1
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Dolińska MM, Kirwan AJ, Megarity CF. Retuning the potential of the electrochemical leaf. Faraday Discuss 2024; 252:188-207. [PMID: 38848142 DOI: 10.1039/d4fd00020j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2024]
Abstract
The electrochemical leaf enables the electrification and control of multi-enzyme cascades by exploiting two discoveries: (i) the ability to electrify the photosynthetic enzyme ferredoxin NADP+ reductase (FNR), driving it to catalyse the interconversion of NADP+/NADPH whilst it is entrapped in a highly porous, metal oxide electrode, and (ii) the evidence that additional enzymes can be co-entrapped in the electrode pores where, through one NADP(H)-dependent enzyme, extended cascades can be driven by electrical connection to FNR, via NADP(H) recycling. By changing a critical active-site tyrosine to serine, FNR's exclusivity for NADP(H) is swapped for unphosphorylated NAD(H). Here we present an electrochemical study of this variant FNR, and show that in addition to the intended inversion of cofactor preference, this change to the active site has altered FNR's tuning of the flavin reduction potential, making it less reductive. Exploiting the ability to monitor the variant's activity with NADP(H) as a function of potential has revealed a trapped intermediate state, relieved only by applying a negative overpotential, which allows catalysis to proceed. Inhibition by NADP+ (very tightly bound) with respect to NAD(H) turnover was also revealed and interestingly, this inhibition changes depending on the applied potential. These findings are of critical importance for future exploitation of the electrochemical leaf.
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Affiliation(s)
- Marta M Dolińska
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Adam J Kirwan
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
| | - Clare F Megarity
- School of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK.
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2
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Silvestri G, Arrigoni F, Persico F, Bertini L, Zampella G, De Gioia L, Vertemara J. Assessing the Performance of Non-Equilibrium Thermodynamic Integration in Flavodoxin Redox Potential Estimation. Molecules 2023; 28:6016. [PMID: 37630271 PMCID: PMC10459689 DOI: 10.3390/molecules28166016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/07/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023] Open
Abstract
Flavodoxins are enzymes that contain the redox-active flavin mononucleotide (FMN) cofactor and play a crucial role in numerous biological processes, including energy conversion and electron transfer. Since the redox characteristics of flavodoxins are significantly impacted by the molecular environment of the FMN cofactor, the evaluation of the interplay between the redox properties of the flavin cofactor and its molecular surroundings in flavoproteins is a critical area of investigation for both fundamental research and technological advancements, as the electrochemical tuning of flavoproteins is necessary for optimal interaction with redox acceptor or donor molecules. In order to facilitate the rational design of biomolecular devices, it is imperative to have access to computational tools that can accurately predict the redox potential of both natural and artificial flavoproteins. In this study, we have investigated the feasibility of using non-equilibrium thermodynamic integration protocols to reliably predict the redox potential of flavodoxins. Using as a test set the wild-type flavodoxin from Clostridium Beijerinckii and eight experimentally characterized single-point mutants, we have computed their redox potential. Our results show that 75% (6 out of 8) of the calculated reaction free energies are within 1 kcal/mol of the experimental values, and none exceed an error of 2 kcal/mol, confirming that non-equilibrium thermodynamic integration is a trustworthy tool for the quantitative estimation of the redox potential of this biologically and technologically significant class of enzymes.
