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Bowling PE, Dasgupta S, Herbert JM. Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. J Chem Inf Model 2024; 64:3912-3922. [PMID: 38648614 DOI: 10.1021/acs.jcim.4c00221] [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: 04/25/2024]
Abstract
In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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2
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Wang J, Ren T, Sun G, Zhang N, Zhao L, Zhong R. Mechanism of AGT-Mediated Repair of dG-dC Cross-Links in the Drug Resistance to Chloroethylnitrosoureas: Molecular Docking, MD Simulation, and ONIOM (QM/MM) Investigation. J Chem Inf Model 2024; 64:3411-3429. [PMID: 38511939 DOI: 10.1021/acs.jcim.3c01958] [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: 03/22/2024]
Abstract
Chloroethylnitrosoureas (CENUs) are important chemotherapies applied in the treatment of cancer. They exert anticancer activity by inducing DNA interstrand cross-links (ICLs) via the formation of two O6-alkylguanine intermediates, O6-chloroethylguanine (O6-ClEtG) and N1,O6-ethanoguanine (N1,O6-EtG). However, O6-alkylguanine-DNA alkyltransferase (AGT), a DNA-repair enzyme, can restore the O6-alkylguanine damages and thereby obstruct the formation of ICLs (dG-dC cross-link). In this study, the inhibitory mechanism of ICL formation was investigated to elucidate the drug resistance of CENUs mediated by AGT in detail. Based on the structures of the substrate-enzyme complexes obtained from docking and MD simulations, two ONIOM (QM/MM) models with different sizes of the QM region were constructed. The model with a larger QM region, which included the substrate (O6-ClEtG or N1,O6-EtG), a water molecule, and five residues (Tyr114, Cys145, His146, Lys165, and Glu172) in the active pocket of AGT, accurately described the repairing reaction and generated the results coinciding with the experimental outcomes. The repair process consists of two sequential steps: hydrogen transfer to form a thiolate anion on Cys145 and alkyl transfer from the O6 site of guanine (the rate-limiting step). The repair of N1,O6-EtG was more favorable than that of O6-ClEtG from both kinetics and thermodynamics aspects. Moreover, the comparison of the repairing process with the formation of dG-dC cross-link and the inhibition of AGT by O6-benzylguanine (O6-BG) showed that the presence of AGT could effectively interrupt the formation of ICLs leading to drug resistance, and the inhibition of AGT by O6-BG that was energetically more favorable than the repair of O6-ClEtG could not prevent the repair of N1,O6-EtG. Therefore, it is necessary to completely eliminate AGT activity before CENUs medication to enhance the chemotherapeutic effectiveness. This work provides reasonable explanations for the supposed mechanism of AGT-mediated drug resistance of CENUs and will assist in the development of novel CENU chemotherapies and their medication strategies.
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Affiliation(s)
- Jiaojiao Wang
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Ting Ren
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Guohui Sun
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Na Zhang
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Chemistry and Life Science, Beijing University of Technology, Beijing 100124, China
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3
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McCarthy E, Ekesan Ş, Giese TJ, Wilson TJ, Deng J, Huang L, Lilley DJ, York DM. Catalytic mechanism and pH dependence of a methyltransferase ribozyme (MTR1) from computational enzymology. Nucleic Acids Res 2023; 51:4508-4518. [PMID: 37070188 PMCID: PMC10201425 DOI: 10.1093/nar/gkad260] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/09/2023] [Accepted: 04/10/2023] [Indexed: 04/19/2023] Open
Abstract
A methyltransferase ribozyme (MTR1) was selected in vitro to catalyze alkyl transfer from exogenous O6-methylguanine (O6mG) to a target adenine N1, and recently, high-resolution crystal structures have become available. We use a combination of classical molecular dynamics, ab initio quantum mechanical/molecular mechanical (QM/MM) and alchemical free energy (AFE) simulations to elucidate the atomic-level solution mechanism of MTR1. Simulations identify an active reactant state involving protonation of C10 that hydrogen bonds with O6mG:N1. The deduced mechanism involves a stepwise mechanism with two transition states corresponding to proton transfer from C10:N3 to O6mG:N1 and rate-controlling methyl transfer (19.4 kcal·mol-1 barrier). AFE simulations predict the pKa for C10 to be 6.3, close to the experimental apparent pKa of 6.2, further implicating it as a critical general acid. The intrinsic rate derived from QM/MM simulations, together with pKa calculations, enables us to predict an activity-pH profile that agrees well with experiment. The insights gained provide further support for a putative RNA world and establish new design principles for RNA-based biochemical tools.
