1
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Wei W, Siegbahn PEM, Liao R. Mechanism of the Dinuclear Iron Enzymep‐Aminobenzoate N‐oxygenase from Density Functional Calculations. ChemCatChem 2018. [DOI: 10.1002/cctc.201801072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Wen‐Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
| | - Per E. M. Siegbahn
- Department of Organic Chemistry, Arrhenius LaboratoryStockholm University Stockholm SE-10691 Sweden
| | - Rong‐Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical EngineeringHuazhong University of Science and Technology Wuhan 430074 P. R. China
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2
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Cai X, Jiang H, Zhang T, Jiang B, Mu W, Miao M. Thermostability and Specific-Activity Enhancement of an Arginine Deiminase from Enterococcus faecalis SK23.001 via Semirational Design for l-Citrulline Production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2018; 66:8841-8850. [PMID: 30047723 DOI: 10.1021/acs.jafc.8b02858] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
l-Citrulline is a nonessential amino acid with a variety of physiological functions and can be enzymatically produced by arginine deiminase (ADI, EC 3.5.3.6). The enzymatic-production approach is of immense interest because of its mild conditions, high yield, low cost, and environmental benignity. However, the major hindrances of l-citrulline industrialization are the poor thermostability and enzyme activity of ADI. Hence, in this work, directed evolution and site-directed mutagenesis aided with in silico screening, including the use of b-factor values and HoTMuSiC, were applied to a previously identified ADI from Enterococcus faecalis SK23.001 ( EfADI), and a triple-site variant R15K-F269Y-G292P was obtained. The triple-site variant displays a 2.5-fold higher specific enzyme activity (333 U mg-1), a lower Km value of 6.4 mM, and a 6.1-fold longer half-life ( t1/2,45°C = 86.7 min) than wild-type EfADI. This work provides a protein-engineering strategy to improve enzyme activity and thermostability, which might be transferrable to other ADIs and enzymes.
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Affiliation(s)
- Xue Cai
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Hangyu Jiang
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Tao Zhang
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Bo Jiang
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
- International Joint Laboratory on Food Safety , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
- International Joint Laboratory on Food Safety , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology , Jiangnan University , Wuxi , Jiangsu 214122 , China
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3
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Fan F, Chen N, Wang Y, Wu R, Cao Z. QM/MM and MM MD Simulations on the Pyrimidine-Specific Nucleoside Hydrolase: A Comprehensive Understanding of Enzymatic Hydrolysis of Uridine. J Phys Chem B 2018; 122:1121-1131. [PMID: 29285933 DOI: 10.1021/acs.jpcb.7b10524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The pyrimidine-specific nucleoside hydrolase Yeik (CU-NH) from Escherichia coli cleaves the N-glycosidic bond of uridine and cytidine with a 102-104-fold faster rate than that of purine nucleoside substrates, such as inosine. Such a remarkable substrate specificity and the plausible hydrolytic mechanisms of uridine have been explored by using QM/MM and MM MD simulations. The present calculations show that the relatively stronger hydrogen-bond interactions between uridine and the active-site residues Gln227 and Tyr231 in CU-NH play an important role in enhancing the substrate binding and thus promoting the N-glycosidic bond cleavage, in comparison with inosine. The estimated energy barrier of 30 kcal/mol for the hydrolysis of inosine is much higher than 22 kcal/mol for uridine. Extensive MM MD simulations on the transportation of substrates to the active site of CU-NH indicate that the uridine binding is exothermic by ∼23 kcal/mol, more remarkable than inosine (∼12 kcal/mol). All of these arise from the noncovalent interactions between the substrate and the active site featured in CU-NH, which account for the substrate specificity. Quite differing from other nucleoside hydrolases, here the enzymatic N-glycosidic bond cleavage of uridine is less influenced by its protonation.
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Affiliation(s)
- Fangfang Fan
- 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
| | - Nanhao Chen
- Department of Chemistry, University of California , Davis, California 95616, United States
| | - Yongheng Wang
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, China
| | - Ruibo Wu
- School of Pharmaceutical Sciences, Sun Yat-sen University , Guangzhou 510006, China
| | - 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
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4
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Wang WJ, Wei WJ, Liao RZ. Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase. Phys Chem Chem Phys 2018; 20:15784-15794. [DOI: 10.1039/c8cp02683a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
QM/MM calculations were performed to elucidate the reaction mechanism and chemoselectivity of 2,4-QueD. The protonation state of the first-shell ligand Glu74 plays an important role in dictating the selectivity.