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Affiliation(s)
| | | | | | | | | | - Luca De Gioia
- Department of Biotechnology and Biosciences BtBs, University of Milano-Bicocca, Piazza dell’Ateneo Nuovo 1, 20126 Milan, Italy
| | - Jacopo Vertemara
- Department of Biotechnology and Biosciences BtBs, University of Milano-Bicocca, Piazza dell’Ateneo Nuovo 1, 20126 Milan, Italy
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3
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Galuzzi B, Mirarchi A, Viganò EL, De Gioia L, Damiani C, Arrigoni F. Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. J Chem Inf Model 2022; 62:4748-4759. [PMID: 36126254 PMCID: PMC9554915 DOI: 10.1021/acs.jcim.2c00858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Indexed: 11/29/2022]
Abstract
Determining the redox potentials of protein cofactors and how they are influenced by their molecular neighborhoods is essential for basic research and many biotechnological applications, from biosensors and biocatalysis to bioremediation and bioelectronics. The laborious determination of redox potential with current experimental technologies pushes forward the need for computational approaches that can reliably predict it. Although current computational approaches based on quantum and molecular mechanics are accurate, their large computational costs hinder their usage. In this work, we explored the possibility of using more efficient QSPR models based on machine learning (ML) for the prediction of protein redox potential, as an alternative to classical approaches. As a proof of concept, we focused on flavoproteins, one of the most important families of enzymes directly involved in redox processes. To train and test different ML models, we retrieved a dataset of flavoproteins with a known midpoint redox potential (Em) and 3D structure. The features of interest, accounting for both short- and long-range effects of the protein matrix on the flavin cofactor, have been automatically extracted from each protein PDB file. Our best ML model (XGB) has a performance error below 1 kcal/mol (∼36 mV), comparing favorably to more sophisticated computational approaches. We also provided indications on the features that mostly affect the Em value, and when possible, we rationalized them on the basis of previous studies.
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Affiliation(s)
- Bruno
Giovanni Galuzzi
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
- SYSBIO
Centre of Systems Biology/ISBE.IT, Piazza della Scienza 2, 20126, Milan, Italy
| | - Antonio Mirarchi
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Edoardo Luca Viganò
- Istituto
di Ricerche Farmacologiche Mario Negri, Via Mario Negri 2, 20156 Milan, Italy
| | - Luca De Gioia
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
| | - Chiara Damiani
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
- SYSBIO
Centre of Systems Biology/ISBE.IT, Piazza della Scienza 2, 20126, Milan, Italy
| | - Federica Arrigoni
- Department
of Biotechnology and Biosciences, University
of Milano-Bicocca, Piazza della Scienza 2, 20126 Milan, Italy
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4
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Berd M, Moussi K, Aouabdia Y, Benchallal L, Chahi G, Kahouadji B. From metallic to semiconductor conversion of single-walled carbon nanotubes by chlorination. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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5
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Samurkas A, Fan X, Ma D, Sundarraj R, Lin L, Yao L, Ma R, Jiang H, Cao P, Gao Q, Yuchi Z. Discovery of Potential Species-Specific Green Insecticides Targeting the Lepidopteran Ryanodine Receptor. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:4528-4537. [PMID: 32207934 DOI: 10.1021/acs.jafc.0c01063] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Ryanodine receptors (RyRs) are homotetrameric intracellular calcium (Ca2+) release channels responsible for excitation-contraction coupling of muscle cells. Diamide insecticides specifically act on RyRs of Lepidoptera and Coleoptera pests and are safe for nontargeted organisms, generating big worldwide sales. Despite their popularity, several devastating agricultural pests have been reported to be resistant to them because of mutations in a small transmembrane region of their RyRs, hinting a binding pocket nearby. A potential solution to overcome resistance is to develop new insecticides targeting different binding sites in pest RyRs. Based on a high-resolution crystal structure of diamondback moth (DBM) RyR N-terminal domain (NTD) determined by our group, we carried out extensive structure-based insecticide screening targeting the intersubunit interface. We identified eight lead compounds that selectively target the open conformation of DBM RyR, which are predicted to act as channel activators similar to diamide insecticides. Binding mode analysis shows selective binding to a hydrophobic pocket of DBM NTD-A but not to the pocket of its mammalian counterpart. We tested three available compounds on the HEK293 cell lines stably expressing DBM or mammalian RyR, one of which shows good potency and selectivity against DBM RyR. The insecticidal effect of the compound was also confirmed using fruit flies. The detailed binding mode, toxicity, absorption, distribution, metabolism, and excretion, and reactivity of the compound were predicted by bioinformatic methods. Together, our study lays a foundation for developing a new class of selective RyR-targeting insecticides to control both wild-type and resistant pests.