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Affiliation(s)
- Erika McCarthy
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Şölen Ekesan
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
| | - Timothy J Wilson
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Jie Deng
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong–Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Lin Huang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Guangdong–Hong Kong Joint Laboratory for RNA Medicine, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
- Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - David M J Lilley
- Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dundee, Dow Street, Dundee DD1 5EH, UK
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, NJ 08854, USA
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4
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Dasgupta S, Herbert JM. Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites. J Phys Chem B 2020; 124:1137-1147. [PMID: 31986049 DOI: 10.1021/acs.jpcb.9b11060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quantum-chemical studies of enzymatic reaction mechanisms sometimes use truncated active-site models as simplified alternatives to mixed quantum mechanics molecular mechanics (QM/MM) procedures. Eliminating the MM degrees of freedom reduces the complexity of the sampling problem, but the trade-off is the need to introduce geometric constraints in order to prevent structural collapse of the model system during geometry optimizations that do not contain a full protein backbone. These constraints may impair the efficiency of the optimization, and care must be taken to avoid artifacts such as imaginary vibrational frequencies. We introduce a simple alternative in which terminal atoms of the model system are placed in soft harmonic confining potentials rather than being rigidly constrained. This modification is simple to implement and straightforward to use in vibrational frequency calculations, unlike iterative constraint-satisfaction algorithms, and allows the optimization to proceed without constraint even though the practical result is to fix the anchor atoms in space. The new approach is more efficient for optimizing minima and transition states, as compared to the use of fixed-atom constraints, and also more robust against unwanted imaginary frequencies. We illustrate the method by application to several enzymatic reaction pathways where entropy makes a significant contribution to the relevant reaction barriers. The use of confining potentials correctly describes reaction paths and facilitates calculation of both vibrational zero-point and finite-temperature entropic corrections to barrier heights.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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5
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Nocentini A, Carta F, Tanc M, Selleri S, Supuran CT, Bazzicalupi C, Gratteri P. Deciphering the Mechanism of Human Carbonic Anhydrases Inhibition with Sulfocoumarins: Computational and Experimental Studies. Chemistry 2018; 24:7840-7844. [DOI: 10.1002/chem.201800941] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Revised: 03/22/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Alessio Nocentini
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics & QSAR; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Fabrizio Carta
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Muhammet Tanc
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Silvia Selleri
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Claudiu T. Supuran
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
| | - Carla Bazzicalupi
- Department of Chemistry “U. Schiff”; University of Florence; Via della Lastruccia 3 50019 Sesto Fiorentino Italy
| | - Paola Gratteri
- Department NEUROFARBA-Pharmaceutical and nutraceutical section; Laboratory of Molecular Modeling Cheminformatics & QSAR; University of Firenze; via Ugo Schiff 6 50019 Sesto Fiorentino Italy
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6
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Osipov I, Gorbachev MY, Gorinchoy NN. Proton-induced accelerated decay of the fungicide, vinclozolin, on TiO 2 surface under solar irradiation: Experimental and DFT study. JOURNAL OF ENVIRONMENTAL SCIENCE AND HEALTH. PART. B, PESTICIDES, FOOD CONTAMINANTS, AND AGRICULTURAL WASTES 2018; 53:222-228. [PMID: 29286876 DOI: 10.1080/03601234.2017.1410406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The photochemical degradation of vinclozolin by addition of titanium dioxide on silica support has been examined both experimental and quantum-chemically. Solar irradiation of vinclozolin on silica with and without addition of titanium dioxide for 6 h resulted in 21% and 97.8% vinclozolin residues, respectively. In both these cases, phototransformation leads to the formation of (3,5-dichlorophenyl isocyanate) and (3,5-dichloroaniline). The presence of the intermediary product resulted from opening of the 2,4-oxazolidine-dione ring is also confirmed by GS-MS and LC-MS chromatography. The proton-induced mechanism of vinclozolin decay at the above experimental conditions is clarified on the base of DFT calculations.
