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Liang J, Xiao K, Wang X, Hou T, Zeng C, Gao X, Wang B, Zhong C. Revisiting Solar Energy Flow in Nanomaterial-Microorganism Hybrid Systems. Chem Rev 2024. [PMID: 38900019 DOI: 10.1021/acs.chemrev.3c00831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
Nanomaterial-microorganism hybrid systems (NMHSs), integrating semiconductor nanomaterials with microorganisms, present a promising platform for broadband solar energy harvesting, high-efficiency carbon reduction, and sustainable chemical production. While studies underscore its potential in diverse solar-to-chemical energy conversions, prevailing NMHSs grapple with suboptimal energy conversion efficiency. Such limitations stem predominantly from an insufficient systematic exploration of the mechanisms dictating solar energy flow. This review provides a systematic overview of the notable advancements in this nascent field, with a particular focus on the discussion of three pivotal steps of energy flow: solar energy capture, cross-membrane energy transport, and energy conversion into chemicals. While key challenges faced in each stage are independently identified and discussed, viable solutions are correspondingly postulated. In view of the interplay of the three steps in affecting the overall efficiency of solar-to-chemical energy conversion, subsequent discussions thus take an integrative and systematic viewpoint to comprehend, analyze and improve the solar energy flow in the current NMHSs of different configurations, and highlighting the contemporary techniques that can be employed to investigate various aspects of energy flow within NMHSs. Finally, a concluding section summarizes opportunities for future research, providing a roadmap for the continued development and optimization of NMHSs.
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Affiliation(s)
- Jun Liang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Kemeng Xiao
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xinyu Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Tianfeng Hou
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Cuiping Zeng
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Xiang Gao
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Bo Wang
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Chao Zhong
- Key Laboratory of Quantitative Synthetic Biology, Center for Materials Synthetic Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
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2
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Yuan F, Su B, Yu Y, Wang J. Study and design of amino acid-based radical enzymes using unnatural amino acids. RSC Chem Biol 2023; 4:431-446. [PMID: 37292061 PMCID: PMC10246556 DOI: 10.1039/d2cb00250g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 05/17/2023] [Indexed: 06/10/2023] Open
Abstract
Radical enzymes harness the power of reactive radical species by placing them in a protein scaffold, and they are capable of catalysing many important reactions. New native radical enzymes, especially those with amino acid-based radicals, in the category of non-heme iron enzymes (including ribonucleotide reductases), heme enzymes, copper enzymes, and FAD-radical enzymes have been discovered and characterized. We discussed recent research efforts to discover new native amino acid-based radical enzymes, and to study the roles of radicals in processes such as enzyme catalysis and electron transfer. Furthermore, design of radical enzymes in a small and simple scaffold not only allows us to study the radical in a well-controlled system and test our understanding of the native enzymes, but also allows us to create powerful enzymes. In the study and design of amino acid-based radical enzymes, the use of unnatural amino acids allows precise control of pKa values and reduction potentials of the residue, as well as probing the location of the radical through spectroscopic methods, making it a powerful research tool. Our understanding of amino acid-based radical enzymes will allow us to tailor them to create powerful catalysts and better therapeutics.
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Affiliation(s)
- Feiyan Yuan
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Binbin Su
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Yang Yu
- Institute of Biochemical Engineering, Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 102488 China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences Beijing 100101 China
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3
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Maqboul I. Profiling charge transport: A new computational approach. Int J Biol Macromol 2023; 237:124065. [PMID: 36948333 DOI: 10.1016/j.ijbiomac.2023.124065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Revised: 03/12/2023] [Accepted: 03/13/2023] [Indexed: 03/24/2023]
Abstract
To maintain life, charge transfer processes must be efficient to allow electrons to migrate across distances as large as 30-50 Å within a timescale from picoseconds to milliseconds, and the free-energy cost should not exceed one electron volt. By employing local ionization and local affinity energies, we calculated the pathway for electron and electron-hole transport, respectively. The pathway is then used to calculate both the driving force and the activation energy. The electronic coupling is calculated using configuration interaction procedure. When the charge acceptor is not known, as in oxidative stress, the charge transport terminals are found using Monte-Carlo simulation. These parameters were used to calculate the rate described by Marcus theory. Our approach has been elaborately explained using the famous androstane example and then applied to two proteins: electron transport in azurin protein and hole-hopping migration route from the heme center of cytochrome c peroxidase to its surface. This model gives an effective method to calculate the charge transport pathway and the free-energy profile within 0.1 eV from the experimental measurements and electronic coupling within 3 meV.