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Affiliation(s)
- Arthur Samurkas
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
- Laboratory of Organic Chemistry, Wageningen University & Research, Wageningen 6708 WE, The Netherlands
| | - Xiaona Fan
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Dan Ma
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | | | - Lianyun Lin
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Li Yao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Ruifang Ma
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Heng Jiang
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Peng Cao
- Key Laboratory of Drug Targets and Drug Leads for Degenerative Diseases, Affiliated Hospital of Integrated Traditional Chinese and Western Medicine, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Qingzhi Gao
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
| | - Zhiguang Yuchi
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin 300072, China
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6
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Aleksandrov A. A Molecular Mechanics Model for Flavins. J Comput Chem 2019; 40:2834-2842. [DOI: 10.1002/jcc.26061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 07/03/2019] [Accepted: 08/04/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Alexey Aleksandrov
- Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique IP Paris, 91128 Palaiseau France
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7
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Valenti G, Iurlo M, Claramunt RM, Accorsi G, Paolucci F, Farrán MÁ, Marcaccio M. Redox Properties and Interchromophoric Electronic Interactions in Isoalloxazine−Anthraquinone Dyads. ChemElectroChem 2018. [DOI: 10.1002/celc.201701374] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Giovanni Valenti
- Department of Chemistry “ G. Ciamician”; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Matteo Iurlo
- Department of Chemistry “ G. Ciamician”; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - Rosa María Claramunt
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias; Universidad Nacional de Educación a Distancia (UNED); Paseo Senda del Rey 9 28040 Madrid Spain
| | - Gianluca Accorsi
- CNR NANOTEC, Institute of Nanotechnology c/o Campus Ecotekne; University of Salento; Via Monteroni 73100 Lecce Italy
| | - Francesco Paolucci
- Department of Chemistry “ G. Ciamician”; University of Bologna; Via Selmi 2 40126 Bologna Italy
| | - M. Ángeles Farrán
- Departamento de Química Orgánica y Bio-Orgánica, Facultad de Ciencias; Universidad Nacional de Educación a Distancia (UNED); Paseo Senda del Rey 9 28040 Madrid Spain
| | - Massimo Marcaccio
- Department of Chemistry “ G. Ciamician”; University of Bologna; Via Selmi 2 40126 Bologna Italy
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8
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Yang Z, Chen J, Zhou Y, Huang H, Xu D, Zhang C. Understanding the hydrogen transfer mechanism for the biodegradation of 2,4,6-trinitrotoluene catalyzed by pentaerythritol tetranitrate reductase: molecular dynamics simulations. Phys Chem Chem Phys 2018; 20:12157-12165. [DOI: 10.1039/c8cp00345a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The explosive 2,4,6-trinitrotoluene (TNT) is a highly toxic pollutant.