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Affiliation(s)
- Ivan Osipov
- a Department of Quantum Chemistry , Institute of Chemistry, Academy of Sciences of Moldova , Kishinev , Republic of Moldova
| | - Mikhail Y Gorbachev
- a Department of Quantum Chemistry , Institute of Chemistry, Academy of Sciences of Moldova , Kishinev , Republic of Moldova
| | - Natalia N Gorinchoy
- a Department of Quantum Chemistry , Institute of Chemistry, Academy of Sciences of Moldova , Kishinev , Republic of Moldova
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7
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Molecular recognition of cyclodecapeptides to ibuprofen and naproxen enantiomers: a theoretical study. Struct Chem 2017. [DOI: 10.1007/s11224-017-0929-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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8
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Delarami HS, Ebrahimi A. Theoretical investigation of the backbone···π and π···π stacking interactions in substituted-benzene||3-methyl-2′-deoxyadenosine: a perspective to the DNA repair. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1118569] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Hojat Samareh Delarami
- Computational Quantum Chemistry Laboratory, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
| | - Ali Ebrahimi
- Computational Quantum Chemistry Laboratory, Department of Chemistry, University of Sistan and Baluchestan, Zahedan, Iran
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9
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Li L, Li S, Sun G, Peng R, Zhao L, Zhong R. Influence of the Expression Level of O6-Alkylguanine-DNA Alkyltransferase on the Formation of DNA Interstrand Crosslinks Induced by Chloroethylnitrosoureas in Cells: A Quantitation Using High-Performance Liquid Chromatography-Mass Spectrometry. PLoS One 2015; 10:e0121225. [PMID: 25799182 PMCID: PMC4370500 DOI: 10.1371/journal.pone.0121225] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 01/29/2015] [Indexed: 11/24/2022] Open
Abstract
Chloroethylnitrosoureas (CENUs), which are bifunctional alkylating agents widely used in the clinical treatment of cancer, exert anticancer activity by inducing crosslink within a guanine-cytosine DNA base pair. However, the formation of dG-dC crosslinks can be prevented by O6-alkylguanine-DNA alkyltransferase (AGT), ultimately leading to drug resistance. Therefore, the level of AGT expression is related to the formation of dG-dC crosslinks and the sensitivity of cells to CENUs. In this work, we determined the CENU-induced dG-dC crosslink in mouse L1210 leukemia cells and in human glioblastoma cells (SF-763, SF-767 and SF-126) containing different levels of AGT using high-performance liquid chromatography coupled with electrospray ionization tandem mass spectrometry. The results indicate that nimustine (ACNU) induced more dG-dC crosslinks in L1210 leukemia cells than those induced by carmustine (BCNU), lomustine (CCNU) and fotemustine (FTMS). This result was consistent with a previously reported cohort study, which demonstrated that ACNU had a better survival gain than BCNU, CCNU and FTMS for patients with high-grade glioma. Moreover, we compared the crosslinking levels and the cytotoxicity in SF-763, SF-767 and SF-126 cells with different AGT expression levels after exposure to ACNU. The levels of dG-dC crosslink in SF-126 cells (low AGT expression) were significantly higher than those in SF-767 (medium AGT expression) and SF-763 (high AGT expression) cells at each time point. Correspondingly, the cytotoxicity of SF-126 was the highest followed by SF-767 and SF-763. The results obtained in this work provided unequivocal evidence for drug resistance to CENUs induced by AGT-mediated repair of DNA ICLs. We postulate that the level of dG-dC crosslink has the potential to be employed as a biomarker for estimating drug resistance and anticancer efficiencies of novel CENU chemotherapies.
