembly into anisotropic monolayers, the collective action of the aligned dipole moments increases the electrical conductivity of the ensemble in one direction and decreases it in the other. When induced to self-assemble into isotropic monolayers, the dipole moments are randomized and the electrical conductivity is approximately equal in both directions. We demonstrate the robustness and utility of these all-protein logic circuits by constructing pulse modulators based on AND and OR logic gates that function nearly identically to simulated circuits. These results show that digital circuits with useful functionality can be derived from readily obtainable biomolecules using simple, straightforward fabrication techniques that exploit molecular self-assembly, realizing one of the primary goals of molecular electronics. Proteins are promising molecular materials for next-generation electronic devices. Here, the authors fabricated printable digital logic circuits comprising resistors and diodes from self-assembled photosystem I complexes that enable pulse modulation.
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Affiliation(s)
- Xinkai Qiu
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. .,Optoelectronics Group, Cavendish Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge, CB3 0HE, UK.
| | - Ryan C Chiechi
- Stratingh Institute for Chemistry, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands. .,Department of Chemistry, North Carolina State University, Raleigh, NC, 27695-8204, United States.
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17
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Kontkanen OV, Biriukov D, Futera Z. Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces. J Chem Phys 2022; 156:175101. [DOI: 10.1063/5.0085141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid QM/MM computational technique based on DFT to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Somewhat surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry, however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.
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Affiliation(s)
| | - Denys Biriukov
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Czech Republic
| | - Zdenek Futera
- University of South Bohemia in Ceske Budejovice Faculty of Science, Czech Republic
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18
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López-Ortiz M, Zamora RA, Giannotti MI, Hu C, Croce R, Gorostiza P. Distance and Potential Dependence of Charge Transport Through the Reaction Center of Individual Photosynthetic Complexes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2104366. [PMID: 34874621 DOI: 10.1002/smll.202104366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Charge separation and transport through the reaction center of photosystem I (PSI) is an essential part of the photosynthetic electron transport chain. A strategy is developed to immobilize and orient PSI complexes on gold electrodes allowing to probe the complex's electron acceptor side, the chlorophyll special pair P700. Electrochemical scanning tunneling microscopy (ECSTM) imaging and current-distance spectroscopy of single protein complex shows lateral size in agreement with its known dimensions, and a PSI apparent height that depends on the probe potential revealing a gating effect in protein conductance. In current-distance spectroscopy, it is observed that the distance-decay constant of the current between PSI and the ECSTM probe depends on the sample and probe electrode potentials. The longest charge exchange distance (lowest distance-decay constant β) is observed at sample potential 0 mV/SSC (SSC: reference electrode silver/silver chloride) and probe potential 400 mV/SSC. These potentials correspond to hole injection into an electronic state that is available in the absence of illumination. It is proposed that a pair of tryptophan residues located at the interface between P700 and the solution and known to support the hydrophobic recognition of the PSI redox partner plastocyanin, may have an additional role as hole exchange mediator in charge transport through PSI.
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Affiliation(s)
- Manuel López-Ortiz
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Ricardo A Zamora
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
| | - Marina Inés Giannotti
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
- Department of Materials Science and Physical Chemistry, University of Barcelona, Martí i Franquès 1-11, Barcelona, 08028, Spain
| | - Chen Hu
- Biophysics of PhotosynthesisDepartment of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam, 1081 HV, The Netherlands
| | - Roberta Croce
- Biophysics of PhotosynthesisDepartment of Physics and Astronomy, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam, 1081 HV, The Netherlands
| | - Pau Gorostiza
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Baldiri Reixac 10-12, Barcelona, 08028, Spain
- Network Biomedical Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, 28029, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08010, Spain
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19
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Zhang B, Ryan E, Wang X, Song W, Lindsay S. Electronic Transport in Molecular Wires of Precisely Controlled Length Built from Modular Proteins. ACS NANO 2022; 16:1671-1680. [PMID: 35029115 PMCID: PMC9279515 DOI: 10.1021/acsnano.1c10830] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
DNA molecular wires have been studied extensively because of the ease with which molecules of controlled length and composition can be synthesized. The same has not been true for proteins. Here, we have synthesized and studied a series of consensus tetratricopeptide repeat (CTPR) proteins, spanning 4 to 20 nm in length, in increments of 4 nm. For lengths in excess of 6 nm, their conductance exceeds that of the canonical molecular wire, oligo(phenylene-ethylenene), because of the more gradual decay of conductance with length in the protein. We show that, while the conductance decay fits an exponential (characteristic of quantum tunneling) and not a linear increase of resistance with length (characteristic of hopping transport), it is also accounted for by a square-law dependence on length (characteristic of weakly driven hopping). Measurements of the energy dependence of the decay length rule out the quantum tunneling case. A resonance in the carrier injection energy shows that allowed states in the protein align with the Fermi energy of the electrodes. Both the energy of these states and the long-range of hopping suggest that the reorganization induced by hole formation is greatly reduced inside the protein. We outline a model for calculating the molecular-electronic properties of proteins.