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Affiliation(s)
- Zhilin Yang
- Institute of Chemical Materials
- Chinese Academy of Engineering and Physics
- 621900 Mianyang
- China
| | - Junxian Chen
- MOE Key Laboratory of Green Chemistry & Technology
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Yang Zhou
- Institute of Chemical Materials
- Chinese Academy of Engineering and Physics
- 621900 Mianyang
- China
| | - Hui Huang
- Institute of Chemical Materials
- Chinese Academy of Engineering and Physics
- 621900 Mianyang
- China
| | - Dingguo Xu
- MOE Key Laboratory of Green Chemistry & Technology
- College of Chemistry
- Sichuan University
- Chengdu
- P. R. China
| | - Chaoyang Zhang
- Institute of Chemical Materials
- Chinese Academy of Engineering and Physics
- 621900 Mianyang
- China
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9
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Gillet N, Lévy B, Moliner V, Demachy I, de la Lande A. Theoretical estimation of redox potential of biological quinone cofactors. J Comput Chem 2017; 38:1612-1621. [PMID: 28470751 DOI: 10.1002/jcc.24802] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/09/2017] [Accepted: 03/10/2017] [Indexed: 11/10/2022]
Abstract
Redox potentials are essential to understand biological cofactor reactivity and to predict their behavior in biological media. Experimental determination of redox potential in biological system is often difficult due to complexity of biological media but computational approaches can be used to estimate them. Nevertheless, the quality of the computational methodology remains a key issue to validate the results. Instead of looking to the best absolute results, we present here the calibration of theoretical redox potential for quinone derivatives in water coupling QM + MM or QM/MM scheme. Our approach allows using low computational cost theoretical level, ideal for long simulations in biological systems, and determination of the uncertainties linked to the calculations. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Natacha Gillet
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France.,Departament de Química Física i Analítica, Universitat Jaume I, Castellón, 12071, Spain
| | - Bernard Lévy
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, Castellón, 12071, Spain.,Department of Chemistry, University of Bath, Bath BA2 7AY, United Kingdom
| | - Isabelle Demachy
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France
| | - Aurélien de la Lande
- Laboratoire de Chimie-Physique, Université Paris Sud, CNRS, UMR 8000. 15, rue Jean Perrin, 91405 Orsay, CEDEX, France
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10
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Li W, Baldus IB, Gräter F. Redox Potentials of Protein Disulfide Bonds from Free-Energy Calculations. J Phys Chem B 2015; 119:5386-91. [DOI: 10.1021/acs.jpcb.5b01051] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Wenjin Li
- Heidelberg Institute
for Theoretical Studies, Schloss-Wolfsbrunnenweg
35, 69118 Heidelberg, Germany
| | - Ilona B. Baldus
- Heidelberg Institute
for Theoretical Studies, Schloss-Wolfsbrunnenweg
35, 69118 Heidelberg, Germany
| | - Frauke Gräter
- Heidelberg Institute
for Theoretical Studies, Schloss-Wolfsbrunnenweg
35, 69118 Heidelberg, Germany
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11
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Marenich AV, Ho J, Coote ML, Cramer CJ, Truhlar DG. Computational electrochemistry: prediction of liquid-phase reduction potentials. Phys Chem Chem Phys 2014; 16:15068-106. [PMID: 24958074 DOI: 10.1039/c4cp01572j] [Citation(s) in RCA: 314] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
This article reviews recent developments and applications in the area of computational electrochemistry. Our focus is on predicting the reduction potentials of electron transfer and other electrochemical reactions and half-reactions in both aqueous and nonaqueous solutions. Topics covered include various computational protocols that combine quantum mechanical electronic structure methods (such as density functional theory) with implicit-solvent models, explicit-solvent protocols that employ Monte Carlo or molecular dynamics simulations (for example, Car-Parrinello molecular dynamics using the grand canonical ensemble formalism), and the Marcus theory of electronic charge transfer. We also review computational approaches based on empirical relationships between molecular and electronic structure and electron transfer reactivity. The scope of the implicit-solvent protocols is emphasized, and the present status of the theory and future directions are outlined.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, MN 55455-0431, USA.
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12
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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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13
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Filippini G, Bonal C, Malfreyt P. Methodological approaches for the free energy calculations in electroactive SAMs. Mol Phys 2012. [DOI: 10.1080/00268976.2011.652680] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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14
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Mechanical force can fine-tune redox potentials of disulfide bonds. Biophys J 2012; 102:622-9. [PMID: 22325286 DOI: 10.1016/j.bpj.2011.12.039] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2011] [Accepted: 12/16/2011] [Indexed: 11/20/2022] Open
Abstract
Mechanical force applied along a disulfide bond alters its rate of reduction. We here aimed at quantifying the direct effect of force onto the chemical reactivity of a sulfur-sulfur bond in contrast to indirect, e.g., steric or mechanistic, influences. To this end, we evaluated the dependency of a disulfide bond's redox potential on a pulling force applied along the system. Our QM/MM simulations of cystine as a model system take conformational dynamics and explicit solvation into account and show that redox potentials increase over the whole range of forces probed here (30-3320 pN), and thus even in the absence of a significant disulfide bond elongation (<500 pN). Instead, at low forces, dihedrals and angles, as the softer degrees of freedom are stretched, contribute to the destabilization of the oxidized state. We find physiological forces to be likely to tune the disulfide's redox potentials to an extent similar to the tuning within proteins by point mutations.
