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Ju H, Cheng L, Li M, Mei K, He S, Jia C, Guo X. Single-Molecule Electrical Profiling of Peptides and Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2401877. [PMID: 38639403 PMCID: PMC11267281 DOI: 10.1002/advs.202401877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 04/03/2024] [Indexed: 04/20/2024]
Abstract
In recent decades, there has been a significant increase in the application of single-molecule electrical analysis platforms in studying proteins and peptides. These advanced analysis methods have the potential for deep investigation of enzymatic working mechanisms and accurate monitoring of dynamic changes in protein configurations, which are often challenging to achieve in ensemble measurements. In this work, the prominent research progress in peptide and protein-related studies are surveyed using electronic devices with single-molecule/single-event sensitivity, including single-molecule junctions, single-molecule field-effect transistors, and nanopores. In particular, the successful commercial application of nanopores in DNA sequencing has made it one of the most promising techniques in protein sequencing at the single-molecule level. From single peptides to protein complexes, the correlation between their electrical characteristics, structures, and biological functions is gradually being established. This enables to distinguish different molecular configurations of these biomacromolecules through real-time electrical monitoring of their life activities, significantly improving the understanding of the mechanisms underlying various life processes.
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Affiliation(s)
- Hongyu Ju
- School of Pharmaceutical Science and TechnologyTianjin UniversityTianjin300072P. R. China
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Li Cheng
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Mengmeng Li
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Kunrong Mei
- School of Pharmaceutical Science and TechnologyTianjin UniversityTianjin300072P. R. China
| | - Suhang He
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Chuancheng Jia
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
| | - Xuefeng Guo
- Center of Single‐Molecule SciencesInstitute of Modern OpticsFrontiers Science Center for New Organic MatterTianjin Key Laboratory of Microscale Optical Information Science and TechnologyCollege of Electronic Information and Optical EngineeringNankai UniversityTianjin300350P. R. China
- Beijing National Laboratory for Molecular SciencesNational Biomedical Imaging CenterCollege of Chemistry and Molecular EngineeringPeking UniversityBeijing100871P. R. China
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Akhtar A, Rashid U, Seth C, Kumar S, Broekmann P, Kaliginedi V. Modulating the charge transport in metal│molecule│metal junctions via electrochemical gating. Electrochim Acta 2021. [DOI: 10.1016/j.electacta.2021.138540] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Belding L, Root SE, Li Y, Park J, Baghbanzadeh M, Rojas E, Pieters PF, Yoon HJ, Whitesides GM. Conformation, and Charge Tunneling through Molecules in SAMs. J Am Chem Soc 2021; 143:3481-3493. [DOI: 10.1021/jacs.0c12571] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Lee Belding
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Samuel E. Root
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Yuan Li
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Junwoo Park
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Mostafa Baghbanzadeh
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Edwin Rojas
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Priscilla F. Pieters
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street, Cambridge, Massachusetts 02138, United States
| | - Hyo Jae Yoon
- Department of Chemistry, Korea University, Seoul 02841, Korea
| | - George M. Whitesides
- Department of Chemistry and Chemical Biology, Harvard University 12 Oxford Street, Cambridge, Massachusetts 02138, United States
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Koronkiewicz B, Swierk J, Regan K, Mayer JM. Shallow Distance Dependence for Proton-Coupled Tyrosine Oxidation in Oligoproline Peptides. J Am Chem Soc 2020; 142:12106-12118. [PMID: 32510937 PMCID: PMC7545454 DOI: 10.1021/jacs.0c01429] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
We have explored the kinetic effect of increasing electron transfer (ET) distance in a biomimetic, proton-coupled electron-transfer (PCET) system. Biological ET often occurs simultaneously with proton transfer (PT) in order to avoid the high-energy, charged intermediates resulting from the stepwise transfer of protons and electrons. These concerted proton-electron-transfer (CPET) reactions are implicated in numerous biological ET pathways. In many cases, PT is coupled to long-range ET. While many studies have shown that the rate of ET is sensitive to the distance between the electron donor and acceptor, extensions to biological CPET reactions are sparse. The possibility of a unique ET distance dependence for CPET reactions deserves further exploration, as this could have implications for how we understand biological ET. We therefore explored the ET distance dependence for the CPET oxidation of tyrosine in a model system. We prepared a series of metallopeptides with a tyrosine separated from a Ru(bpy)32+ complex by an oligoproline bridge of increasing length. Rate constants for intramolecular tyrosine oxidation were measured using the flash-quench transient absorption technique in aqueous solutions. The rate constants for tyrosine oxidation decreased by 125-fold with three added proline residues between tyrosine and the oxidant. By comparison, related intramolecular ET rate constants in very similar constructs were reported to decrease by 4-5 orders of magnitude over the same number of prolines. The observed shallow distance dependence for tyrosine oxidation is proposed to originate in part from the requirement for stronger oxidants, leading to a smaller hole-transfer effective tunneling barrier height. The shallow distance dependence observed here and extensions to distance-dependent CPET reactions have potential implications for long-range charge transfers.
