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Monajemi H, M Zain S, Wan Abdullah WAT. A new step in kinetic proofreading due to misacylated-tRNA during ribosomal peptide bond formation. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2021; 40:635-646. [PMID: 34047250 DOI: 10.1080/15257770.2021.1923742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 04/03/2021] [Accepted: 04/26/2021] [Indexed: 10/21/2022]
Abstract
The translational accuracy in protein synthesis is contributed to by several mechanisms in the ribosome, generally called kinetic proofreading. This process in the ribosome inhibits the non-cognate codon-anticodon interaction. However, it is not sufficient for fidelity of protein synthesis since a wrong amino acid can easily be added to the growing polypeptide chain if a tRNA while cognate to the mRNA, carries a non-cognate amino acid. Therefore, additional to the kinetic proofreading, there must be some hitherto unknown characteristic in misacylated-tRNAs to stop the process of protein synthesis if such misacylated-tRNA is accommodated in the ribosomal A-site. In order to understand this characteristic, we have performed computational quantum chemistry analysis on five different tRNA molecules, each one attached to five different amino acids with one being cognate to the tRNA and the other four non-cognate. This study shows the importance of aminoacyl-tRNA binding energy in ensuring fidelity of protein synthesis.
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Affiliation(s)
- Hadieh Monajemi
- Department of Chemistry, University of Malaya, Kuala Lumpur, Malaysia
- Data Intensive Computing Centre, Research & Innovation Complex, University of Malaya, Kuala Lumpur, Malaysia
- Department of Physics, University of Malaya, Kuala Lumpur, Malaysia
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2
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MATSUBARA T. Molecular Dynamics Study of the S<sub>N</sub>2 Reaction. How Does the Rare Event Take Place? JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2019. [DOI: 10.2477/jccj.2019-0011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Toshiaki MATSUBARA
- Department of Chemistry, Faculty of Science, Kanagawa University, 2946, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
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3
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Covalent simulations of covalent/irreversible enzyme inhibition in drug discovery: a reliable technical protocol. Future Med Chem 2018; 10:2265-2275. [DOI: 10.4155/fmc-2017-0304] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: Irreversible covalent inhibition of biological targets in disease pathogenesis is an emerging field in drug design. Computational techniques have assumed a critical role in understanding covalent enzyme inhibition. However, a gap currently exists with regards to the reliability and reproducibility of currently available protocols available in literature and open scientific forums. Methodology/results: Appropriate ligand and protein target are selected, docked covalently or noncovalently using respective docking tools. Both components are subjected to premolecular dynamic preparations. This was followed by parameterization of the ligand, protein and covalent complex, respectively. The production runs were initiated and the resulting trajectories are saved and analyzed. Conclusion: This protocol is reliable and reproducible, hence would advance the development of irreversible covalent inhibitors toward disease treatment.
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Zhao Y, She N, Zhang X, Wang C, Mo Y. Product release mechanism and the complete enzyme catalysis cycle in yeast cytosine deaminase (yCD): A computational study. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2017; 1865:1020-1029. [PMID: 28478051 DOI: 10.1016/j.bbapap.2017.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2017] [Accepted: 05/02/2017] [Indexed: 11/24/2022]
Abstract
Yeast cytosine deaminase (yCD) is critical in gene-directed enzyme prodrug therapy as it catalyzes the hydrolytic deamination of cytosine. The product (uracil) release process is considered as rate-limiting in the whole enzymatic catalysis and includes the cleavage of the uracil-metal bond and the delivery of free uracil out of the reactive site. Herein extensive combined random acceleration molecular dynamics (RAMD) and molecular dynamics (MD) simulations coupled with the umbrella sampling technique have been performed to study the product transport mechanism. Five channels have been identified, and the thermodynamic and dynamic characterizations for the two most favorable channels have been determined and analyzed. The free energy barrier for the most beneficial pathway is about 13kcal/mol and mainly results from the cleavage of hydrogen bonds between the ligand uracil and surrounding residues Asn51, Glu64, and Asp155. The conjugated rings of Phe114 and Trp152 play gating and guiding roles in the product delivery via π⋯π van der Waals interactions with the product. Finally, the full cycle of the enzymatic catalysis has been determined, making the whole process computationally more precise.
