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Chen CG, Nardi AN, Amadei A, D’Abramo M. Theoretical Modeling of Redox Potentials of Biomolecules. Molecules 2022; 27:molecules27031077. [PMID: 35164342 PMCID: PMC8838479 DOI: 10.3390/molecules27031077] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/28/2022] Open
Abstract
The estimation of the redox potentials of biologically relevant systems by means of theoretical-computational approaches still represents a challenge. In fact, the size of these systems typically does not allow a full quantum-mechanical treatment needed to describe electron loss/gain in such a complex environment, where the redox process takes place. Therefore, a number of different theoretical strategies have been developed so far to make the calculation of the redox free energy feasible with current computational resources. In this review, we provide a survey of such theoretical-computational approaches used in this context, highlighting their physical principles and discussing their advantages and limitations. Several examples of these approaches applied to the estimation of the redox potentials of both proteins and nucleic acids are described and critically discussed. Finally, general considerations on the most promising strategies are reported.
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Affiliation(s)
- Cheng Giuseppe Chen
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
| | | | - Andrea Amadei
- Department of Chemical and Technological Sciences, Tor Vergata University, 00133 Rome, Italy;
| | - Marco D’Abramo
- Department of Chemistry, Sapienza University of Rome, 00185 Rome, Italy; (C.G.C.); (A.N.N.)
- Correspondence:
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2
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Randell NM, Rendon J, Demeunynck M, Bayle P, Gambarelli S, Artero V, Mouesca J, Chavarot‐Kerlidou M. Tuning the Electron Storage Potential of a Charge‐Photoaccumulating Ru
II
Complex by a DFT‐Guided Approach. Chemistry 2019; 25:13911-13920. [DOI: 10.1002/chem.201902312] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/19/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Nicholas M. Randell
- Univ. Grenoble Alpes, CNRS, CEAIRIG, Laboratoire de Chimie et Biologie des Métaux 38000 Grenoble France
| | - Julia Rendon
- Univ. Grenoble Alpes, CNRS, CEAIRIG, Laboratoire de Chimie et Biologie des Métaux 38000 Grenoble France
- Univ. Grenoble Alpes, CEA, CNRSIRIG-DIESE-SyMMES-CAMPE 38000 Grenoble France
| | | | | | - Serge Gambarelli
- Univ. Grenoble Alpes, CEA, CNRSIRIG-DIESE-SyMMES-CAMPE 38000 Grenoble France
| | - Vincent Artero
- Univ. Grenoble Alpes, CNRS, CEAIRIG, Laboratoire de Chimie et Biologie des Métaux 38000 Grenoble France
| | - Jean‐Marie Mouesca
- Univ. Grenoble Alpes, CEA, CNRSIRIG-DIESE-SyMMES-CAMPE 38000 Grenoble France
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3
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Tran KN, Niu S, Ichiye T. Reduction potential calculations of the Fe–S clusters in
Thermus thermophilus
respiratory complex I. J Comput Chem 2019; 40:1248-1256. [DOI: 10.1002/jcc.25785] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 12/12/2018] [Accepted: 01/06/2019] [Indexed: 01/12/2023]
Affiliation(s)
- Kelly N. Tran
- Department of ChemistryGeorgetown University Washington District of Columbia, 20057
| | - Shuqiang Niu
- Department of ChemistryGeorgetown University Washington District of Columbia, 20057
| | - Toshiko Ichiye
- Department of ChemistryGeorgetown University Washington District of Columbia, 20057
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4
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Volbeda A, Mouesca JM, Darnault C, Roessler MM, Parkin A, Armstrong FA, Fontecilla-Camps JC. X-ray structural, functional and computational studies of the O 2-sensitive E. coli hydrogenase-1 C19G variant reveal an unusual [4Fe-4S] cluster. Chem Commun (Camb) 2018; 54:7175-7178. [PMID: 29888350 DOI: 10.1039/c8cc02896f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The crystal structure of the Escherichia coli O2-sensitive C19G [NiFe]-hydrogenase-1 variant shows that the mutation results in a novel FeS cluster, proximal to the Ni-Fe active site. While the proximal cluster of the native O2-tolerant enzyme can transfer two electrons to that site, EPR spectroscopy shows that the modified cluster can transfer only one electron, this shortfall coinciding with O2 sensitivity. Computational studies on electron transfer help to explain how the structural and redox properties of the novel FeS cluster modulate the observed phenotype.
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Affiliation(s)
- A Volbeda
- Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France.