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Affiliation(s)
- Lili Li
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, P. R. China
| | - Sisi Li
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, P. R. China
| | - Guohui Sun
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, P. R. China
| | - Ruizeng Peng
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, P. R. China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, P. R. China
- * E-mail:
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental and Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing, P. R. China
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10
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EBRAHIMI ALI, HABIBI-KHORASANI MOSTAFA, REZAZADEH SHIVA, BEHAZIN ROYA, AZIZI ABOLFAZL. Theoretical study on the detailed repair of O6-methyl guanine to guanine by cysteine. J CHEM SCI 2015. [DOI: 10.1007/s12039-014-0724-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Sun G, Zhao L, Fan T, Li S, Zhong R. Investigations on the Effect of O6-Benzylguanine on the Formation of dG-dC Interstrand Cross-Links Induced by Chloroethylnitrosoureas in Human Glioma Cells Using Stable Isotope Dilution High-Performance Liquid Chromatography Electrospray Ionization Tandem Mass Spectrometry. Chem Res Toxicol 2014; 27:1253-62. [PMID: 24914620 DOI: 10.1021/tx500143b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Guohui Sun
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Lijiao Zhao
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Tengjiao Fan
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Sisi Li
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
| | - Rugang Zhong
- Beijing Key Laboratory of Environmental & Viral Oncology, College of Life Science and Bioengineering, Beijing University of Technology, Beijing 100124, P. R. China
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12
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Larabi R, Abtouche S, Brahimi M. Theoretical study of methyl group transfer assisted by proton transfer reaction in the N-acylated imidates. J Mol Model 2014; 20:2302. [DOI: 10.1007/s00894-014-2302-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/12/2014] [Indexed: 11/28/2022]
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13
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Torabifard H, Fattahi A. DFT study on Thiotepa and Tepa interactions with their DNA receptor. Struct Chem 2012. [DOI: 10.1007/s11224-012-0020-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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14
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Torabifard H, Fattahi A. Mechanisms and kinetics of thiotepa and tepa hydrolysis: DFT study. J Mol Model 2012; 18:3563-76. [DOI: 10.1007/s00894-012-1354-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2011] [Accepted: 01/03/2012] [Indexed: 10/28/2022]
Affiliation(s)
- Hedieh Torabifard
- Department of Chemistry, Sharif University of Technology, P.O. BOX:11365-9516, Tehran, Iran
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15
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Cui FC, Pan XL, Liu W, Liu JY. Elucidation of the methyl transfer mechanism catalyzed by chalcone O-methyltransferase: A density functional study. J Comput Chem 2011; 32:3068-74. [DOI: 10.1002/jcc.21890] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Revised: 05/17/2011] [Accepted: 06/22/2011] [Indexed: 11/07/2022]
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16
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Pegg AE. Multifaceted roles of alkyltransferase and related proteins in DNA repair, DNA damage, resistance to chemotherapy, and research tools. Chem Res Toxicol 2011; 24:618-39. [PMID: 21466232 DOI: 10.1021/tx200031q] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
O(6)-Alkylguanine-DNA alkyltransferase (AGT) is a widely distributed, unique DNA repair protein that acts as a single agent to directly remove alkyl groups located on the O(6)-position of guanine from DNA restoring the DNA in one step. The protein acts only once, and its alkylated form is degraded rapidly. It is a major factor in counteracting the mutagenic, carcinogenic, and cytotoxic effects of agents that form such adducts including N-nitroso-compounds and a number of cancer chemotherapeutics. This review describes the structure, function, and mechanism of action of AGTs and of a family of related alkyltransferase-like proteins, which do not act alone to repair O(6)-alkylguanines in DNA but link repair to other pathways. The paradoxical ability of AGTs to stimulate the DNA-damaging ability of dihaloalkanes and other bis-electrophiles via the formation of AGT-DNA cross-links is also described. Other important properties of AGTs include the ability to provide resistance to cancer therapeutic alkylating agents, and the availability of AGT inhibitors such as O(6)-benzylguanine that might overcome this resistance is discussed. Finally, the properties of fusion proteins in which AGT sequences are linked to other proteins are outlined. Such proteins occur naturally, and synthetic variants engineered to react specifically with derivatives of O(6)-benzylguanine are the basis of a valuable research technique for tagging proteins with specific reagents.
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Affiliation(s)
- Anthony E Pegg
- Department of Cellular and Molecular Physiology, Milton S. Hershey Medical Center, Pennsylvania State University College of Medicine , Pennsylvania 17033, United States.