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Affiliation(s)
- Yuan Zhao
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
| | - Nai She
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China
| | - Xin Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology, Beijing 100029, China
| | - Chaojie Wang
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University, Kaifeng 475004, China.
| | - Yirong Mo
- Department of Chemistry, Western Michigan University, Kalamazoo, MI 49008, USA
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5
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Matsubara T, Ito T. Theoretical Study of the Heterolytic σ Bond Cleavage on the Ge═O Bond of Germanone. An Insight into the Driving Force from Both Electronic and Dynamical Aspects. J Phys Chem A 2017; 121:1768-1778. [DOI: 10.1021/acs.jpca.6b12478] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toshiaki Matsubara
- Department of Chemistry, Faculty of Science, Kanagawa University, 2946, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
| | - Tomoyoshi Ito
- Department of Chemistry, Faculty of Science, Kanagawa University, 2946, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
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Matsubara T, Ito T. Quantum Mechanical and Molecular Dynamics Studies of the Reaction Mechanism of the Nucleophilic Substitution at the Si Atom. J Phys Chem A 2016; 120:2636-46. [PMID: 27046773 DOI: 10.1021/acs.jpca.6b02308] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of the nucleophilic substitution at the Si atom, SiH3Cl + Cl*(-) → SiH3Cl* + Cl(-), is examined by both quantum mechanical (QM) and molecular dynamics (MD) methods. This reaction proceeds by two steps with the inversion or retention of the configuration passing through an intermediate with the trigonal bipyramid (TBP) structure, although the conventional SN2 reaction at the C atom proceeds by one step with the inversion of the configuration passing through a transition state with the TBP structure. We followed by the QM calculations all the possible paths of the substitution reaction that undergo the TBP intermediates with the cis and trans forms produced by the frontside and backside attacks of Cl(-). As a result, it was thought that TBPcis1 produced with a high probability is readily transformed to the energetically more stable TBPtrans. This fact was also shown by the MD simulations. In order to obtain more information concerning the trajectory of Cl(-) on the dissociation from TBPtrans, which we cannot clarify on the basis of the energy profile determined by the QM method, the MD simulations with and without the water solvent were conducted and analyzed in detail. The QM-MD simulations without the water solvent revealed that the dissociation of Cl(-) from TBPtrans occurs without passing through TBPcis1'. The ONIOM-MD simulations with the water solvent further suggested that the thermal fluctuation of the water solvent significantly affects the oscillation of the kinetic and potential energies of the substrate to facilitate the isomerization of the TBP intermediate from the cis form to the trans form and the subsequent dissociation of Cl(-) from TBPtrans.
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Affiliation(s)
- Toshiaki Matsubara
- Department of Chemistry, Faculty of Science, Kanagawa University , 2946, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
| | - Tomoyoshi Ito
- Department of Chemistry, Faculty of Science, Kanagawa University , 2946, Tsuchiya, Hiratsuka, Kanagawa 259-1293, Japan
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7
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Zhang X, Zhao Y, Yan H, Cao Z, Mo Y. Combined QM(DFT)/MM molecular dynamics simulations of the deamination of cytosine by yeast cytosine deaminase (yCD). J Comput Chem 2016; 37:1163-74. [DOI: 10.1002/jcc.24306] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Revised: 01/04/2016] [Accepted: 01/05/2016] [Indexed: 12/16/2022]
Affiliation(s)
- Xin Zhang
- State Key Laboratory of Chemical Resource Engineering, Institute of Materia Medica, College of Science, Beijing University of Chemical Technology; Beijing 100029 China
- Department of Chemistry; Western Michigan University; Kalamazoo Michigan 49008
| | - Yuan Zhao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University; Xiamen 360015 China
- The Key Laboratory of Natural Medicine and Immuno-Engineering, Henan University; Kaifeng 475004 China
| | - Honggao Yan
- Department of Biochemistry; The Center for Biological Modeling, Michigan State University; East Lansing Michigan 48824
- Department of Chemistry; The Center for Biological Modeling, Michigan State University; East Lansing Michigan 48824
| | - Zexing Cao
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry College of Chemistry and Chemical Engineering, Xiamen University; Xiamen 360015 China
| | - Yirong Mo
- Department of Chemistry; Western Michigan University; Kalamazoo Michigan 49008
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Abstract