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5
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Tan ML, Perrin BS, Niu S, Huang Q, Ichiye T. Protein dynamics and the all-ferrous [Fe4 S4 ] cluster in the nitrogenase iron protein. Protein Sci 2015; 25:12-8. [PMID: 26271353 PMCID: PMC4815322 DOI: 10.1002/pro.2772] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 08/12/2015] [Accepted: 08/12/2015] [Indexed: 01/09/2023]
Abstract
In nitrogen fixation by Azotobacter vinelandii nitrogenase, the iron protein (FeP) binds to and subsequently transfers electrons to the molybdenum–FeP, which contains the nitrogen fixation site, along with hydrolysis of two ATPs. However, the nature of the reduced state cluster is not completely clear. While reduced FeP is generally thought to contain an [Fe4S4]1+ cluster, evidence also exists for an all‐ferrous [Fe4S4]0 cluster. Since the former indicates a single electron is transferred per two ATPs hydrolyzed while the latter indicates two electrons could be transferred per two ATPs hydrolyzed, an all‐ferrous [Fe4S4]0 cluster in FeP is potenially two times more efficient. However, the 1+/0 reduction potential has been measured in the protein at both 460 and 790 mV, causing the biological significance to be questioned. Here, “density functional theory plus Poisson Boltzmann” calculations show that cluster movement relative to the protein surface observed in the crystal structures could account for both measured values. In addition, elastic network mode analysis indicates that such movement occurs in low frequency vibrations of the protein, implying protein dynamics might lead to variations in reduction potential. Furthermore, the different reductants used in the conflicting measurements of the reduction potential could be differentially affecting the protein dynamics. Moreover, even if the all‐ferrous cluster is not the biologically relevant cluster, mutagenesis to stabilize the conformation with the more exposed cluster may be useful for bioengineering more efficient enzymes.
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Affiliation(s)
- Ming-Liang Tan
- Department of Chemistry, Georgetown University, Washington, District of Columbia, 20057
| | - B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
| | - Shuqiang Niu
- Department of Chemistry, Georgetown University, Washington, District of Columbia, 20057
| | - Qi Huang
- Department of Chemistry, Georgetown University, Washington, District of Columbia, 20057
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, District of Columbia, 20057.,Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
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6
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Miller BT, Singh RP, Schalk V, Pevzner Y, Sun J, Miller CS, Boresch S, Ichiye T, Brooks BR, Woodcock HL. Web-based computational chemistry education with CHARMMing I: Lessons and tutorial. PLoS Comput Biol 2014; 10:e1003719. [PMID: 25057988 PMCID: PMC4109840 DOI: 10.1371/journal.pcbi.1003719] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
This article describes the development, implementation, and use of web-based “lessons” to introduce students and other newcomers to computer simulations of biological macromolecules. These lessons, i.e., interactive step-by-step instructions for performing common molecular simulation tasks, are integrated into the collaboratively developed CHARMM INterface and Graphics (CHARMMing) web user interface (http://www.charmming.org). Several lessons have already been developed with new ones easily added via a provided Python script. In addition to CHARMMing's new lessons functionality, web-based graphical capabilities have been overhauled and are fully compatible with modern mobile web browsers (e.g., phones and tablets), allowing easy integration of these advanced simulation techniques into coursework. Finally, one of the primary objections to web-based systems like CHARMMing has been that “point and click” simulation set-up does little to teach the user about the underlying physics, biology, and computational methods being applied. In response to this criticism, we have developed a freely available tutorial to bridge the gap between graphical simulation setup and the technical knowledge necessary to perform simulations without user interface assistance.