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Affiliation(s)
- Bintian Zhang
- Biodesign Institute, Arizona State University, Tempe, AZ 85281
| | - Eathen Ryan
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281
| | - Xu Wang
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281
| | - Weisi Song
- Biodesign Institute, Arizona State University, Tempe, AZ 85281
| | - Stuart Lindsay
- Biodesign Institute, Arizona State University, Tempe, AZ 85281
- School of Molecular Sciences, Arizona State University, Tempe, AZ 85281
- Department of Physics, Arizona State University, Tempe, AZ 85281
- Corresponding Author: Stuart Lindsay: Phone 480 205 6432
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20
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Nanosecond heme-to-heme electron transfer rates in a multiheme cytochrome nanowire reported by a spectrally unique His/Met-ligated heme. Proc Natl Acad Sci U S A 2021; 118:2107939118. [PMID: 34556577 PMCID: PMC8488605 DOI: 10.1073/pnas.2107939118] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2021] [Indexed: 11/29/2022] Open
Abstract
Multiheme cytochromes have been identified as essential proteins for electron exchange between bacterial enzymes and redox substrates outside of the cell. In microbiology, these proteins contribute to efficient energy storage and conversion. For biotechnology, multiheme cytochromes contribute to the production of green fuels and electricity. Furthermore, these proteins inspire the design of molecular-scale electronic devices. Here, we report exceptionally high rates of heme-to-heme electron transfer in a multiheme cytochrome. We expect similarly high rates, among the highest reported for ground-state electron transfer in biology, in other multiheme cytochromes as the close-packed hemes adopt similar configurations despite very different amino acid sequences and protein folds. Proteins achieve efficient energy storage and conversion through electron transfer along a series of redox cofactors. Multiheme cytochromes are notable examples. These proteins transfer electrons over distance scales of several nanometers to >10 μm and in so doing they couple cellular metabolism with extracellular redox partners including electrodes. Here, we report pump-probe spectroscopy that provides a direct measure of the intrinsic rates of heme–heme electron transfer in this fascinating class of proteins. Our study took advantage of a spectrally unique His/Met-ligated heme introduced at a defined site within the decaheme extracellular MtrC protein of Shewanella oneidensis. We observed rates of heme-to-heme electron transfer on the order of 109 s−1 (3.7 to 4.3 Å edge-to-edge distance), in good agreement with predictions based on density functional and molecular dynamics calculations. These rates are among the highest reported for ground-state electron transfer in biology. Yet, some fall 2 to 3 orders of magnitude below the Moser–Dutton ruler because electron transfer at these short distances is through space and therefore associated with a higher tunneling barrier than the through-protein tunneling scenario that is usual at longer distances. Moreover, we show that the His/Met-ligated heme creates an electron sink that stabilizes the charge separated state on the 100-μs time scale. This feature could be exploited in future designs of multiheme cytochromes as components of versatile photosynthetic biohybrid assemblies.