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Affiliation(s)
- Ibrahim Maqboul
- Computer Chemistry Center (CCC), Department of Chemistry and Pharmacy, Faculty of Sciences, Friedrich-Alexander-University, Erlangen, Germany; Computer Chemistry Center (CCC), Department of Chemistry and Pharmacy, Faculty of Sciences, Friedrich-Alexander-University, Nägelsbachstraße 25, 91052 Erlangen, Germany..
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Ledray AP, Dwaraknath S, Chakarawet K, Sponholtz MR, Merchen C, Van Stappen C, Rao G, Britt RD, Lu Y. Tryptophan Can Promote Oxygen Reduction to Water in a Biosynthetic Model of Heme Copper Oxidases. Biochemistry 2023; 62:388-395. [PMID: 36215733 DOI: 10.1021/acs.biochem.2c00300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Heme-copper oxidases (HCOs) utilize tyrosine (Tyr) to donate one of the four electrons required for the reduction of O2 to water in biological respiration, while tryptophan (Trp) is speculated to fulfill the same role in cyt bd oxidases. We previously engineered myoglobin into a biosynthetic model of HCOs and demonstrated the critical role that Tyr serves in the oxygen reduction reaction (ORR). To address the roles of Tyr and Trp in these oxidases, we herein report the preparation of the same biosynthetic model with the Tyr replaced by Trp and further demonstrate that Trp can also promote the ORR, albeit with lower activity. An X-ray crystal structure of the Trp variant shows a hydrogen-bonding network involving two water molecules that are organized by Trp, similar to that in the Tyr variant, which is absent in the crystal structure with the native Phe residue. Additional electron paramagnetic resonance measurements are consistent with the formation of a Trp radical species upon reacting with H2O2. We attribute the lower activity of the Trp variant to Trp's higher reduction potential relative to Tyr. Together, these findings demonstrate, for the first time, that Trp can indeed promote the ORR and provides a structural basis for the observation of varying activities. The results support a redox role for the conserved Trp in bd oxidase while suggesting that HCOs use Tyr instead of Trp to achieve higher reactivity.
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Affiliation(s)
- Aaron P Ledray
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Sudharsan Dwaraknath
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Khetpakorn Chakarawet
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Madeline R Sponholtz
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Claire Merchen
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Casey Van Stappen
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Guodong Rao
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - R David Britt
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - Yi Lu
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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5
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Aboelnga MM. Exploring the structure function relationship of heme peroxidases: Molecular dynamics study on cytochrome c peroxidase variants. Comput Biol Med 2022; 146:105544. [DOI: 10.1016/j.compbiomed.2022.105544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/16/2022] [Accepted: 04/17/2022] [Indexed: 11/03/2022]
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Aboelnga MM. Mechanistic insights into the chemistry of compound I formation in heme peroxidases: quantum chemical investigations of cytochrome c peroxidase. RSC Adv 2022; 12:15543-15554. [PMID: 35685178 PMCID: PMC9125774 DOI: 10.1039/d2ra01073a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/17/2022] [Indexed: 11/21/2022] Open
Abstract