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Affiliation(s)
- Benjamin T. Miller
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
- * E-mail: (BTM); (HLW)
| | - Rishi P. Singh
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Vinushka Schalk
- Department of Natural Sciences, New College of Florida, Sarasota, Florida, United States of America
| | - Yuri Pevzner
- Department of Chemistry, University of South Florida, Tampa, Florida, United States of America
| | - Jingjun Sun
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - Carrie S. Miller
- Department of Chemistry, Georgetown University, Washington, D.C., United States of America
| | - Stefan Boresch
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, D.C., United States of America
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, Bethesda, Maryland, United States of America
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida, United States of America
- * E-mail: (BTM); (HLW)
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Perrin BS, Miller BT, Schalk V, Woodcock HL, Brooks BR, Ichiye T. Web-based computational chemistry education with CHARMMing III: Reduction potentials of electron transfer proteins. PLoS Comput Biol 2014; 10:e1003739. [PMID: 25058418 PMCID: PMC4110074 DOI: 10.1371/journal.pcbi.1003739] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A module for fast determination of reduction potentials, E°, of redox-active proteins has been implemented in the CHARMM INterface and Graphics (CHARMMing) web portal (www.charmming.org). The free energy of reduction, which is proportional to E°, is composed of an intrinsic contribution due to the redox site and an environmental contribution due to the protein and solvent. Here, the intrinsic contribution is selected from a library of pre-calculated density functional theory values for each type of redox site and redox couple, while the environmental contribution is calculated from a crystal structure of the protein using Poisson-Boltzmann continuum electrostatics. An accompanying lesson demonstrates a calculation of E°. In this lesson, an ionizable residue in a [4Fe-4S]-protein that causes a pH-dependent E° is identified, and the E° of a mutant that would test the identification is predicted. This demonstration is valuable to both computational chemistry students and researchers interested in predicting sequence determinants of E° for mutagenesis.
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Affiliation(s)
- B. Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Benjamin T. Miller
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Vinushka Schalk
- Department of Natural Sciences, New College of Florida, Sarasota, Florida, United States of America
| | - H. Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida, United States of America
| | - Bernard R. Brooks
- Laboratory of Computational Biology, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Washington, D.C., United States of America
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8
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Structures of benzylsuccinate synthase elucidate roles of accessory subunits in glycyl radical enzyme activation and activity. Proc Natl Acad Sci U S A 2014; 111:10161-6. [PMID: 24982148 DOI: 10.1073/pnas.1405983111] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Anaerobic degradation of the environmental pollutant toluene is initiated by the glycyl radical enzyme benzylsuccinate synthase (BSS), which catalyzes the radical addition of toluene to fumarate, forming benzylsuccinate. We have determined crystal structures of the catalytic α-subunit of BSS with its accessory subunits β and γ, which both bind a [4Fe-4S] cluster and are essential for BSS activity in vivo. We find that BSSα has the common glycyl radical enzyme fold, a 10-stranded β/α-barrel that surrounds the glycyl radical cofactor and active site. Both accessory subunits β and γ display folds related to high potential iron-sulfur proteins but differ substantially from each other in how they interact with the α-subunit. BSSγ binds distally to the active site, burying a hydrophobic region of BSSα, whereas BSSβ binds to a hydrophilic surface of BSSα that is proximal to the active site. To further investigate the function of BSSβ, we determined the structure of a BSSαγ complex. Remarkably, we find that the barrel partially opens, allowing the C-terminal region of BSSα that houses the glycyl radical to shift within the barrel toward an exit pathway. The structural changes that we observe in the BSSαγ complex center around the crucial glycyl radical domain, thus suggesting a role for BSSβ in modulating the conformational dynamics required for enzyme activity. Accompanying proteolysis experiments support these structural observations.
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9
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Wei C, Lazim R, Zhang D. Importance of polarization effect in the study of metalloproteins: application of polarized protein specific charge scheme in predicting the reduction potential of azurin. Proteins 2014; 82:2209-19. [PMID: 24753270 DOI: 10.1002/prot.24584] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/07/2014] [Accepted: 04/12/2014] [Indexed: 11/08/2022]
Abstract
Molecular dynamics (MD) simulation is commonly used in the study of protein dynamics, and in recent years, the extension of MD simulation to the study of metalloproteins is gaining much interest. Choice of force field is crucial in MD studies, and the inclusion of metal centers complicates the process of accurately describing the electrostatic environment that surrounds the redox centre. Herein, we would like to explore the importance of including electrostatic contribution from both protein and solvent in the study of metalloproteins. MD simulations with the implementation of thermodynamic integration will be conducted to model the reduction process of azurin from Pseudomonas aeruginosa. Three charge schemes will be used to derive the partial charges of azurin. These charge schemes differ in terms of the amount of immediate environment, respective to copper, considered during charge fitting, which ranges from the inclusion of copper and residues in the first coordination sphere during density functional theory charge fitting to the comprehensive inclusion of protein and solvent effect surrounding the metal centre using polarized protein-specific charge scheme. From the simulations conducted, the relative reduction potential of the mutated azurins respective to that of wild-type azurin (ΔEcal) were calculated and compared with experimental values. The ΔEcal approached experimental value with increasing consideration of environmental effect hence substantiating the importance of polarization effect in the study of metalloproteins. This study also attests the practicality of polarized protein-specific charge as a computational tool capable of incorporating both protein environment and solvent effect into MD simulations.