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17
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Tiwari S, Agnihotri N, Mishra PC. Quantum theoretical study of cleavage of the glycosidic bond of 2'-deoxyadenosine: base excision-repair mechanism of DNA by MutY. J Phys Chem B 2011; 115:3200-7. [PMID: 21384840 DOI: 10.1021/jp1109256] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The enzyme adenine DNA glycosylase, also called MutY, is known to catalyze base excision repair by removal of adenine from the abnormal 2'-deoxyadenosine:8-oxo-2'-deoxyguanosine pair in DNA. The active site of the enzyme was considered to consist of a glutamic acid residue along with two water molecules. The relevant reaction mechanism involving different barrier energies was studied theoretically. Molecular geometries of the various molecules and complexes involved in the reaction, e.g., the reactant, intermediate, and product complexes as well as transition states, were optimized employing density functional theory at the B3LYP/6-31G(d,p) level in the gas phase. It was followed by single-point energy calculations at the B3LYP/AUG-cc-pVDZ, BHandHLYP/AUG-cc-pVDZ, and MP2/AUG-cc-pVDZ levels in the gas phase. Single-point energy calculations were also carried out at the B3LYP/AUG-cc-pVDZ and BHandHLYP/AUG-cc-pVDZ levels in aqueous media as well as in the solvents chlorobenzene and dichloroethane. For the solvation calculations, the integral equation formalism of the polarizable continuum model (IEF-PCM) was employed. It is found that glutamic acid along with two water molecules would effectively cleave the glycosidic bond of adenosine by a new two-step reaction mechanism proposed here which is different from the three-step mechanism proposed by other authors earlier regarding the working mechanism of MutY.
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Affiliation(s)
- Saumya Tiwari
- Department of Physics, Banaras Hindu University, Varanasi, India
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18
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Li X, Zheng QC, Zhang JL, Zhang HX. Theoretical study on the mechanism of rearrangement reaction catalyzed by N5-carboxyaminoimidazole ribonucleotide mutase. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2010.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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19
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Liao RZ, Georgieva P, Yu JG, Himo F. Mechanism of mycolic acid cyclopropane synthase: a theoretical study. Biochemistry 2011; 50:1505-13. [PMID: 21241051 DOI: 10.1021/bi101493p] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The reaction mechanism of mycolic acid cyclopropane synthase is investigated using hybrid density functional theory. The direct methylation mechanism is examined with a large model of the active site constructed on the basis of the crystal structure of the native enzyme. The important active site residue Glu140 is modeled in both ionized and neutral forms. We demonstrate that the reaction starts via the transfer of a methyl to the substrate double bond, followed by the transfer of a proton from the methyl cation to the bicarbonate present in the active site. The first step is calculated to be rate-limiting, in agreement with experimental kinetic results. The protonation state of Glu140 has a rather weak influence on the reaction energetics. In addition to the natural reaction, a possible side reaction, namely a carbocation rearrangement, is also considered and is shown to have a low barrier. Finally, the energetics for the sulfur ylide proposal, which has already been ruled out, is also estimated, showing a large energetic penalty for ylide formation.
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Affiliation(s)
- Rong-Zhen Liao
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-10691 Stockholm, Sweden
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20
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21
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Hou Q, Du L, Gao J, Liu Y, Liu C. QM/MM study on the reaction mechanism of O6-alkylguanine-DNA alkyltransferase. J Phys Chem B 2010; 114:15296-300. [PMID: 21038902 DOI: 10.1021/jp106714m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Combined quantum-mechanical/molecular-mechanical (QM/MM) approaches have been applied to investigate the detailed reaction mechanism of human O(6)-alkylguanine-DNA alkyltransferase (AGT). AGT is a direct DNA repair protein that is capable of repairing alkylated DNA by transferring the methyl group to the thiol group of a cysteine residue (Cys145) in the active site in an irreversible and stoichiometric reaction. Our QM/MM calculations reveal that the methyl group transferring step is expected to occur through two steps, in which the methyl carbocation generating step is the rate-determining step with an energy barrier of 14.4 kcal/mol at the QM/MM B3LYP/6-31G(d,p)//CHARMM22 level of theory. It is different from the previous theoretical studies based on QM calculations by using a cluster model in which the methyl group transferring step is a one-step process with a higher energy barrier.
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Affiliation(s)
- Qianqian Hou
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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22
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Georgieva P, Himo F. Quantum chemical modeling of enzymatic reactions: the case of histone lysine methyltransferase. J Comput Chem 2010; 31:1707-14. [PMID: 20082388 DOI: 10.1002/jcc.21458] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods.