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Affiliation(s)
- Wen-Juan Wang
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Wen-Jie Wei
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
| | - Rong-Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage
- Ministry of Education
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica
- Hubei Key Laboratory of Materials Chemistry and Service Failure
- School of Chemistry and Chemical Engineering
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5
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Zhao C, Ling B, Dong L, Liu Y. Theoretical insights into the protonation states of active site cysteine and citrullination mechanism of Porphyromonas gingivalis peptidylarginine deiminase. Proteins 2017; 85:1518-1528. [PMID: 28486790 DOI: 10.1002/prot.25313] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 04/24/2017] [Accepted: 05/02/2017] [Indexed: 12/29/2022]
Abstract
Porphyromonas gingivalis peptidylarginine deiminase (PPAD) catalyzes the citrullination of peptidylarginine, which plays a critical role in the rheumatoid arthritis (RA) and gene regulation. For a better understanding of citrullination mechanism of PPAD, it is required to establish the protonation states of active site cysteine, which is still a controversial issue for the members of guanidino-group-modifying enzyme superfamily. In this work, we first explored the transformation between the two states: State N (both C351 and H236 are neutral) and State I (both residues exist as a thiolate-imidazolium ion pair), and then investigated the citrullination reaction of peptidylarginine, using a combined QM/MM approach. State N is calculated to be more stable than State I by 8.46 kcal/mol, and State N can transform to State I via two steps of substrate-assisted proton transfer. Citrullination of the peptidylarginine contains deamination and hydrolysis. Starting from State N, the deamination reaction corresponds to an energy barrier of 18.82 kcal/mol. The deprotonated C351 initiates the nucleophilic attack to the substrate, which is the key step for deamination reaction. The hydrolysis reaction contains two chemical steps. Both the deprotonated D238 and H236 can act as the bases to activate the hydrolytic water, which correspond to similar energy barriers (∼17 kcal/mol). On the basis of our calculations, C351, D238, and H236 constitute a catalytic triad, and their protonation states are critical for both the deamination and hydrolysis processes. In view of the sequence similarity, these findings may be shared with human PAD1-PAD4 and other guanidino-group-modifying enzymes. Proteins 2017; 85:1518-1528. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Chenxiao Zhao
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Baoping Ling
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
| | - Lihua Dong
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China.,School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, Shandong, 250013, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong, 250100, China
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6
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Sirin GS, Zhang Y. How is acetylcholinesterase phosphonylated by soman? An ab initio QM/MM molecular dynamics study. J Phys Chem A 2014; 118:9132-9. [PMID: 24786171 PMCID: PMC4183371 DOI: 10.1021/jp502712d] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
![]()
Acetylcholinesterase (AChE) is a
crucial enzyme in the cholinergic
nerve system that hydrolyzes acetylcholine (ACh) and terminates synaptic
signals by reducing the effective concentration of ACh in the synaptic
clefts. Organophosphate compounds irreversibly inhibit AChEs, leading
to irreparable damage to nerve cells. By employing Born–Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella
sampling, a state-of-the-art approach to simulate enzyme reactions,
we have characterized the covalent inhibition mechanism between AChE
and the nerve toxin soman and determined its free energy profile for
the first time. Our results indicate that phosphonylation of the catalytic
serine by soman employs an addition–elimination mechanism,
which is highly associative and stepwise: in the initial addition
step, which is also rate-limiting, His440 acts as a general base to
facilitate the nucleophilic attack of Ser200 on the soman’s
phosphorus atom to form a trigonal bipyrimidal pentacovalent intermediate;
in the subsequent elimination step, Try121 of the catalytic gorge
stabilizes the leaving fluorine atom prior to its dissociation from
the active site. Together with our previous characterization of the
aging mechanism of soman inhibited AChE, our simulations have revealed
detailed molecular mechanistic insights into the damaging function
of the nerve agent soman.
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Affiliation(s)
- Gulseher Sarah Sirin
- Sackler Institute of Graduate Biomedical Sciences, New York University School of Medicine , New York, New York 10016, United States
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7
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Mlýnský V, Banáš P, Šponer J, van der Kamp MW, Mulholland AJ, Otyepka M. Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme. J Chem Theory Comput 2014; 10:1608-22. [PMID: 26580373 DOI: 10.1021/ct401015e] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have analyzed the capability of state-of-the-art multiscale computational approaches to provide atomic-resolution electronic structure insights into possible catalytic scenarios of the hairpin ribozyme by evaluating potential and free energy surfaces of the reactions by various hybrid QM/MM methods. The hairpin ribozyme is a unique catalytic RNA that achieves rate acceleration similar to other small self-cleaving ribozymes but without direct metal ion participation. Guanine 8 (G8) and adenine 38 (A38) have been identified as the catalytically essential nucleobases. However, their exact catalytic roles are still being investigated. In line with the available experimental data, we considered two reaction scenarios involving protonated A38H(+) as a general acid which is further assisted by either canonical G8 or deprotonated G8(-) forms. We used the spin-component scaled Møller-Plesset (SCS-MP2) method at the complete basis set limit as the reference method. The semiempirical AM1/d-PhoT and SCC-DFTBPR methods provided acceptable activation barriers with respect to the SCS-MP2 data but predicted significantly different reaction pathways. DFT functionals (BLYP and MPW1K) yielded the same reaction pathway as the SCS-MP2 method. The activation barriers were slightly underestimated by the GGA BLYP functional, although with accuracy comparable to the semiempirical methods. The SCS-MP2 method and hybrid MPW1K functional gave activation barriers that were closest to those derived from experimentally measured rate constants.
