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Gholami S, Nenov A, Rivalta I, Bocola M, Bordbar AK, Schwaneberg U, Davari MD, Garavelli M. Theoretical Model of the Protochlorophyllide Oxidoreductase from a Hierarchy of Protocols. J Phys Chem B 2018; 122:7668-7681. [PMID: 29996651 DOI: 10.1021/acs.jpcb.8b04231] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The enzyme protochlorophyllide oxidoreductase (LPOR) catalyzes the light-driven reduction of protochlorophyllide (Pchlide), a crucial step in chlorophyll biosynthesis. Molecular understanding of the photocatalytic mechanism of LPOR is essential for harnessing light energy to mediate enzymatic reactions. The absence of X-ray crystal structure has promoted the development of LPOR homology models that lack a catalytically competent active site and could not explain the variously reported spectroscopic evidence, including time-resolved optical spectroscopy data. We have refined previous structural models to account for the catalytic active site and the characteristic experimental spectral features of Pchlide binding, including the 26 cm-1 red shift of the C13(1) carbonyl stretch vibration in the mid-infrared (IR) and the 12 nm red shift of the Q x electronic band. A hierarchy of theoretical methods, including homology modeling, molecular dynamics simulations, hybrid quantum mechanics [(TD-)DFT]/molecular mechanics [AMBER] calculations, and computational vibrational and electronic spectroscopies, have been combined in an iterative protocol to reproduce experimental evidence and to predict ultrafast transient IR spectroscopic fingerprints associated with the catalytic process. The successful application to the LPOR enzyme indicates that the presented hierarchical protocol provides a general workflow to protein structure refinement.
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Affiliation(s)
- Samira Gholami
- Department of Chemistry , University of Isfahan , Isfahan 81746-73441 , Iran.,Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Artur Nenov
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
| | - Ivan Rivalta
- Université de Lyon , École Normale Supérieure de Lyon, CNRS, Université Claude Bernard Lyon 1, Laboratoire de Chimie UMR 5182, F-69342 , Lyon , France
| | - Marco Bocola
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , 52074 Aachen , Germany
| | - A Khalegh Bordbar
- Department of Chemistry , University of Isfahan , Isfahan 81746-73441 , Iran
| | - Ulrich Schwaneberg
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , 52074 Aachen , Germany.,DWI-Leibniz Institute for Interactive Materials , Forckenbeckstraße 50 , 52056 Aachen , Germany
| | - Mehdi D Davari
- Institute of Biotechnology , RWTH Aachen University , Worringer Weg 3 , 52074 Aachen , Germany
| | - Marco Garavelli
- Dipartimento di Chimica Industriale , Università degli Studi di Bologna , Viale del Risorgimento 4 , I-40136 Bologna , Italy
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Hoeven R, Hardman SJO, Heyes DJ, Scrutton NS. Cross-Species Analysis of Protein Dynamics Associated with Hydride and Proton Transfer in the Catalytic Cycle of the Light-Driven Enzyme Protochlorophyllide Oxidoreductase. Biochemistry 2016; 55:903-13. [DOI: 10.1021/acs.biochem.5b01355] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robin Hoeven
- Centre for Synthetic Biology
of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Samantha J. O. Hardman
- Centre for Synthetic Biology
of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J. Heyes
- Centre for Synthetic Biology
of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Nigel S. Scrutton
- Centre for Synthetic Biology
of Fine and Speciality Chemicals, Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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Heyes DJ, Hardman SJO, Hedison TM, Hoeven R, Greetham GM, Towrie M, Scrutton NS. Excited-state charge separation in the photochemical mechanism of the light-driven enzyme protochlorophyllide oxidoreductase. Angew Chem Int Ed Engl 2015; 54:1512-5. [PMID: 25488797 PMCID: PMC4531822 DOI: 10.1002/anie.201409881] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Indexed: 11/11/2022]
Abstract
The unique light-driven enzyme protochlorophyllide oxidoreductase (POR) is an important model system for understanding how light energy can be harnessed to power enzyme reactions. The ultrafast photochemical processes, essential for capturing the excitation energy to drive the subsequent hydride- and proton-transfer chemistry, have so far proven difficult to detect. We have used a combination of time-resolved visible and IR spectroscopy, providing complete temporal resolution over the picosecond-microsecond time range, to propose a new mechanism for the photochemistry. Excited-state interactions between active site residues and a carboxyl group on the Pchlide molecule result in a polarized and highly reactive double bond. This so-called "reactive" intramolecular charge-transfer state creates an electron-deficient site across the double bond to trigger the subsequent nucleophilic attack of NADPH, by the negatively charged hydride from nicotinamide adenine dinucleotide phosphate. This work provides the crucial, missing link between excited-state processes and chemistry in POR. Moreover, it provides important insight into how light energy can be harnessed to drive enzyme catalysis with implications for the design of light-activated chemical and biological catalysts.
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Affiliation(s)
- Derren J Heyes
- Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester131 Princess Street, Manchester M1 7DN (UK)
| | - Samantha J O Hardman
- Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester131 Princess Street, Manchester M1 7DN (UK)
| | - Tobias M Hedison
- Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester131 Princess Street, Manchester M1 7DN (UK)
| | - Robin Hoeven
- Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester131 Princess Street, Manchester M1 7DN (UK)
| | - Greg M Greetham
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities CouncilHarwell Oxford, Didcot, OX11 0QX (UK)
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities CouncilHarwell Oxford, Didcot, OX11 0QX (UK)
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Photon Science Institute, University of Manchester131 Princess Street, Manchester M1 7DN (UK)
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Heyes DJ, Hardman SJO, Hedison TM, Hoeven R, Greetham GM, Towrie M, Scrutton NS. Excited-State Charge Separation in the Photochemical Mechanism of the Light-Driven Enzyme Protochlorophyllide Oxidoreductase. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409881] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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