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21
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Blake RC, Nautiyal A, Smith KA, Walton NN, Pendleton B, Wang Z. Ferrimicrobium acidiphilum Exchanges Electrons With a Platinum Electrode via a Cytochrome With Reduced Absorbance Maxima at 448 and 605 nm. Front Microbiol 2021; 12:705187. [PMID: 34381433 PMCID: PMC8350767 DOI: 10.3389/fmicb.2021.705187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 07/02/2021] [Indexed: 01/22/2023] Open
Abstract
Ferrimicrobium acidiphilum is a Gram-positive member of the Actinobacteria phylum that can respire aerobically or anaerobically with soluble Fe(II) or Fe(III), respectively, in sulfuric acid at pH 1.5. Cyclic voltammetry measurements using intact F. acidiphilum at pH 1.5 produced fully reversible voltammograms that were highly reproducible. The maximum current observed with the anodic peak was considerably less than was the maximum current observed with the cathodic peak. This difference was attributed to the competition between the platinum electrode and the soluble oxygen for the available electrons that were introduced by the cathodic wave into this facultative aerobic organism. The standard reduction potential of the intact organism was determined to be 786 mV vs. the standard hydrogen electrode, slightly more positive than that of 735 mV that was determined for soluble iron at pH 1.5 using the same apparatus. Chronocoulometry measurements conducted at different cell densities revealed that the intact organism remained in close proximity to the working electrode during the measurement, whereas soluble ionic iron did not. When the cyclic voltammetry of intact F. acidiphilum was monitored using an integrating cavity absorption meter, the only small changes in absorbance that were detected were consistent with the participation of a cellular cytochrome with reduced absorbance peaks at 448 and 605 nm. The cytochrome that participated in the exchange of electrons between the intact organism and extracellular solid electrodes like platinum was the same cytochrome whose oxidation was previously shown to be rate-limiting when the organism respired aerobically on extracellular soluble iron.
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Affiliation(s)
- Robert C Blake
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Amit Nautiyal
- Department of Chemistry, Xavier University of Louisiana, New Orleans, LA, United States
| | - Kayla A Smith
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Noelle N Walton
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Brealand Pendleton
- Division of Basic Pharmaceutical Sciences, College of Pharmacy, Xavier University of Louisiana, New Orleans, LA, United States
| | - Zhe Wang
- Department of Chemistry, Oakland University, Rochester, NY, United States
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22
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Abstract
Steady progress is being made in unveiling nature's long-range charge transport mechanisms in redox proteins and in the development of versatile self-assembling scaffolds and de novo proteins by design-two separate fields that soon may intersect to yield the first artificial bioelectronic wires. Here, we summarize compelling developments in these areas that put a spotlight on the prospect of their convergence, featuring, in particular, work by Dai et al. in this issue of ACS Nano that illustrates success in intentional design with nuanced control, binding multiple c-type hemes into a specific ordered array bearing the essential hallmarks of heme chains in bacterial multiheme cytochromes.
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Affiliation(s)
- Kevin M Rosso
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Piotr Zarzycki
- Energy Geosciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
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23
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Futera Z. Amino-acid interactions with the Au(111) surface: adsorption, band alignment, and interfacial electronic coupling. Phys Chem Chem Phys 2021; 23:10257-10266. [PMID: 33899874 DOI: 10.1039/d1cp00218j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The charge transport properties of biological molecules like peptides and proteins are intensively studied for the great flexibility, redox-state variability, long-range efficiency, and biocompatibility of potential bioelectronic applications. Yet, the electronic interactions of biomolecules with solid metal surfaces, determining the conductivities of the biomolecular junctions, are hard to predict and usually unavailable. Here, we present accurate adsorption structures and energies, electronic band alignment, and interfacial electronic coupling data for all 20 natural amino acids computed using the DFT+Σ scheme based on the vdW-DF and OT-RSH functionals. For comparison, data obtained using the popular PBE functional are provided as well. Tryptophan, compared to other amino acids, is shown to be distinctly exceptional in terms of the electronic properties related to charge transport. Its high adsorption energy, frontier-orbital levels aligned relatively close to the Fermi energy of gold and strong interfacial electronic coupling make it an ideal candidate for facilitating charge transfer on such heterogeneous interfaces. Although the amino acids in peptides and proteins are affected by the structural interactions hindering their contact with the surface, knowledge of the single-molecule surface interactions is necessary for a detailed understanding of such structural effects and tuning of potential applications.