Entropic effects have often been invoked to explain the extraordinary catalytic power of enzymes. In particular, the hypothesis that enzymes can use part of the substrate-binding free energy to reduce the entropic penalty associated with the subsequent chemical transformation has been very influential. The enzymatic reaction of cytidine deaminase appears to be a distinct example. Here, substrate binding is associated with a significant entropy loss that closely matches the activation entropy penalty for the uncatalyzed reaction in water, whereas the activation entropy for the rate-limiting catalytic step in the enzyme is close to zero. Herein, we report extensive computer simulations of the cytidine deaminase reaction and its temperature dependence. The energetics of the catalytic reaction is first evaluated by density functional theory calculations. These results are then used to parametrize an empirical valence bond description of the reaction, which allows efficient sampling by molecular dynamics simulations and computation of Arrhenius plots. The thermodynamic activation parameters calculated by this approach are in excellent agreement with experimental data and indeed show an activation entropy close to zero for the rate-limiting transition state. However, the origin of this effect is a change of reaction mechanism compared the uncatalyzed reaction. The enzyme operates by hydroxide ion attack, which is intrinsically associated with a favorable activation entropy. Hence, this has little to do with utilization of binding free energy to pay the entropic penalty but rather reflects how a preorganized active site can stabilize a reaction path that is not operational in solution.
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9
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 760] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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10
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Manta B, Raushel FM, Himo F. Reaction Mechanism of Zinc-Dependent Cytosine Deaminase from Escherichia coli: A Quantum-Chemical Study. J Phys Chem B 2014; 118:5644-52. [DOI: 10.1021/jp501228s] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bianca Manta
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Frank M. Raushel
- Department of Chemistry, Texas A&M University, P.O. Box 30012, College Station, Texas 77842-3012, United States
| | - Fahmi Himo
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
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11
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Monajemi H, Daud MN, Mohd Zain S, Wan Abdullah WAT. ONIOM and ab-initio calculations on the mechanism of uncatalyzed peptide bond formation. Biochem Cell Biol 2012; 90:691-700. [PMID: 23016605 DOI: 10.1139/o2012-027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Finding a proper transition structure for the peptide bond formation process can lead one to a better understanding of the role of ribosome in catalyzing this reaction. Using computer simulations, we performed the potential energy surface scan on the ester bond dissociation of P-site aminoacyl-tRNA and the peptide bond formation of P-site and A-site amino acids. The full fragments of initiator tRNA(i)(met) and elongator tRNA(phe) are attached to both cognate and non-cognate amino acids as the P-site substrate. The A-site amino acid for all four calculations is methionine. We used ONIOM calculations to reduce the computational cost. Our study illustrates the reduced rate of peptide bond formation for misacylated tRNA(i)(met) in the absence of ribosomal bases. The misacylated elongator tRNA(phe), however, did not show any difference in its PES compared with that for the phe-tRNA(phe). This demonstrates the structural specification of initiator tRNA(i)(met) for the amino acids side chain.
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Affiliation(s)
- Hadieh Monajemi
- Department of Physics, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
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12
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Monajemi H, Omar NYM, Daud MN, Zain SM, Abdullah WATW. The role of initiator tRNAimet in fidelity of initiation of protein synthesis. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2012; 30:726-39. [PMID: 21902474 DOI: 10.1080/15257770.2011.605780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
The proper arrangement of amino acids in a protein determines its proper function, which is vital for the cellular metabolism. This indicates that the process of peptide bond formation requires high fidelity. One of the most important processes for this fidelity is kinetic proofreading. As biochemical experiments suggest that kinetic proofreading plays a major role in ensuring the fidelity of protein synthesis, it is not certain whether or not a misacylated tRNA would be corrected by kinetic proofreading during the peptide bond formation. Using 2-layered ONIOM (QM/MM) computational calculations, we studied the behavior of misacylated tRNAs and compared the results with these for cognate aminoacyl-tRNAs during the process of peptide bond formation to investigate the effect of nonnative amino acids on tRNAs. The difference between the behavior of initiator tRNA(i) (met) compared to the one for the elongator tRNAs indicates that only the initiator tRNA(i) (met) specifies the amino acid side chain.
