1
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Cicek E, Monard G, Sungur FA. Molecular Mechanism of Protein Arginine Deiminase 2: A Study Involving Multiple Microsecond Long Molecular Dynamics Simulations. Biochemistry 2022; 61:1286-1297. [PMID: 35737372 PMCID: PMC9260958 DOI: 10.1021/acs.biochem.2c00158] [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] [Indexed: 11/29/2022]
Abstract
Peptidylarginine deiminase 2 (PAD2) is a Ca2+-dependent enzyme that catalyzes the conversion of protein arginine residues to citrulline. This kind of structural modification in histone molecules may affect gene regulation, leading to effects that may trigger several diseases, including breast cancer, which makes PAD2 an attractive target for anticancer drug development. To design new effective inhibitors to control activation of PAD2, improving our understanding of the molecular mechanisms of PAD2 using up-to-date computational techniques is essential. We have designed five different PAD2-substrate complex systems based on varying protonation states of the active site residues. To search the conformational space broadly, multiple independent molecular dynamics simulations of the complexes have been performed. In total, 50 replica simulations have been performed, each of 1 μs, yielding a total simulation time of 50 μs. Our findings identify that the protonation states of Cys647, Asp473, and His471 are critical for the binding and localization of the N-α-benzoyl-l-arginine ethyl ester substrate within the active site. A novel mechanism for enzyme activation is proposed according to near attack conformers. This represents an important step in understanding the mechanism of citrullination and developing PAD2-inhibiting drugs for the treatment of breast cancer.
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Affiliation(s)
- Erdem Cicek
- Informatics Institute, Computational Science and Engineering, Istanbul Technical University, TR-34469 Istanbul, Turkey
| | - Gerald Monard
- Université de Lorraine, CNRS, LPCT, F-54000 Nancy, France
| | - Fethiye Aylin Sungur
- Informatics Institute, Computational Science and Engineering, Istanbul Technical University, TR-34469 Istanbul, Turkey
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2
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Osswald M, Fingerhut BP. Electron Transfer-Induced Active Site Structural Relaxation in 64-Photolyase of Drosophila melanogaster. J Phys Chem B 2021; 125:8690-8702. [PMID: 34323497 DOI: 10.1021/acs.jpcb.1c02951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While catalytic electron flow and photoreactivation of CPD-photolyases are increasingly understood, the microscopic details of the 64-photolyase repair mechanism are perpetually debated. Here, we investigate in long-time (μs) molecular dynamics simulations combined with extensive quantum mechanical/molecular mechanical (QM/MM) simulations the primary electron transfer (ET) reactions in 64-photolyase of Drosophila melanogaster (D. melanogaster). The characterization of the relative energetics of locally excited and charge separated states in the (6-4) photoproduct enzyme repair complex reveals a charge-separated state involving the adenine moiety of the FADH- cofactor that facilitates reduction of the photoproduct. Microscopic details of the collective reaction coordinate of ET reactions are identified that involve the reorganization of the hydrogen bond network and structural relaxation of the active site. The simulations reveal complex active site relaxation dynamics involving distinguished amino acids (Lys246, His365, and His369), conformational reorganization of the hydroxyl group of the (6-4) photoproduct, and a strengthening of hydrogen bonds with immobilized water molecules. In particular, rotation of the Lys246 side chain is found to impose a double-well character along the reaction coordinate of the ET reaction. Our findings suggest that the primary ET reactions in the (6-4) photoproduct enzyme repair complex of D. melanogaster are governed by a complex multi-minima active site relaxation dynamics and potentially precede the equilibration of the protein. ET pathways mediated by the adenine moiety and the 5' side of the photoproduct are proposed to be relevant for triggering the catalytic (6-4) photoproduct reactivation.