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Affiliation(s)
- Zdenek Futera
- Faculty of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic.
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24
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The Role of Metal Ions in the Electron Transport through Azurin-Based Junctions. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11093732] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We studied the coherent electron transport through metal–protein–metal junctions based on a blue copper azurin, in which the copper ion was replaced by three different metal ions (Co, Ni and Zn). Our results show that neither the protein structure nor the transmission at the Fermi level change significantly upon metal replacement. The discrepancy with previous experimental observations suggests that the transport mechanism taking place in these types of junctions is probably not fully coherent.
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25
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Futera Z, Ide I, Kayser B, Garg K, Jiang X, van Wonderen JH, Butt JN, Ishii H, Pecht I, Sheves M, Cahen D, Blumberger J. Coherent Electron Transport across a 3 nm Bioelectronic Junction Made of Multi-Heme Proteins. J Phys Chem Lett 2020; 11:9766-9774. [PMID: 33142062 PMCID: PMC7681787 DOI: 10.1021/acs.jpclett.0c02686] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Multi-heme cytochromes (MHCs) are fascinating proteins used by bacterial organisms to shuttle electrons within, between, and out of their cells. When placed in solid-state electronic junctions, MHCs support temperature-independent currents over several nanometers that are 3 orders of magnitude higher compared to other redox proteins of similar size. To gain molecular-level insight into their astonishingly high conductivities, we combine experimental photoemission spectroscopy with DFT+Σ current-voltage calculations on a representative Gold-MHC-Gold junction. We find that conduction across the dry, 3 nm long protein occurs via off-resonant coherent tunneling, mediated by a large number of protein valence-band orbitals that are strongly delocalized over heme and protein residues. This picture is profoundly different from the electron hopping mechanism induced electrochemically or photochemically under aqueous conditions. Our results imply that the current output in solid-state junctions can be even further increased in resonance, for example, by applying a gate voltage, thus allowing a quantum jump for next-generation bionanoelectronic devices.
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Affiliation(s)
- Zdenek Futera
- Faculty
of Science, University of South Bohemia, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, U.K.
| | - Ichiro Ide
- Graduate
School of Science and Engineering, Chiba
University, Chiba, Japan
| | - Ben Kayser
- Department
of Materials and Interfaces, Weizmann Institute
of Science, Rehovot, Israel
| | - Kavita Garg
- Department
of Materials and Interfaces, Weizmann Institute
of Science, Rehovot, Israel
| | - Xiuyun Jiang
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, U.K.
| | - Jessica H. van Wonderen
- School
of Chemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Julea N. Butt
- School
of Chemistry, School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, U.K.
| | - Hisao Ishii
- Graduate
School of Science and Engineering, Chiba
University, Chiba, Japan
| | - Israel Pecht
- Department
of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Mordechai Sheves
- Department
of Organic Chemistry, Weizmann Institute
of Science, Rehovot, Israel
| | - David Cahen
- Department
of Materials and Interfaces, Weizmann Institute
of Science, Rehovot, Israel
| | - Jochen Blumberger
- Department
of Physics and Astronomy, University College
London, Gower Street, London WC1E
6BT, U.K.
- (J.B.)