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Affiliation(s)
- Vojtěch Mlýnský
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Pavel Banáš
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics , Academy of Sciences of the Czech Republic, Kralovopolska 135, 612 65 Brno, Czech Republic
- CEITEC-Central European Institute of Technology, Masaryk University , Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Marc W van der Kamp
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Adrian J Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Cantock's Close, Bristol BS8 1TS, U.K
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University , tr. 17 listopadu 12, 771 46, Olomouc, Czech Republic
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8
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Chen N, Zhou J, Li J, Xu J, Wu R. Concerted Cyclization of Lanosterol C-Ring and D-Ring Under Human Oxidosqualene Cyclase Catalysis: An ab Initio QM/MM MD Study. J Chem Theory Comput 2014; 10:1109-20. [PMID: 26580186 DOI: 10.1021/ct400949b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Nanhao Chen
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Jingwei Zhou
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Jiabo Li
- Schrödinger, LLC., 120 West 45th Street,
17th Floor, New York, New York, 10036 United States
| | - Jun Xu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
| | - Ruibo Wu
- School
of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, P.R. China
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9
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Zhao Y, Chen N, Wu R, Cao Z. A QM/MM MD study of the pH-dependent ring-opening catalysis and lid motif flexibility in glucosamine 6-phosphate deaminase. Phys Chem Chem Phys 2014; 16:18406-17. [DOI: 10.1039/c4cp01609b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
QM/MM MD and MM MD simulations reveal pH-dependent proton-shuttle ring-opening mechanisms of GlcN6P and dynamical behavior of the lid motif inSmuNagB.
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Affiliation(s)
- 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 361005, P. R. China
| | - Nanhao Chen
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, P. R. China
| | - Ruibo Wu
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, P. R. China
| | - 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 361005, P. R. China
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10
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Zhao Y, Chen N, Mo Y, Cao Z. A full picture of enzymatic catalysis by hydroxynitrile lyases from Hevea brasiliensis: protonation dependent reaction steps and residue-gated movement of the substrate and the product. Phys Chem Chem Phys 2014; 16:26864-75. [DOI: 10.1039/c4cp04032e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydroxynitrile lyases (HNLs) defend plants from herbivores and microbial attack by releasing cyanide from hydroxynitriles.
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Affiliation(s)
- 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 361005, P. R. China
| | - Nanhao Chen
- School of Pharmaceutical Sciences
- Sun Yat-sen University
- Guangzhou 510006, P. R. China
| | - Yirong Mo
- Department of Chemistry
- Western Michigan University
- Kalamazoo, USA
| | - 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 361005, P. R. China
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11
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Enhanced Sampling in Molecular Dynamics Using Metadynamics, Replica-Exchange, and Temperature-Acceleration. ENTROPY 2013. [DOI: 10.3390/e16010163] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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12
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Paasche A, Schirmeister T, Engels B. Benchmark Study for the Cysteine-Histidine Proton Transfer Reaction in a Protein Environment: Gas Phase, COSMO, QM/MM Approaches. J Chem Theory Comput 2013; 9:1765-77. [PMID: 26587634 DOI: 10.1021/ct301082y] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Proton transfer reactions are of crucial interest for the investigation of proteins. We have investigated the accuracy of commonly used quantum chemical methods for the description of proton transfer reactions in different environments (gas phase, COSMO, QM/MM) using the proton transfer between the catalytic dyad residues cysteine 145 and histidine 41 of SARS coronavirus main protease as a case study. The test includes thermodynamic, kinetic, and structural properties. The study comprises computationally demanding ab initio approaches (HF, CC2, MP2, SCS-CC2, SCS-MP2, CCSD(T)), popular density functional theories (BLYP, B3LYP, M06-2X), and semiempirical methods (MNDO/d, AM1, RM1, PM3, PM6). The approximated coupled cluster approach LCCSD(T) is taken as a reference method. We find that the robustness of the tested methods with respect to the environment correlates well with the level of theory. As an example HF, CC2, MP2, and their SCS variants show similar errors for gas phase, COSMO, or QM/MM computations. In contrast for semiempirical methods, the errors strongly diversify if one goes from gas phase to COSMO or QM/MM. Particular problems are observed for the recent semiempirical methods PM6 and RM1, which show the best performance for gas phase calculations but possess larger errors in conjunction with COSMO. Finally, a combination of SCS-MP2 and B3LYP or M06-2X allows reliable estimates about remaining errors.