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Affiliation(s)
- Mara Osswald
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
| | - Benjamin P Fingerhut
- Max-Born-Institut für Nichtlineare Optik und Kurzzeitspektroskopie, D-12489 Berlin, Germany
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3
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Dokainish HM, Kitao A. Similarities and Differences between Thymine(6-4)Thymine/Cytosine DNA Lesion Repairs by Photolyases. J Phys Chem B 2018; 122:8537-8547. [PMID: 30124048 DOI: 10.1021/acs.jpcb.8b07048] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Photolyases are ancient enzymes that harvest sunlight to repair DNA pyrimidine lesions such as pyrimidine(6-4)pyrimidone and cyclobutane dimers. Particularly, (6-4) photolyase ((6-4)PHR) plays an important role in maintaining genetic integrity by repairing thymine(6-4)thymine (T(6-4)T) and thymine(6-4)cytosine (T(6-4)C) photolesions. The majority of (6-4)PHR studies have been performed on the basis of the former's activity and assuming the equivalence of the two repair mechanisms, although the latter's activity remains poorly studied. Here, we describe investigations of the repair process of the T(6-4)C dimer using several computational methods from molecular dynamics (MD) simulations to large quantum mechanical/molecular mechanical approaches. Two possible mechanisms, the historically proposed azetidine four-member ring intermediate and the free NH3 formation pathways, were considered. The MD results predicted that important active site histidine residues employed for the repair of the T(6-4)C dimer have protonation states similar to those seen in the (6-4)PHR/T(6-4)T complex. More importantly, despite chemical differences between the two substrates, a similar repair mechanism was identified: His365 protonates NH2, resulting in formation/activation mechanism of a free NH3, inducing NH2 transfer to the 5' base, and ultimately leading to pyrimidine restoration. This reaction is thermodynamically favorable with a rate-limiting barrier of 20.4 kcal mol-1. In contrast, the azetidine intermediate is unfeasible, possessing an energy barrier of 60 kcal mol-1; this barrier is similar to that predicted for the oxetane intermediate in T(6-4)T repair. Although both substrates are repaired with comparable quantum yields, the reactive complex in T(6-4)C was shown to be a 3' base radical with a lower driving force for back electron transfer combined with higher energy barrier for catalysis. These results showed the similarity in the general repair mechanisms between the two substrates while emphasizing differences in the electron dynamics in the repair cycle.
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Affiliation(s)
- Hisham M Dokainish
- School of Life Science and Technology , Tokyo Institute of Technology , M6-13, 2-12-1 Ookayama , Meguro , Tokyo 152-8550 , Japan
| | - Akio Kitao
- School of Life Science and Technology , Tokyo Institute of Technology , M6-13, 2-12-1 Ookayama , Meguro , Tokyo 152-8550 , Japan
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4
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Kovačević B, Barić D, Babić D, Bilić L, Hanževački M, Sandala GM, Radom L, Smith DM. Computational Tale of Two Enzymes: Glycerol Dehydration With or Without B12. J Am Chem Soc 2018; 140:8487-8496. [DOI: 10.1021/jacs.8b03109] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Borislav Kovačević
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Danijela Barić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Darko Babić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Luka Bilić
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Marko Hanževački
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
| | - Gregory M. Sandala
- Department of Chemistry and Biochemistry, Mount Allison University, Sackville, New Brunswick E4L 1G8, Canada
| | - Leo Radom
- School of Chemistry, University of Sydney, Sydney, NSW 2006, Australia
| | - David M. Smith
- Department of Physical Chemistry, Ruđer Bošković Institute, 10000 Zagreb, Croatia
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5
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Uppula P. Exploration of Conformations, Analysis of Protein and Biological Significance of Histidine Dimers. ChemistrySelect 2018. [DOI: 10.1002/slct.201702559] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Purushotham Uppula
- Center for molecular modelling; Indian Institute of Chemical Technology; Tarnaka Hyderabad-500 007 India
- Department of Chemistry; K L Education Foundation, Guntur; Andhra Pradesh India- 522502
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6
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Yamamoto J, Plaza P, Brettel K. Repair of (6-4) Lesions in DNA by (6-4) Photolyase: 20 Years of Quest for the Photoreaction Mechanism. Photochem Photobiol 2017; 93:51-66. [PMID: 27992654 DOI: 10.1111/php.12696] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 12/09/2016] [Indexed: 01/05/2023]
Abstract
Exposure of DNA to ultraviolet (UV) light from the Sun or from other sources causes the formation of harmful and carcinogenic crosslinks between adjacent pyrimidine nucleobases, namely cyclobutane pyrimidine dimers and pyrimidine(6-4)pyrimidone photoproducts. Nature has developed unique flavoenzymes, called DNA photolyases, that utilize blue light, that is photons of lower energy than those of the damaging light, to repair these lesions. In this review, we focus on the chemically challenging repair of the (6-4) photoproducts by (6-4) photolyase and describe the major events along the quest for the reaction mechanisms, over the 20 years since the discovery of (6-4) photolyase.