. Phone: ++44-(0)20-7679-4373. Fax: ++44-(0)20-7679-7145
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26
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Jiang X, van Wonderen JH, Butt JN, Edwards MJ, Clarke TA, Blumberger J. Which Multi-Heme Protein Complex Transfers Electrons More Efficiently? Comparing MtrCAB from Shewanella with OmcS from Geobacter. J Phys Chem Lett 2020; 11:9421-9425. [PMID: 33104365 DOI: 10.1021/acs.jpclett.0c02842] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Microbial nanowires are fascinating biological structures that allow bacteria to transport electrons over micrometers for reduction of extracellular substrates. It was recently established that the nanowires of both Shewanella and Geobacter are made of multi-heme proteins; but, while Shewanella employs the 20-heme protein complex MtrCAB, Geobacter uses a redox polymer made of the hexa-heme protein OmcS, begging the question as to which protein architecture is more efficient in terms of long-range electron transfer. Using a multiscale computational approach we find that OmcS supports electron flows about an order of magnitude higher than MtrCAB due to larger heme-heme electronic couplings and better insulation of hemes from the solvent. We show that heme side chains are an essential structural element in both protein complexes, accelerating rate-limiting electron tunnelling steps up to 1000-fold. Our results imply that the alternating stacked/T-shaped heme arrangement present in both protein complexes may be an evolutionarily convergent design principle permitting efficient electron transfer over very long distances.
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Affiliation(s)
- Xiuyun Jiang
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Jessica H van Wonderen
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Julea N Butt
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Marcus J Edwards
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Thomas A Clarke
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas Young Centre, University College London, London WC1E 6BT, United Kingdom
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27
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Li DB, Edwards MJ, Blake AW, Newton-Payne SE, Piper SEH, Jenner LP, Sokol KP, Reisner E, Van Wonderen JH, Clarke TA, Butt JN. His/Met heme ligation in the PioA outer membrane cytochrome enabling light-driven extracellular electron transfer by Rhodopseudomonas palustris TIE-1. NANOTECHNOLOGY 2020; 31:354002. [PMID: 32403091 DOI: 10.1088/1361-6528/ab92c7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
A growing number of bacterial species are known to move electrons across their cell envelopes. Naturally this occurs in support of energy conservation and carbon-fixation. For biotechnology it allows electron exchange between bacteria and electrodes in microbial fuel cells and during microbial electrosynthesis. In this context Rhodopseudomonas palustris TIE-1 is of much interest. These bacteria respond to light by taking electrons from their external environment, including electrodes, to drive CO2-fixation. The PioA cytochrome, that spans the bacterial outer membrane, is essential for this electron transfer and yet little is known about its structure and electron transfer properties. Here we reveal the ten c-type hemes of PioA are redox active across the window +250 to -400 mV versus Standard Hydrogen Electrode and that the hemes with most positive reduction potentials have His/Met and His/H2O ligation. These chemical and redox properties distinguish PioA from the more widely studied family of MtrA outer membrane decaheme cytochromes with ten His/His ligated hemes. We predict a structure for PioA in which the hemes form a chain spanning the longest dimension of the protein, from Heme 1 to Heme 10. Hemes 2, 3 and 7 are identified as those most likely to have His/Met and/or His/H2O ligation. Sequence analysis suggests His/Met ligation of Heme 2 and/or 7 is a defining feature of decaheme PioA homologs from over 30 different bacterial genera. His/Met ligation of Heme 3 appears to be less common and primarily associated with PioA homologs from purple non-sulphur bacteria belonging to the alphaproteobacteria class.