Peroxidases are heme containing enzymes that catalyze peroxide-dependant oxidation of a variety of substrates through forming key ferryl intermediates, compounds I and II. Cytochrome c peroxidase (Ccp1) has served for decades as a chemical model toward understanding the chemical biology of this heme family of enzymes. It is known to feature a distinctive electronic behaviour for its compound I despite significant structural similarity to other peroxidases. A water-assisted mechanism has been proposed over a dry one for the formation of compound I in similar peroxidases. To better identify the viability of these mechanisms, we employed quantum chemistry calculations for the heme pocket of Ccp1 in three different spin states. We provided comparative energetic and structural results for the six possible pathways that suggest the preference of the dry mechanism energetically and structurally. The doublet state is found to be the most preferable spin state for the mechanism to proceed and for the formation of the Cpd I ferryl-intermediate irrespective of the considered dielectric constant used to represent the solvent environment. The nature of the spin state has negligible effects on the calculated structures but great impact on the energetics. Our analysis was also expanded to explain the major contribution of key residues to the peroxidase activity of Ccp1 through exploring the mechanism at various in silico generated Ccp1 variants. Overall, we provide valuable findings toward solving the current ambiguity of the exact mechanism in Ccp1, which could be applied to peroxidases with similar heme pockets. Discerning the feasibility of a no-water peroxidase mechanism in the doublet spin state irrespective of the environment surrounding the heme pocket.![]()
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Affiliation(s)
- Mohamed M Aboelnga
- Chemistry Department, Faculty of Science, Damietta University New Damietta 34517 Egypt
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7
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Ru X, Crane BR, Zhang P, Beratan DN. Why Do Most Aromatics Fail to Support Hole Hopping in the Cytochrome c Peroxidase-Cytochrome c Complex? J Phys Chem B 2021; 125:7763-7773. [PMID: 34235935 DOI: 10.1021/acs.jpcb.1c05064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron transport through aromatic species (especially tryptophan and tyrosine) plays a central role in water splitting, redox signaling, oxidative damage protection, and bioenergetics. The cytochrome c peroxidase (CcP)-cytochrome c (Cc) complex (CcP:Cc) is used widely to study interprotein electron transfer (ET) mechanisms. Tryptophan 191 (Trp191) of CcP supports hole hopping charge recombination in the CcP:Cc complex. Experimental studies find that when Trp191 is substituted by tyrosine, phenylalanine, or redox-active aniline derivatives bound in the W191G cavity, enzymatic activity and charge recombination rates both decrease. Theoretical analysis of these CcP:Cc complexes finds that the ET kinetics depend strongly on the chemistry of the modified Trp site. The computed electronic couplings in the W191F and W191G species are orders of magnitude smaller than in the native protein, due largely to the absence of a hopping intermediate and the large tunneling distance. Small molecules bound in the W191G cavity are weakly coupled electronically to the Cc heme, and the structural disorder of the guest molecule in the binding pocket may contribute further to the lack of enzymatic activity. The couplings in W191Y are not substantially weakened compared to the native species, but the redox potential difference for tyrosine vs tryptophan oxidation accounts for the slower rate in the Tyr mutant. Thus, theoretical analysis explains why only the native Trp supports rapid hole hopping in the CcP:Cc complex. Favorable free energies and electronic couplings are essential for establishing an efficient hole hopping relay in this protein-protein complex.