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Affiliation(s)
- Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Osaka, Japan
| | - Pascal Plaza
- Ecole Normale Supérieure, PSL Research University, UPMC Univ Paris 06, CNRS, Département de Chimie, PASTEUR, Paris, France.,Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, PASTEUR, Paris, France
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC), IBITECS, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
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Faraji S, Dreuw A. Insights into Light-driven DNA Repair by Photolyases: Challenges and Opportunities for Electronic Structure Theory. Photochem Photobiol 2017; 93:37-50. [PMID: 27925218 DOI: 10.1111/php.12679] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 11/18/2016] [Indexed: 01/25/2023]
Abstract
Ultraviolet radiation causes two of the most abundant mutagenic and cytotoxic DNA lesions: cyclobutane pyrimidine dimers and 6-4 photoproducts. (6-4) Photolyases are light-activated enzymes that selectively bind to DNA and trigger repair of mutagenic 6-4 photoproducts via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH- ) to the lesion triggering repair. This review provides an overview of the sequential steps of the repair process, that is light absorption and resonance energy transfer, photoinduced electron transfer and electron-induced splitting mechanisms, with an emphasis on the role of theory and computation. In addition, theoretical calculations and physical properties that can be used to classify specific mechanism are discussed in an effort to trace the fundamental aspects of each individual step and assist the interpretation of experimental data. The current challenges and suggested future directions are outlined for each step, concluding with a view on the future.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Heidelberg, Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Heidelberg, Germany
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8
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Dokainish HM, Kitao A. Computational Assignment of the Histidine Protonation State in (6-4) Photolyase Enzyme and Its Effect on the Protonation Step. ACS Catal 2016. [DOI: 10.1021/acscatal.6b01094] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Hisham M. Dokainish
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Akio Kitao
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
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9
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Faraji S, Zhong D, Dreuw A. Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-4) Photolesions by Photolyases. Angew Chem Int Ed Engl 2016; 55:5175-8. [PMID: 26996356 PMCID: PMC4921128 DOI: 10.1002/anie.201511950] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 01/27/2016] [Indexed: 11/09/2022]
Abstract
Quantum mechanics/molecular mechanics calculations are employed to assign previously recorded experimental spectroscopic signatures of the intermediates occurring during the photo-induced repair of (6-4) photolesions by photolyases to specific molecular structures. Based on this close comparison of experiment and theory it is demonstrated that the acting repair mechanism involves proton transfer from the protonated His365 to the N3' nitrogen of the lesion, which proceeds simultaneously with intramolecular OH transfer along an oxetane-like transition state.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
| | - Dongping Zhong
- Departments of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics and Biochemistry, The Ohio State University, Columbus Ohio 43210, USA,
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls Heidelberg University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany,
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10
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Faraji S, Zhong D, Dreuw A. Characterization of the Intermediate in and Identification of the Repair Mechanism of (6-
4) Photolesions by Photolyases. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201511950] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing; Ruprecht-Karls University Heidelberg; Im Neuenheimer Feld 205A 69120 Heidelberg Germany
| | - Dongping Zhong
- Department of Physics, Department of Chemistry and Biochemistry, and Programs of Biophysics, Chemical Physics and Biochemistry; The Ohio State University; Columbus OH 43210 USA
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing; Ruprecht-Karls University Heidelberg; Im Neuenheimer Feld 205A 69120 Heidelberg Germany
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11