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Affiliation(s)
- Polina Georgieva
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
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23
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Cui FC, Pan XL, Liu JY. Catalytic Mechanism of Hydroxynitrile Lyase from Hevea brasiliensis: A Theoretical Investigation. J Phys Chem B 2010; 114:9622-8. [DOI: 10.1021/jp100373e] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Feng-Chao Cui
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Xiao-Liang Pan
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
| | - Jing-Yao Liu
- State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun 130023, China
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24
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Idupulapati NB, Mainardi DS. Quantum Chemical Modeling of Methanol Oxidation Mechanisms by Methanol Dehydrogenase Enzyme: Effect of Substitution of Calcium by Barium in the Active Site. J Phys Chem A 2010; 114:1887-96. [DOI: 10.1021/jp9083025] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nagesh B. Idupulapati
- Institute for Micromanufacturing, Chemical Engineering Program, Louisiana Tech University, Ruston, Louisiana 71272
| | - Daniela S. Mainardi
- Institute for Micromanufacturing, Chemical Engineering Program, Louisiana Tech University, Ruston, Louisiana 71272
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25
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Jena NR, Shukla PK, Jena HS, Mishra PC, Suhai S. O6-Methylguanine Repair by O6-Alkylguanine-DNA Alkyltransferase. J Phys Chem B 2009; 113:16285-90. [DOI: 10.1021/jp907836w] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- N. R. Jena
- Division Molecular Biophysics (B020), Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India, Department of Physics, Banaras Hindu University, Varanasi-221005, India, and Department of Chemistry, Indian Institute of Technology, Guwahati-781039, Assam, India
| | - P. K. Shukla
- Division Molecular Biophysics (B020), Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India, Department of Physics, Banaras Hindu University, Varanasi-221005, India, and Department of Chemistry, Indian Institute of Technology, Guwahati-781039, Assam, India
| | - H. S. Jena
- Division Molecular Biophysics (B020), Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India, Department of Physics, Banaras Hindu University, Varanasi-221005, India, and Department of Chemistry, Indian Institute of Technology, Guwahati-781039, Assam, India
| | - P. C. Mishra
- Division Molecular Biophysics (B020), Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India, Department of Physics, Banaras Hindu University, Varanasi-221005, India, and Department of Chemistry, Indian Institute of Technology, Guwahati-781039, Assam, India
| | - S. Suhai
- Division Molecular Biophysics (B020), Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, D-69120 Heidelberg, Germany, Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India, Department of Physics, Banaras Hindu University, Varanasi-221005, India, and Department of Chemistry, Indian Institute of Technology, Guwahati-781039, Assam, India
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26
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Shukla PK, Mishra PC. Repair of O6-methylguanine to guanine by cysteine in the absence and presence of histidine and by cysteine thiolate anion: a quantum chemical study. Phys Chem Chem Phys 2009; 11:8191-202. [PMID: 19756275 DOI: 10.1039/b908295f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
O6-methylguanine (O6mG) is known to be a potential mutagenic modification of guanine as it mispairs with thymine in DNA and causes GC to AT transversion mutation. It is experimentally known that O6mG can be repaired to guanine by the protein O6-alkylguanine-DNA alkyltransferase (AGT), a cysteine residue being the main active site. In the present work, the mechanisms of repair of cis-O6-methylguanine (O6mG) to guanine due to its reaction with cysteine in the absence and presence of histidine and with cysteine thiolate anion were investigated theoretically using the B3LYP hybrid functional of density functional theory and the second order Møller-Plesset perturbation (MP2) theory. Reactant, intermediate and product complexes as well as transition states involved in these reactions were fully optimized at the B3LYP/6-31 + G* level of theory in the gas phase. The solvent effect of water was treated using the polarizable continuum model (PCM). Single point energy calculations were performed at the B3LYP/AUG-cc-pVDZ and MP2/6-31 + G* levels of theory in the gas phase and aqueous media. It is found that cysteine alone can repair the cis-O6mG to guanine, but the involvement of histidine along with cysteine lowers down the barrier energy significantly. However, when cysteine thiolate anion is used in place of cysteine, the barrier energy is strongly reduced. These results broadly support the suggestions based on experimental studies.