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Affiliation(s)
- Brian Koronkiewicz
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - John Swierk
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Kevin Regan
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - James M Mayer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
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Li S, Chen W, Hu X, Feng F. Self-Assembly of Albumin and [FeFe]-Hydrogenase Mimics for Photocatalytic Hydrogen Evolution. ACS APPLIED BIO MATERIALS 2020; 3:2482-2488. [DOI: 10.1021/acsabm.0c00194] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shuyi Li
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Weijian Chen
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiantao Hu
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Fude Feng
- Key Laboratory of High Performance Polymer Material and Technology of Ministry of Education, Department of Polymer Science & Engineering, School of Chemistry & Chemical Engineering, Nanjing University, Nanjing 210023, China
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Fianchini M. Synthesis meets theory: Past, present and future of rational chemistry. PHYSICAL SCIENCES REVIEWS 2017. [DOI: 10.1515/psr-2017-0134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Abstract
Chemical synthesis has its roots in the empirical approach of alchemy. Nonetheless, the birth of the scientific method, the technical and technological advances (exploiting revolutionary discoveries in physics) and the improved management and sharing of growing databases greatly contributed to the evolution of chemistry from an esoteric ground into a mature scientific discipline during these last 400 years. Furthermore, thanks to the evolution of computational resources, platforms and media in the last 40 years, theoretical chemistry has added to the puzzle the final missing tile in the process of “rationalizing” chemistry. The use of mathematical models of chemical properties, behaviors and reactivities is nowadays ubiquitous in literature. Theoretical chemistry has been successful in the difficult task of complementing and explaining synthetic results and providing rigorous insights when these are otherwise unattainable by experiment. The first part of this review walks the reader through a concise historical overview on the evolution of the “model” in chemistry. Salient milestones have been highlighted and briefly discussed. The second part focuses more on the general description of recent state-of-the-art computational techniques currently used worldwide by chemists to produce synergistic models between theory and experiment. Each section is complemented by key-examples taken from the literature that illustrate the application of the technique discussed therein.
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Soo HS, Agiral A, Bachmeier A, Frei H. Visible Light-Induced Hole Injection into Rectifying Molecular Wires Anchored on Co3O4 and SiO2 Nanoparticles. J Am Chem Soc 2012; 134:17104-16. [DOI: 10.1021/ja306162g] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Han Sen Soo
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley,
California 94720, United States
| | - Anil Agiral
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley,
California 94720, United States
| | - Andreas Bachmeier
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley,
California 94720, United States
| | - Heinz Frei
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley,
California 94720, United States
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Villani G. Theoretical Investigation of Hydrogen Atom Transfer in the Cytosine-Guanine Base Pair and Its Coupling with Electronic Rearrangement. Concerted vs Stepwise Mechanism. J Phys Chem B 2010; 114:9653-62. [DOI: 10.1021/jp102457s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Giovanni Villani
- Istituto per i Processi Chimico-Fisici, IPCF-CNR, Via G. Moruzzi, 1, I-56124 Pisa, Italy
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de la Lande A, Salahub DR. Derivation of interpretative models for long range electron transfer from constrained density functional theory. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.11.012] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Affiliation(s)
- My Hang V Huynh
- DE-1: High Explosive Science and Technology Group, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Schlag EW, Sheu SY, Yang DY, Selzle HL, Lin SH. Distal charge transport in peptides. Angew Chem Int Ed Engl 2007; 46:3196-210. [PMID: 17372995 DOI: 10.1002/anie.200601623] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Biological systems often transport charges and reactive processes over substantial distances. Traditional models of chemical kinetics generally do not describe such extreme distal processes. In this Review, an atomistic model for a distal transport of information, which was specifically developed for peptides, is considered. Chemical reactivity is taken as the result of distal effects based on two-step bifunctional kinetics involving unique, very rapid motional properties of peptides in the subpicosecond regime. The bifunctional model suggests highly efficient transport of charge and reactivity in an isolated peptide over a substantial distance; conversely, a very low efficiency in a water environment was found. The model suggests ultrafast transport of charge and reactivity over substantial molecular distances in a peptide environment. Many such domains can be active in a protein.
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Affiliation(s)
- Edward W Schlag
- Institut für Physikalische und Theoretische Chemie, Technische Universität München, Lichtenbergstrasse 4, 85748 Garching, Germany.