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Yamada D, Yamamoto J, Zhang Y, Iwata T, Hitomi K, Getzoff ED, Iwai S, Kandori H. Structural Changes of the Active Center during the Photoactivation of Xenopus (6-4) Photolyase. Biochemistry 2016; 55:715-23. [PMID: 26719910 DOI: 10.1021/acs.biochem.5b01111] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Photolyases (PHRs) repair the UV-induced photoproducts, cyclobutane pyrimidine dimer (CPD) or pyrimidine-pyrimidone (6-4) photoproduct [(6-4) PP], restoring normal bases to maintain genetic integrity. CPD and (6-4) PP are repaired by substrate-specific PHRs, CPD PHR and (6-4) PHR, respectively. Flavin adenine dinucleotide (FAD) is the chromophore of both PHRs, and the resting oxidized form (FAD(ox)), at least under in vitro purified conditions, is first photoconverted to the neutral semiquinoid radical (FADH(•)) form, followed by photoconversion into the enzymatically active fully reduced (FADH(-)) form. Previously, we reported light-induced difference Fourier transform infrared (FTIR) spectra corresponding to the photoactivation process of Xenopus (6-4) PHR. Spectral differences between the absence and presence of (6-4) PP were observed in the photoactivation process. To identify the FTIR signals where these differences appeared, we compared the FTIR spectra of photoactivation (i) in the presence and absence of (6-4) PP, (ii) of (13)C labeling, (15)N labeling, and [(14)N]His/(15)N labeling, and (iii) of H354A and H358A mutants. We successfully assigned the vibrational bands for (6-4) PP, the α-helix and neutral His residue(s). In particular, we assigned three bands to the C ═ O groups of (6-4) PP in the three different redox states of FAD. Furthermore, the changed hydrogen bonding environments of C ═ O groups of (6-4) PP suggested restructuring of the binding pocket of the DNA lesion in the process of photoactivation.
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Affiliation(s)
- Daichi Yamada
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Yu Zhang
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Tatsuya Iwata
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
| | - Kenichi Hitomi
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States.,Life Sciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
| | - Shigenori Iwai
- Graduate School of Engineering Science, Osaka University , Toyonaka, Osaka 560-8531, Japan
| | - Hideki Kandori
- Department of Frontier Materials, Nagoya Institute of Technology , Showa-ku, Nagoya 466-8555, Japan
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12
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Dreuw A, Faraji S. A quantum chemical perspective on (6-4) photolesion repair by photolyases. Phys Chem Chem Phys 2014; 15:19957-69. [PMID: 24145385 DOI: 10.1039/c3cp53313a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
(6-4)-Photolyases are fascinating enzymes which repair (6-4)-DNA photolesions utilizing light themselves. It is well known that upon initial photo-excitation of an antenna pigment an electron is transferred from an adjacent FADH(-) cofactor to the photolesion initiating repair, i.e. restoration of the original undamaged DNA bases. Concerning the molecular details of this amazing repair mechanism, the early steps of energy transfer and catalytic electron generation are well understood, the terminal repair mechanism, however, is still a matter of ongoing debate. In this perspective article, recent results of quantum chemical investigations are presented, and their meaning for the repair mechanism under natural conditions is outlined. Consequences of natural light conditions, temperature and thermal equilibration are highlighted when issues like the initial protonation state of the relevant histidines and the lesion, or the direction of electron transfer are discussed.
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Affiliation(s)
- Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
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13
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Faraji S, Dreuw A. Physicochemical Mechanism of Light-Driven DNA Repair by (6-4) Photolyases. Annu Rev Phys Chem 2014; 65:275-92. [DOI: 10.1146/annurev-physchem-040513-103626] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, 69120 Heidelberg, Germany; ,
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, 69120 Heidelberg, Germany; ,
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Domratcheva T, Udvarhelyi A, Shahi ARM. Computational spectroscopy, dynamics, and photochemistry of photosensory flavoproteins. Methods Mol Biol 2014; 1146:191-228. [PMID: 24764094 DOI: 10.1007/978-1-4939-0452-5_10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Extensive interest in photosensory proteins stimulated computational studies of flavins and flavoproteins in the past decade. This review is dedicated to the three central topics of these studies: calculations of flavin UV-visible and IR spectra, simulated dynamics of photoreceptor proteins, and flavin photochemistry. Accordingly, this chapter is divided into three parts; each part describes corresponding computational protocols, summarizes computational results, and discusses the emerging mechanistic picture.