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Affiliation(s)
- Hadieh Monajemi
- Department of Physics, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
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13
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Chung LW, Hirao H, Li X, Morokuma K. The ONIOM method: its foundation and applications to metalloenzymes and photobiology. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.85] [Citation(s) in RCA: 132] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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14
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Mullin JM, Roskop LB, Pruitt SR, Collins MA, Gordon MS. Systematic fragmentation method and the effective fragment potential: an efficient method for capturing molecular energies. J Phys Chem A 2010; 113:10040-9. [PMID: 19739681 DOI: 10.1021/jp9036183] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The systematic fragmentation method fragments a large molecular system into smaller pieces, in such a way as to greatly reduce the computational cost while retaining nearly the accuracy of the parent ab initio electronic structure method. In order to attain the desired (sub-kcal/mol) accuracy, one must properly account for the nonbonded interactions between the separated fragments. Since, for a large molecular species, there can be a great many fragments and therefore a great many nonbonded interactions, computations of the nonbonded interactions can be very time-consuming. The present work explores the efficacy of employing the effective fragment potential (EFP) method to obtain the nonbonded interactions since the EFP method has been shown previously to capture nonbonded interactions with an accuracy that is often comparable to that of second-order perturbation theory. It is demonstrated that for nonbonded interactions that are not high on the repulsive wall (generally >2.7 A), the EFP method appears to be a viable approach for evaluating the nonbonded interactions. The efficacy of the EFP method for this purpose is illustrated by comparing the method to ab initio methods for small water clusters, the ZOVGAS molecule, retinal, and the alpha-helix. Using SFM with EFP for nonbonded interactions yields an error of 0.2 kcal/mol for the retinal cis-trans isomerization and a mean error of 1.0 kcal/mol for the isomerization energies of five small (120-170 atoms) alpha-helices.
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15
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Selvam L, Vasilyev V, Wang F. Methylation of Zebularine: A Quantum Mechanical Study Incorporating Interactive 3D pdf Graphs. J Phys Chem B 2009; 113:11496-504. [DOI: 10.1021/jp901678g] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lalitha Selvam
- Centre for Molecular Simulation, Swinburne University
of Technology, Hawthorn, Melbourne, Victoria 3122, Australia, National
Computational Infrastructure, Australian National University, Canberra,
ACT 0200, Australia
| | - Vladislav Vasilyev
- Centre for Molecular Simulation, Swinburne University
of Technology, Hawthorn, Melbourne, Victoria 3122, Australia, National
Computational Infrastructure, Australian National University, Canberra,
ACT 0200, Australia
| | - Feng Wang
- Centre for Molecular Simulation, Swinburne University
of Technology, Hawthorn, Melbourne, Victoria 3122, Australia, National
Computational Infrastructure, Australian National University, Canberra,
ACT 0200, Australia
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Matsubara T. Dynamical Behavior of the H2 Molecule of the PtH(H2)[P(t-Bu)3]2+ Complex. A Theory of Chemical Reactivity. J Phys Chem A 2009; 113:3227-36. [DOI: 10.1021/jp810336u] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toshiaki Matsubara
- Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima 739-8530, Japan
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17
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The Oniom Method and its Applications to Enzymatic Reactions. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2009. [DOI: 10.1007/978-1-4020-9956-4_2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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18
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Matsubara T. Application of the ONIOM-Molecular Dynamics Method to the Organometallic Reaction Cis-(H)2Pt(PR3)2 → H2 + Pt(PR3)2 (R = H, Me, Ph, and t-Bu). An Insight into the Dynamical Environmental Effects. J Phys Chem A 2008; 112:9886-94. [DOI: 10.1021/jp803070t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Toshiaki Matsubara
- Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima 739-8530, Japan
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19