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Affiliation(s)
- Caiyi Wei
- Division of Chemistry and Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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10
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Perrin BS, Ichiye T. Identifying sequence determinants of reduction potentials of metalloproteins. J Biol Inorg Chem 2013; 18:599-608. [PMID: 23690205 PMCID: PMC3723707 DOI: 10.1007/s00775-013-1004-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Accepted: 05/01/2013] [Indexed: 10/26/2022]
Abstract
The reduction potential of an electron transfer protein is one of its most important functional characteristics. Although the type of redox site and the protein fold are the major determinants of the reduction potential of a redox-active protein, its amino acid sequence may tune the reduction potential as well. Thus, homologous proteins can often be divided into different classes, with each class characterized by a biological function and a reduction potential. Site-specific mutagenesis of the sequence determinants of the differences in the reduction potential between classes should change the reduction potential of a protein in one class to that of the other class. Here, a procedure is presented that combines energetic and bioinformatic analysis of homologous proteins to identify sequence determinants that are also good candidates for site-specific mutations, using the [4Fe-4S] ferredoxins and the [4Fe-4S] high-potential iron-sulfur proteins as examples. This procedure is designed to guide site-specific mutations or more computationally expensive studies, such as molecular dynamics simulations. To make the procedure more accessible to the general scientific community, it is being implemented into CHARMMing, a Web-based portal, with a library of density functional theory results for the redox site that are used in the setting up of Poisson-Boltzmann continuum electrostatics calculations for the protein energetics.
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Affiliation(s)
- Bradley Scott Perrin
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
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11
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Bergeler M, Stiebritz MT, Reiher M. Structure-Property Relationships of Fe4S4Clusters. Chempluschem 2013; 78:1082-1098. [DOI: 10.1002/cplu.201300186] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Indexed: 11/08/2022]
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12
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Perrin BS, Ichiye T. Identifying residues that cause pH-dependent reduction potentials. Biochemistry 2013; 52:3022-4. [PMID: 23607577 DOI: 10.1021/bi4002858] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The pH dependence of the reduction potential E° for a metalloprotein indicates that the protonation state of at least one residue near the redox site changes and may be important for its activity. The responsible residue is usually identified by site-specific mutagenesis, which may be time-consuming. Here, the titration of E° for Chromatium vinosum high-potential iron-sulfur protein is predicted to be in good agreement with experiment using density functional theory and Poisson-Boltzmann calculations if only the sole histidine undergoes changes in protonation. The implementation of this approach into CHARMMing, a user-friendly web-based portal, allows users to identify residues in other proteins causing similar pH dependence.
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Affiliation(s)
- B Scott Perrin
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
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13
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Perrin BS, Niu S, Ichiye T. Calculating standard reduction potentials of [4Fe-4S] proteins. J Comput Chem 2013; 34:576-82. [PMID: 23115132 PMCID: PMC3570669 DOI: 10.1002/jcc.23169] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Revised: 09/20/2012] [Accepted: 09/30/2012] [Indexed: 11/08/2022]
Abstract
The oxidation-reduction potentials of electron transfer proteins determine the driving forces for their electron transfer reactions. Although the type of redox site determines the intrinsic energy required to add or remove an electron, the electrostatic interaction energy between the redox site and its surrounding environment can greatly shift the redox potentials. Here, a method for calculating the reduction potential versus the standard hydrogen electrode, E°, of a metalloprotein using a combination of density functional theory and continuum electrostatics is presented. This work focuses on the methodology for the continuum electrostatics calculations, including various factors that may affect the accuracy. The calculations are demonstrated using crystal structures of six homologous HiPIPs, which give E° that are in excellent agreement with experimental results.
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Affiliation(s)
- Bradley Scott Perrin
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
| | - Shuqiang Niu
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
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Perrin BS, Ichiye T. Characterizing the effects of the protein environment on the reduction potentials of metalloproteins. J Biol Inorg Chem 2013; 18:103-10. [PMID: 23229112 PMCID: PMC3567609 DOI: 10.1007/s00775-012-0955-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/18/2012] [Indexed: 11/26/2022]
Abstract
The reduction potentials of electron transfer proteins are critically determined by the degree of burial of the redox site within the protein and the degree of permanent polarization of the polypeptide around the redox site. Although continuum electrostatics calculations of protein structures can predict the net effect of these factors, quantifying each individual contribution is a difficult task. Here, the burial of the redox site is characterized by a dielectric radius R(p) (a Born-type radius for the protein), the polarization of the polypeptide is characterized by an electret potential ϕ(p) (the average electrostatic potential at the metal atoms), and an electret-dielectric spheres (EDS) model of the entire protein is then defined in terms of R(p) and ϕ(p). The EDS model shows that for a protein with a redox site of charge Q, the dielectric response free energy is a function of Q(2), while the electret energy is a function of Q. In addition, R(p) and ϕ(p) are shown to be characteristics of the fold of a protein and are predictive of the most likely redox couple for redox sites that undergo different redox couples.