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Affiliation(s)
- Dao-Bo Li
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom. Present address: Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application, Guangdong Institute of Microbiology, Guangdong Academy of Sciences, Guangzhou, China and State Key Laboratory of Applied Microbiology Southern China, Guangzhou, People's Republic of China
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28
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Roy S, Xie O, Dorval Courchesne N. Challenges in engineering conductive protein fibres: Disentangling the knowledge. CAN J CHEM ENG 2020. [DOI: 10.1002/cjce.23836] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sophia Roy
- Department of Chemical Engineering McGill University Montréal Québec Canada
| | - Oliver Xie
- Department of Chemical Engineering McGill University Montréal Québec Canada
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29
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Huang J, Zarzycki J, Gunner MR, Parson WW, Kern JF, Yano J, Ducat DC, Kramer DM. Mesoscopic to Macroscopic Electron Transfer by Hopping in a Crystal Network of Cytochromes. J Am Chem Soc 2020; 142:10459-10467. [DOI: 10.1021/jacs.0c02729] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Jingcheng Huang
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - Jan Zarzycki
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - M. R. Gunner
- Department of Physics, City College of New York, New York, New York 10031, United States
| | - William W. Parson
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jan F. Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Daniel C. Ducat
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
| | - David M. Kramer
- DOE-Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824, United States
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
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30
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Kayser B, Fereiro JA, Bhattacharyya R, Cohen SR, Vilan A, Pecht I, Sheves M, Cahen D. Solid-State Electron Transport via the Protein Azurin is Temperature-Independent Down to 4 K. J Phys Chem Lett 2020; 11:144-151. [PMID: 31821001 DOI: 10.1021/acs.jpclett.9b03120] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Solid-state electronic transport (ETp) via the electron-transfer copper protein azurin (Az) was measured in Au/Az/Au junction configurations down to 4 K, the lowest temperature for solid-state protein-based junctions. Not only does lowering the temperature help when observing fine features of electronic transport, but it also limits possible electron transport mechanisms. Practically, wire-bonded devices-on-chip, carrying Az-based microscopic junctions, were measured in liquid He, minimizing temperature gradients across the samples. Much smaller junctions, in conducting-probe atomic force microscopy measurements, served, between room temperature and the protein's denaturation temperature (∼323 K), to check that conductance behavior is independent of device configuration or contact nature and thus is a property of the protein itself. Temperature-independent currents were observed from ∼320 to 4 K. The experimental results were fitted to a single-level Landauer model to extract effective energy barrier and electrode-molecule coupling strength values and to compare data sets. Our results strongly support that quantum tunneling, rather than hopping, dominates ETp via Az.
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Affiliation(s)
- Ben Kayser
- Department of Materials and Interfaces , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Jerry A Fereiro
- Department of Materials and Interfaces , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Rajarshi Bhattacharyya
- Braun Center for Submicron Research, Department of Condensed Matter Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Sidney R Cohen
- Department of Chemical Research Support , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Ayelet Vilan
- Department of Chemical and Biological Physics , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Israel Pecht
- Department of Immunology , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - Mordechai Sheves
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot 76100 , Israel
| | - David Cahen
- Department of Materials and Interfaces , Weizmann Institute of Science , Rehovot 76100 , Israel
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31
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Mishra S, Pirbadian S, Mondal AK, El-Naggar MY, Naaman R. Spin-Dependent Electron Transport through Bacterial Cell Surface Multiheme Electron Conduits. J Am Chem Soc 2019; 141:19198-19202. [DOI: 10.1021/jacs.9b09262] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Suryakant Mishra
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Sahand Pirbadian
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
| | - Amit Kumar Mondal
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Mohamed Y. El-Naggar
- Department of Physics and Astronomy, University of Southern California, Los Angeles, California 90089, United States
- Department of Chemistry, University of Southern California, Los Angeles, California 90089, United States
- Department of Biological Sciences, University of Southern California, Los Angeles, California 91030, United States
| | - Ron Naaman
- Department of Chemical and Biological Physics, Weizmann Institute of Science, Rehovot 76100, Israel
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32
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van Wonderen JH, Hall CR, Jiang X, Adamczyk K, Carof A, Heisler I, Piper SEH, Clarke TA, Watmough NJ, Sazanovich IV, Towrie M, Meech SR, Blumberger J, Butt JN. Ultrafast Light-Driven Electron Transfer in a Ru(II)tris(bipyridine)-Labeled Multiheme Cytochrome. J Am Chem Soc 2019; 141:15190-15200. [DOI: 10.1021/jacs.9b06858] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Jessica H. van Wonderen