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Affiliation(s)
- P K Shukla
- Department of Physics, Banaras Hindu University, Varanasi - 221005, India
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27
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Tiwari S, Mishra PC. A quantum chemical study of repair of O6-methylguanine to guanine by tyrosine: evaluation of the winged helix-turn-helix model. J Mol Model 2009; 15:1407-15. [PMID: 19421793 DOI: 10.1007/s00894-009-0499-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2009] [Accepted: 04/16/2009] [Indexed: 11/24/2022]
Abstract
The winged helix-turn-helix model for the repair of O6-MeG to guanine involving the reaction of O6-MeG with a tyrosine residue of the protein O6-alkylguanine-DNA alkyltransferase (AGT) was examined by studying the reaction mechanism and barrier energies. Molecular geometries of the species and complexes involved in the reaction, i.e. the reactant, intermediate and product complexes as well as transition states, were optimized employing density functional theory in gas phase. It was followed by single point energy calculations using density functional theory along with a higher basis set and second order M(phi)ller-Plesset perturbation theory (MP2) along with two different basis sets in gas phase and aqueous media. For the solvation calculations in aqueous media, the integral equation formalism of the polarizable continuum model (IEF-PCM) was employed. Vibrational frequency analysis was performed for each optimized structure and genuineness of transition states was ensured by visualizing the vibrational modes. It is found that tyrosine can repair O6-MeG to guanine by a two-step reaction. The present results have been compared with those obtained considering the helix-turn-helix model where the repair reaction primarily involves cysteine and occurs in a single-step. It is concluded that the repair through tyrosine envisaged in the winged helix-turn-helix model would be less efficient than that through cysteine envisaged in the helix-turn-helix model.
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Affiliation(s)
- Saumya Tiwari
- Department of Physics, Banaras Hindu University, Varanasi, India
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Kamerlin SCL, Haranczyk M, Warshel A. Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies. J Phys Chem B 2009; 113:1253-72. [PMID: 19055405 PMCID: PMC2679392 DOI: 10.1021/jp8071712] [Citation(s) in RCA: 253] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Hybrid quantum mechanical/molecular mechanical (QM/MM) approaches have been used to provide a general scheme for chemical reactions in proteins. However, such approaches still present a major challenge to computational chemists, not only because of the need for very large computer time in order to evaluate the QM energy but also because of the need for proper computational sampling. This review focuses on the sampling issue in QM/MM evaluations of electrostatic energies in proteins. We chose this example since electrostatic energies play a major role in controlling the function of proteins and are key to the structure-function correlation of biological molecules. Thus, the correct treatment of electrostatics is essential for the accurate simulation of biological systems. Although we will be presenting different types of QM/MM calculations of electrostatic energies (and related properties) here, our focus will be on pKa calculations. This reflects the fact that pKa's of ionizable groups in proteins provide one of the most direct benchmarks for the accuracy of electrostatic models of macromolecules. While pKa calculations by semimacroscopic models have given reasonable results in many cases, existing attempts to perform pKa calculations using QM/MM-FEP have led to discrepancies between calculated and experimental values. In this work, we accelerate our QM/MM calculations using an updated mean charge distribution and a classical reference potential. We examine both a surface residue (Asp3) of the bovine pancreatic trypsin inhibitor and a residue buried in a hydrophobic pocket (Lys102) of the T4-lysozyme mutant. We demonstrate that, by using this approach, we are able to reproduce the relevant side chain pKa's with an accuracy of 3 kcal/mol. This is well within the 7 kcal/mol energy difference observed in studies of enzymatic catalysis, and is thus sufficient accuracy to determine the main contributions to the catalytic energies of enzymes. We also provide an overall perspective of the potential of QM/MM calculations in general evaluations of electrostatic free energies, pointing out that our approach should provide a very powerful and accurate tool to predict the electrostatics of not only solution but also enzymatic reactions, as well as the solvation free energies of even larger systems, such as nucleic acid bases incorporated into DNA.
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Affiliation(s)
- Shina C. L. Kamerlin
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
| | - Maciej Haranczyk
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Mail Stop 50F-1650, Berkeley, CA 94720-8139, USA
| | - Arieh Warshel
- Department of Chemistry, University of Southern California, 418 SGM Building, 3620 McClintock Avenue, Los Angeles, CA 90089-1062, USA
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