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Affiliation(s)
- Bradley Scott Perrin
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
| | - Toshiko Ichiye
- Department of Chemistry, Georgetown University, Box 571227, Washington, DC 20057-1227
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15
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Luo Y, Niu S, Ichiye T. Understanding rubredoxin redox sites by density functional theory studies of analogues. J Phys Chem A 2012; 116:8918-24. [PMID: 22881577 DOI: 10.1021/jp3057509] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Determining the redox energetics of redox site analogues of metalloproteins is essential in unraveling the various contributions to electron transfer properties of these proteins. Since studies of the [4Fe-4S] analogues show that the energies are dependent on the ligand dihedral angles, broken symmetry density functional theory (BS-DFT) with the B3LYP functional and double-ζ basis sets calculations of optimized geometries and electron detachment energies of [1Fe] rubredoxin analogues are compared to crystal structures and gas-phase photoelectron spectroscopy data, respectively, for [Fe(SCH(3))(4)](0/1-/2-), [Fe(S(2)-o-xyl)(2)](0/1-/2-), and Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) in different conformations. In particular, the study of Na(+)[Fe(S(2)-o-xyl)(2)](1-/2-) is the only direct comparison of calculated and experimental gas phase detachment energies for the 1-/2- couple found in the rubredoxins. These results show that variations in the inner sphere energetics by up to ∼0.4 eV can be caused by differences in the ligand dihedral angles in either or both redox states. Moreover, these results indicate that the protein stabilizes the conformation that favors reduction. In addition, the free energies and reorganization energies of oxidation and reduction as well as electrostatic potential charges are calculated, which can be used as estimates in continuum electrostatic calculations of electron transfer properties of [1Fe] proteins.
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Affiliation(s)
- Yan Luo
- Department of Chemistry, Georgetown University, Washington, DC 20057, USA
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16
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Valetti F, Fantuzzi A, Sadeghi SJ, Gilardi G. Iron-based redox centres of reductase and oxygenase components of phenol hydroxylase from A. radioresistens: a redox chain working at highly positive redox potentials. Metallomics 2011; 4:72-7. [PMID: 21984271 DOI: 10.1039/c1mt00136a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This is the first report of the direct electrochemistry of the reductase (PHR) and oxygenase (PHO) components of phenol hydroxylase from Acinetobacter radioresistens S13 studied by cyclic and differential pulse voltammetry. The PHR contains one 2Fe2S cluster and one FAD that mediate the transfer of electrons from NAD(P)H to the non-heme diiron cluster of PHO. Cyclic and differential pulse voltammetry (CV and DPV) on glassy carbon showed two redox pairs with midpoint potentials at +131.5 ± 13 mV and -234 ± 3 mV versus normal hydrogen electrode (NHE). The first redox couple is attributed to the FeS centre, while the second one corresponds to free FAD released by the protein. DPV scans on native and guanidinium chloride treated PHR highlighted the presence of a split signal (ΔE ≈ 100 mV) attributed to heterogeneous properties of the 2Fe2S cluster interacting with the electrode, possibly due to the presence of two protein conformers and consistently with the large peak-to-peak separation and the peak broadening observed in CV. DPV experiments on gold electrodes performed on PHO confirm a consistently higher reduction potential at +396 mV vs. NHE. The positive redox potentials measured by direct electrochemistry for the FeS cluster in PHR and for the non-heme diiron cluster of PHO show that the entire phenol hydroxylase system works at higher potentials than those reported for structurally similar enzymes, for example methane monooxygenases.
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Affiliation(s)
- Francesca Valetti
- Department of Human and Animal Biology, University of Torino, via Accademia Albertina 13, 10123, Torino, Italy
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17
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Niu S, Ichiye T. Density functional theory calculations of redox properties of iron–sulphur protein analogues. MOLECULAR SIMULATION 2011. [DOI: 10.1080/08927022.2011.582111] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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