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Velardez GF, Lemke HT, Breiby DW, Nielsen MM, Møller KB, Henriksen NE. Theoretical Investigation of Perylene Dimers and Excimers and Their Signatures in X-Ray Diffraction. J Phys Chem A 2008; 112:8179-87. [DOI: 10.1021/jp8016375] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Gustavo Fabián Velardez
- Center for Molecular Movies and Department of Chemistry, Technical University of Denmark (DTU), Building 207, DK-2800 Kgs. Lyngby, Denmark, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and Department of Physics, Norwegian University of Science and Technology, Høgskoleringen 5, N-7491 Trondheim, Norway
| | - Henrik T. Lemke
- Center for Molecular Movies and Department of Chemistry, Technical University of Denmark (DTU), Building 207, DK-2800 Kgs. Lyngby, Denmark, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and Department of Physics, Norwegian University of Science and Technology, Høgskoleringen 5, N-7491 Trondheim, Norway
| | - Dag W. Breiby
- Center for Molecular Movies and Department of Chemistry, Technical University of Denmark (DTU), Building 207, DK-2800 Kgs. Lyngby, Denmark, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and Department of Physics, Norwegian University of Science and Technology, Høgskoleringen 5, N-7491 Trondheim, Norway
| | - Martin M. Nielsen
- Center for Molecular Movies and Department of Chemistry, Technical University of Denmark (DTU), Building 207, DK-2800 Kgs. Lyngby, Denmark, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and Department of Physics, Norwegian University of Science and Technology, Høgskoleringen 5, N-7491 Trondheim, Norway
| | - Klaus Braagaard Møller
- Center for Molecular Movies and Department of Chemistry, Technical University of Denmark (DTU), Building 207, DK-2800 Kgs. Lyngby, Denmark, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and Department of Physics, Norwegian University of Science and Technology, Høgskoleringen 5, N-7491 Trondheim, Norway
| | - Niels E. Henriksen
- Center for Molecular Movies and Department of Chemistry, Technical University of Denmark (DTU), Building 207, DK-2800 Kgs. Lyngby, Denmark, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark, and Department of Physics, Norwegian University of Science and Technology, Høgskoleringen 5, N-7491 Trondheim, Norway
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Matsubara T, Dupuis M, Aida M. Ab Initio ONIOM−Molecular Dynamics (MD) Study on the Deamination Reaction by Cytidine Deaminase. J Phys Chem B 2007; 111:9965-74. [PMID: 17661509 DOI: 10.1021/jp072732k] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We applied the ONIOM-molecular dynamics (MD) method to the hydrolytic deamination of cytidine by cytidine deaminase, which is an essential step of the activation process of the anticancer drug inside the human body. The direct MD simulations were performed for the realistic model of cytidine deaminase by calculating the energy and its gradient by the ab initio ONIOM method on the fly. The ONIOM-MD calculations including the thermal motion show that the neighboring amino acid residue is an important factor of the environmental effects and significantly affects not only the geometry and energy of the substrate trapped in the pocket of the active site but also the elementary step of the catalytic reaction. We successfully simulate the second half of the catalytic cycle, which has been considered to involve the rate-determining step, and reveal that the rate-determining step is the release of the NH3 molecule.
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Affiliation(s)
- Toshiaki Matsubara
- Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
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21
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Matsubara T, Dupuis M, Aida M. An insight into the environmental effects of the pocket of the active site of the enzyme.Ab initio ONIOM-molecular dynamics (MD) study on cytosine deaminase. J Comput Chem 2007; 29:458-65. [PMID: 17663441 DOI: 10.1002/jcc.20805] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
We applied the ONIOM-molecular dynamics (MD) method to cytosine deaminase to examine the environmental effects of the amino acid residues in the pocket of the active site on the substrate taking account of their thermal motion. The ab initio ONIOM-MD simulations show that the substrate uracil is strongly perturbed by the amino acid residue Ile33, which sandwiches the uracil with His62, through the steric contact due to the thermal motion. As a result, the magnitude of the thermal oscillation of the potential energy and structure of the substrate uracil significantly increases.
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Affiliation(s)
- Toshiaki Matsubara
- Center for Quantum Life Sciences and Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima 739-8530, Japan.
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