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Affiliation(s)
- Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstraße 29, 69120, Heidelberg, Germany,
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15
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Moughal Shahi AR, Domratcheva T. Challenges in Computing Electron-Transfer Energies of DNA Repair Using Hybrid QM/MM Models. J Chem Theory Comput 2013; 9:4644-52. [DOI: 10.1021/ct400537b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abdul Rehaman Moughal Shahi
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
| | - Tatiana Domratcheva
- Department
of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Jahnstrasse 29, 69120, Heidelberg, Germany
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16
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Faraji S, Groenhof G, Dreuw A. Combined QM/MM investigation on the light-driven electron-induced repair of the (6-4) thymine dimer catalyzed by DNA photolyase. J Phys Chem B 2013; 117:10071-9. [PMID: 23915283 DOI: 10.1021/jp401662z] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The (6-4) photolyases are blue-light-activated enzymes that selectively bind to DNA and initiate splitting of mutagenic thymine (6-4) thymine photoproducts (T(6-4)T-PP) via photoinduced electron transfer from flavin adenine dinucleotide anion (FADH(-)) to the lesion triggering repair. In the present work, the repair mechanism after the initial electron transfer and the effect of the protein/DNA environment are investigated theoretically by means of hybrid quantum mechanical/molecular mechanical (QM/MM) simulations using X-ray structure of the enzyme-DNA complex. By comparison of three previously proposed repair mechanisms, we found that the lowest activation free energy is required for the pathway in which the key step governing the repair photocycle is electron transfer coupled with the proton transfer from the protonated histidine, His365, to the N3' nitrogen of the pyrimidone thymine. The transfer simultaneously occurs with concerted intramolecular OH transfer without formation of an oxetane or isolated water molecule intermediate. In contrast to previously suggested mechanisms, this newly identified pathway requires neither a subsequent two-photon process nor electronic excitation of the photolesion.
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Affiliation(s)
- Shirin Faraji
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany.
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17
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Witwicki M, Jezierska J. DFT insight into o-semiquinone radicals and Ca2+ ion interaction: structure, g tensor, and stability. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1383-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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18
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Benjdia A. DNA photolyases and SP lyase: structure and mechanism of light-dependent and independent DNA lyases. Curr Opin Struct Biol 2012; 22:711-20. [PMID: 23164663 DOI: 10.1016/j.sbi.2012.10.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/30/2012] [Accepted: 10/02/2012] [Indexed: 10/27/2022]
Abstract
Light is essential for many critical biological processes including vision, circadian rhythms, photosynthesis and DNA repair. DNA photolyases use light energy and a fully reduced flavin cofactor to repair the major UV-induced DNA damages, the cis-syn cyclobutane pyrimidine dimers (CPDs) and the pyrimidine-pyrimidone (6-4) photoproducts. Catalysis involves two photoreactions, the photoactivation which leads to the conversion of the flavin cofactor to its catalytic active form and the photorepair whose efficiency depends on a light-harvesting antenna chromophore. Very interestingly, an alternative and light-independent direct reversal mechanism to repair a distinct photolesion is found in bacterial spores, catalyzed by spore photoproduct lyase. This radical SAM enzyme uses an iron-sulfur cluster and S-adenosyl-l-methionine (SAM) to split a specific photoproduct, the so-called spore photoproduct (SP), back to two thymidine residues. The recently solved crystal structure of SP lyase provides new insights into this unique DNA repair mechanism and allows a detailed comparison with DNA photolyases. Similarities as well as divergences between DNA photolyases and SP lyase are highlighted in this review.
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Affiliation(s)
- Alhosna Benjdia
- Department of Biomolecular Mechanisms, Max-Planck Institute for Medical Research, Jahnstrasse 29, Heidelberg, Germany.
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