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Meyer TJ, Huynh MHV, Thorp HH. The Possible Role of Proton-Coupled Electron Transfer (PCET) in Water Oxidation by Photosystem II. Angew Chem Int Ed Engl 2007; 46:5284-304. [PMID: 17604381 DOI: 10.1002/anie.200600917] [Citation(s) in RCA: 410] [Impact Index Per Article: 24.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
All higher life forms use oxygen and respiration as their primary energy source. The oxygen comes from water by solar-energy conversion in photosynthetic membranes. In green plants, light absorption in photosystem II (PSII) drives electron-transfer activation of the oxygen-evolving complex (OEC). The mechanism of water oxidation by the OEC has long been a subject of great interest to biologists and chemists. With the availability of new molecular-level protein structures from X-ray crystallography and EXAFS, as well as the accumulated results from numerous experiments and theoretical studies, it is possible to suggest how water may be oxidized at the OEC. An integrated sequence of light-driven reactions that exploit coupled electron-proton transfer (EPT) could be the key to water oxidation. When these reactions are combined with long-range proton transfer (by sequential local proton transfers), it may be possible to view the OEC as an intricate structure that is "wired for protons".
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Affiliation(s)
- Thomas J Meyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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Abstract
We have probed single-molecule metal-to-ligand charge transfer (MLCT) dynamics of a ruthenium complex at room temperature. Using photon antibunching measurements under continuous wave (CW) laser excitation, nonclassical photon statistics, and excitation power dependent measurements, we were able to selectively measure the single-molecule MLCT state lifetime. This work demonstrated, as the first single-molecule photon antibunching measurement of the triplet excited state, a new application of single-molecule spectroscopy on excited-state dynamics and ground-state recovering dynamics of an important class of chemical species that have often been used and studied in energy conversion and electron transfer.
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Schlag E, Sheu SY, Yang DY, Selzle H, Lin S. Distaler Ladungstransport in Peptiden. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200601623] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Chi Q, Farver O, Ulstrup J. Long-range protein electron transfer observed at the single-molecule level: In situ mapping of redox-gated tunneling resonance. Proc Natl Acad Sci U S A 2005; 102:16203-8. [PMID: 16260751 PMCID: PMC1275599 DOI: 10.1073/pnas.0508257102] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A biomimetic long-range electron transfer (ET) system consisting of the blue copper protein azurin, a tunneling barrier bridge, and a gold single-crystal electrode was designed on the basis of molecular wiring self-assembly principles. This system is sufficiently stable and sensitive in a quasi-biological environment, suitable for detailed observations of long-range protein interfacial ET at the nanoscale and single-molecule levels. Because azurin is located at clearly identifiable fixed sites in well controlled orientation, the ET configuration parallels biological ET. The ET is nonadiabatic, and the rate constants display tunneling features with distance-decay factors of 0.83 and 0.91 A(-1) in H(2)O and D(2)O, respectively. Redox-gated tunneling resonance is observed in situ at the single-molecule level by using electrochemical scanning tunneling microscopy, exhibiting an asymmetric dependence on the redox potential. Maximum resonance appears around the equilibrium redox potential of azurin with an on/off current ratio of approximately 9. Simulation analyses, based on a two-step interfacial ET model for the scanning tunneling microscopy redox process, were performed and provide quantitative information for rational understanding of the ET mechanism.
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Affiliation(s)
- Qijin Chi
- Department of Chemistry and Nano-DTU, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark.
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Tenger K, Khoroshyy P, Leitgeb B, Rákhely G, Borovok N, Kotlyar A, Dolgikh DA, Zimányi L. Complex Kinetics of the Electron Transfer between the Photoactive Redox Label TUPS and the Heme of Cytochrome c. J Chem Inf Model 2005; 45:1520-6. [PMID: 16309248 DOI: 10.1021/ci050181u] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The photoinduced covalent redox label 8-thiouredopyrene-1,3,6-trisulfonate (TUPS) has been attached to two lysine residues (K8 and K39) at opposite sides of horse heart cytochrome c, as well as to cysteines, at the same positions, introduced by site-directed mutagenesis. Electron transfer between TUPS and the heme of cytochrome c deviates from the expected monoexponential kinetic behavior. Neither the overall rate nor the individual exponential components of electron transfer, as followed by kinetic absorption spectroscopy, correlate with the length of the covalent link connecting the dye with the protein. Molecular dynamics calculations show that TUPS can approach the protein surface and occupy several such positions. This heterogeneity may explain the multiexponential electron-transfer kinetics. The calculated optimal electron-transfer pathways do not follow the covalent link but involve through space jumps from the dye to the protein moiety, effectively decoupling the length of the covalent link and the electron-transfer rates.
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Affiliation(s)
- Katalin Tenger
- Institute of Biophysics, Biological Research Center of the Hungarian Academy of Sciences, Szeged, Hungary
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