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Christopher R. Hall
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Xiuyun Jiang
- Department of Physics and Astronomy and Thomas-Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Katrin Adamczyk
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Antoine Carof
- Department of Physics and Astronomy and Thomas-Young Centre, University College London, London WC1E 6BT, United Kingdom
| | - Ismael Heisler
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Samuel E. H. Piper
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Thomas A. Clarke
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Nicholas J. Watmough
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Igor V. Sazanovich
- Central Laser Facility, Research Complex at Harwell, Harwell Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Harwell Campus, Didcot, Oxon OX11 0QX, United Kingdom
| | - Stephen R. Meech
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas-Young Centre, University College London, London WC1E 6BT, United Kingdom
- Institute for Advanced Study, Technische Universität München, Lichtenbergstrasse 2 a, D-85748 Garching, Germany
| | - Julea N. Butt
- School of Chemistry and School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, United Kingdom
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33
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Kinetics of trifurcated electron flow in the decaheme bacterial proteins MtrC and MtrF. Proc Natl Acad Sci U S A 2019; 116:3425-3430. [PMID: 30755526 DOI: 10.1073/pnas.1818003116] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The bacterium Shewanella oneidensis has evolved a sophisticated electron transfer (ET) machinery to export electrons from the cytosol to extracellular space during extracellular respiration. At the heart of this process are decaheme proteins of the Mtr pathway, MtrC and MtrF, located at the external face of the outer bacterial membrane. Crystal structures have revealed that these proteins bind 10 c-type hemes arranged in the peculiar shape of a staggered cross that trifurcates the electron flow, presumably to reduce extracellular substrates while directing electrons to neighboring multiheme cytochromes at either side along the membrane. Especially intriguing is the design of the heme junctions trifurcating the electron flow: they are made of coplanar and T-shaped heme pair motifs with relatively large and seemingly unfavorable tunneling distances. Here, we use electronic structure calculations and molecular simulations to show that the side chains of the heme rings, in particular the cysteine linkages inserting in the space between coplanar and T-shaped heme pairs, strongly enhance electronic coupling in these two motifs. This results in an [Formula: see text]-fold speedup of ET steps at heme junctions that would otherwise be rate limiting. The predicted maximum electron flux through the solvated proteins is remarkably similar for all possible flow directions, suggesting that MtrC and MtrF shuttle electrons with similar efficiency and reversibly in directions parallel and orthogonal to the outer membrane. No major differences in the ET properties of MtrC and MtrF are found, implying that the different expression levels of the two proteins during extracellular respiration are not related to redox function.
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34
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Futera Z, Blumberger J. Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Force Field and Parametrization of Au-S Bonds. J Chem Theory Comput 2018; 15:613-624. [PMID: 30540462 DOI: 10.1021/acs.jctc.8b00992] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The interaction of amino acids with metal electrodes plays a crucial role in bioelectrochemistry and the emerging field of bionanoelectronics. Here we present benchmark calculations of the adsorption structure and energy of all natural amino acids on Au(111) in vacuum using a van-der-Waals density functional (revPBE-vdW) that showed good performance on the S22 set of weakly bound dimers (mean relative unsigned error (MRUE) wrt CCSD(T)/CBS = 13.3%) and adsorption energies of small organic molecules on Au(111) (MRUE wrt experiment = 11.2%). The vdW-DF results are then used to assess the accuracy of a popular force field for Au-amino acid interactions, GolP-CHARMM, which explicitly describes image charge interactions via rigid-rod dipoles. We find that while the force field underestimates adsorption distances, it does reproduce the binding energy rather well (MRUE wrt revPBE-vdW = 11.3%) with the MRUE decreasing in the order Cys, Met > amines > aliphatic > carboxylic > aromatic. We also present a parametrization of the bonding interaction between sulfur-containing molecules and the Au(111) surface and report force field parameters that are compatible with GolP-CHARMM. We believe the vdW-DF calculations presented herein will provide useful reference data for further force field development, and that the new Au-S bonding parameters will enable improved simulations of proteins immobilized on Au-electrodes via S-linkages.
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Affiliation(s)
- Zdenek Futera
- Department of Physics and Astronomy and Thomas-Young-Centre , University College London , Gower Street , London , WC1E 6BT , U.K
| | - Jochen Blumberger
- Department of Physics and Astronomy and Thomas-Young-Centre , University College London , Gower Street , London , WC1E 6BT , U.K.,Institute for Advanced Study , Technische Universität München , Lichtenbergstrasse 2 a , D-85748 Garching , Germany
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