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Affiliation(s)
- Xuyan Ru
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Peng Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - David N Beratan
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States.,Department of Biochemistry, Duke University, Durham, North Carolina 27710, United States.,Department of Physics, Duke University, Durham, North Carolina 27708, United States
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Yee EF, Dzikovski B, Crane BR. Tuning Radical Relay Residues by Proton Management Rescues Protein Electron Hopping. J Am Chem Soc 2019; 141:17571-17587. [PMID: 31603693 DOI: 10.1021/jacs.9b05715] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Transient tyrosine and tryptophan radicals play key roles in the electron transfer (ET) reactions of photosystem (PS) II, ribonucleotide reductase (RNR), photolyase, and many other proteins. However, Tyr and Trp are not functionally interchangeable, and the factors controlling their reactivity are often unclear. Cytochrome c peroxidase (CcP) employs a Trp191•+ radical to oxidize reduced cytochrome c (Cc). Although a Tyr191 replacement also forms a stable radical, it does not support rapid ET from Cc. Here we probe the redox properties of CcP Y191 by non-natural amino acid substitution, altering the ET driving force and manipulating the protic environment of Y191. Higher potential fluorotyrosine residues increase ET rates marginally, but only addition of a hydrogen bond donor to Tyr191• (via Leu232His or Glu) substantially alters activity by increasing the ET rate by nearly 30-fold. ESR and ESEEM spectroscopies, crystallography, and pH-dependent ET kinetics provide strong evidence for hydrogen bond formation to Y191• by His232/Glu232. Rate measurements and rapid freeze quench ESR spectroscopy further reveal differences in radical propagation and Cc oxidation that support an increased Y191• formal potential of ∼200 mV in the presence of E232. Hence, Y191 inactivity results from a potential drop owing to Y191•+ deprotonation. Incorporation of a well-positioned base to accept and donate back a hydrogen bond upshifts the Tyr• potential into a range where it can effectively oxidize Cc. These findings have implications for the YZ/YD radicals of PS II, hole-hopping in RNR and cryptochrome, and engineering proteins for long-range ET reactions.
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Affiliation(s)
- Estella F Yee
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
| | - Boris Dzikovski
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States.,National Biomedical Center for Advanced ESR Technologies (ACERT) , Cornell University , Ithaca , New York 14850 , United States
| | - Brian R Crane
- Department of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States
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Abstract
A recently proposed oxidative damage protection mechanism in proteins relies on hole hopping escape routes formed by redox-active amino acids. We present a computational tool to identify the dominant charge hopping pathways through these residues based on the mean residence times of the transferring charge along these hopping pathways. The residence times are estimated by combining a kinetic model with well-known rate expressions for the charge-transfer steps in the pathways. We identify the most rapid hole hopping escape routes in cytochrome P450 monooxygenase, cytochrome c peroxidase, and benzylsuccinate synthase (BSS). This theoretical analysis supports the existence of hole hopping chains as a mechanism capable of providing hole escape from protein catalytic sites on biologically relevant timescales. Furthermore, we find that pathways involving the [4Fe4S] cluster as the terminal hole acceptor in BSS are accessible on the millisecond timescale, suggesting a potential protective role of redox-active cofactors for preventing protein oxidative damage.
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Bostick CD, Mukhopadhyay S, Pecht I, Sheves M, Cahen D, Lederman D. Protein bioelectronics: a review of what we do and do not know. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2018; 81:026601. [PMID: 29303117 DOI: 10.1088/1361-6633/aa85f2] [Citation(s) in RCA: 136] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We review the status of protein-based molecular electronics. First, we define and discuss fundamental concepts of electron transfer and transport in and across proteins and proposed mechanisms for these processes. We then describe the immobilization of proteins to solid-state surfaces in both nanoscale and macroscopic approaches, and highlight how different methodologies can alter protein electronic properties. Because immobilizing proteins while retaining biological activity is crucial to the successful development of bioelectronic devices, we discuss this process at length. We briefly discuss computational predictions and their connection to experimental results. We then summarize how the biological activity of immobilized proteins is beneficial for bioelectronic devices, and how conductance measurements can shed light on protein properties. Finally, we consider how the research to date could influence the development of future bioelectronic devices.
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Affiliation(s)
- Christopher D Bostick
- Department of Pharmaceutical Sciences, West Virginia University, Morgantown, WV 26506, United States of America. Institute for Genomic Medicine, Columbia University Medical Center, New York, NY 10032, United States of America
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11
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Genome scale identification, structural analysis, and classification of periplasmic binding proteins from Mycobacterium tuberculosis. Curr Genet 2016; 63:553-576. [DOI: 10.1007/s00294-016-0664-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 11/04/2016] [Accepted: 11/05/2016] [Indexed: 01/26/2023]
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