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15
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The impact of Trichoderma reesei Cel7A carbohydrate binding domain mutations on its binding to a cellulose surface: a molecular dynamics free energy study. J Mol Model 2011; 18:1355-64. [DOI: 10.1007/s00894-011-1167-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Accepted: 06/27/2011] [Indexed: 10/18/2022]
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16
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Filippini G, Goujon F, Bonal C, Malfreyt P. Toward a Prediction of the Redox Properties of Electroactive SAMs: A Free Energy Calculation by Molecular Simulation. J Phys Chem B 2010; 114:12897-907. [DOI: 10.1021/jp105632w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Gaëlle Filippini
- Clermont Université, Université Blaise Pascal, Laboratoire de Thermodynamique et Interactions Moléculaires, UMR CNRS 6272, BP 10448, F-63000 Clermont-Ferrand, France
| | - Florent Goujon
- Clermont Université, Université Blaise Pascal, Laboratoire de Thermodynamique et Interactions Moléculaires, UMR CNRS 6272, BP 10448, F-63000 Clermont-Ferrand, France
| | - Christine Bonal
- Clermont Université, Université Blaise Pascal, Laboratoire de Thermodynamique et Interactions Moléculaires, UMR CNRS 6272, BP 10448, F-63000 Clermont-Ferrand, France
| | - Patrice Malfreyt
- Clermont Université, Université Blaise Pascal, Laboratoire de Thermodynamique et Interactions Moléculaires, UMR CNRS 6272, BP 10448, F-63000 Clermont-Ferrand, France
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17
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Aleksandrov A, Thompson D, Simonson T. Alchemical free energy simulations for biological complexes: powerful but temperamental.... J Mol Recognit 2010; 23:117-27. [PMID: 19693787 DOI: 10.1002/jmr.980] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Free energy simulations compare multiple ligand:receptor complexes by "alchemically" transforming one into another, yielding binding free energy differences. Since their introduction in the 1980s, many technical and theoretical obstacles were surmounted, and the method ("MDFE," since molecular dynamics are often used) has matured into a powerful tool. We describe its current status, its effectiveness, and the challenges it faces. MDFE has provided chemical accuracy for many systems but remains expensive, with significant human overhead costs. The bottlenecks have shifted, partly due to increased computer power. To study diverse sets of ligands, force field availability and accuracy can be a major difficulty. Another difficulty is the frequent need to consider multiple states, related to sidechain protonation or buried waters, for example. Sophisticated, automated methods to sample these states are maturing, such as constant pH simulations. Meanwhile, combinations of MDFE and simpler approaches, like continuum dielectric models, can be very effective. As illustrations, we show how, with careful force field parameterization, MDFE accurately predicts binding specificities between complex tetracycline ligands and their targets. We describe substrate binding to the aspartyl-tRNA synthetase enzyme, where many distinct electrostatic states play a role, and a histidine and a Mg(2+) ion act as coupled switches that help enforce a strict preference for the aspartate substrate, relative to several analogs. Overall, MDFE has achieved a predictive status, where novel ligands can be studied and molecular recognition elucidated in depth. It should play an increasing role in the analysis of complex cellular processes and biomolecular engineering.
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Affiliation(s)
- Alexey Aleksandrov
- Laboratoire de Biochimie (CNRS UMR7654), Department of Biology, Ecole Polytechnique, 91128 Palaiseau, France
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