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Affiliation(s)
- Alexander Paasche
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie, Johannes Gutenberg-Universität Mainz, Staudinger Weg 5, 55128 Mainz, Germany
| | - Bernd Engels
- Institut für Physikalische und Theoretische Chemie, Universität Würzburg, Emil-Fischer-Str. 42, 97074 Würzburg, Germany
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13
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Semimicroscopic investigation of active site pK a values in peptidylarginine deiminase 4. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1293-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Roca M, Aranda J, Moliner V, Tuñón I. Modeling methods for studying post-translational and transcriptional modifying enzymes. Curr Opin Chem Biol 2012; 16:465-71. [PMID: 23127358 DOI: 10.1016/j.cbpa.2012.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 09/20/2012] [Accepted: 10/11/2012] [Indexed: 10/27/2022]
Abstract
Biological catalysis is a complex chemical process that involves not only electronic reorganization in the substrate but also the reorganization of the catalyst. This complexity is even larger in the case of post-transcriptional and post-translational modifications which may involve the interaction between two biomacromolecules. However, the development over the past decades of new computational methods and strategies is offering a detailed molecular picture of the catalytic event and a deep understanding of the mechanisms of chemical reactions in biological environments. Here we review the efforts made in the last years to model catalysis in post-transcriptional and post-translational processes. We stress on the advantages and problems of the different computational strategies and their applicability in different cases.
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Affiliation(s)
- Maite Roca
- Departamento de Química Física, Universitat de València, 46100 Burjassot, Spain
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15
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Lodola A, Branduardi D, De Vivo M, Capoferri L, Mor M, Piomelli D, Cavalli A. A catalytic mechanism for cysteine N-terminal nucleophile hydrolases, as revealed by free energy simulations. PLoS One 2012; 7:e32397. [PMID: 22389698 PMCID: PMC3289653 DOI: 10.1371/journal.pone.0032397] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2011] [Accepted: 01/29/2012] [Indexed: 12/22/2022] Open
Abstract
The N-terminal nucleophile (Ntn) hydrolases are a superfamily of enzymes specialized in the hydrolytic cleavage of amide bonds. Even though several members of this family are emerging as innovative drug targets for cancer, inflammation, and pain, the processes through which they catalyze amide hydrolysis remains poorly understood. In particular, the catalytic reactions of cysteine Ntn-hydrolases have never been investigated from a mechanistic point of view. In the present study, we used free energy simulations in the quantum mechanics/molecular mechanics framework to determine the reaction mechanism of amide hydrolysis catalyzed by the prototypical cysteine Ntn-hydrolase, conjugated bile acid hydrolase (CBAH). The computational analyses, which were confirmed in water and using different CBAH mutants, revealed the existence of a chair-like transition state, which might be one of the specific features of the catalytic cycle of Ntn-hydrolases. Our results offer new insights on Ntn-mediated hydrolysis and suggest possible strategies for the creation of therapeutically useful inhibitors.
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Affiliation(s)
- Alessio Lodola
- Pharmaceutical Department, University of Parma, Parma, Italy
| | - Davide Branduardi
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
| | - Marco De Vivo
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
| | - Luigi Capoferri
- Pharmaceutical Department, University of Parma, Parma, Italy
| | - Marco Mor
- Pharmaceutical Department, University of Parma, Parma, Italy
| | - Daniele Piomelli
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
- Department of Pharmacology, University of California Irvine, Irvine, California, United States of America
| | - Andrea Cavalli
- Drug Discovery and Development, Italian Institute of Technology, Genova, Italy
- Department of Pharmaceutical Sciences, University of Bologna, Bologna, Italy
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16
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Wu R, Gong W, Liu T, Zhang Y, Cao Z. QM/MM Molecular Dynamics Study of Purine-Specific Nucleoside Hydrolase. J Phys Chem B 2012; 116:1984-91. [DOI: 10.1021/jp211403j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Ruibo Wu
- School of
Pharmaceutical Sciences,
East Campus, Sun Yat-sen University, Guangzhou
510006, China
- 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 361005, China
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Wengjin Gong
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - Ting, Liu
- 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 361005, China
| | - Yingkai Zhang
- Department
of Chemistry, New York University, New
York, New York 10003, United
States
| | - 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 361005, China
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17
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Smith GK, Ke Z, Guo H, Hengge AC. Insights into the phosphoryl transfer mechanism of cyclin-dependent protein kinases from ab initio QM/MM free-energy studies. J Phys Chem B 2011; 115:13713-22. [PMID: 21999515 DOI: 10.1021/jp207532s] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Phosphorylation reactions catalyzed by kinases and phosphatases play an indispensible role in cellular signaling, and their malfunctioning is implicated in many diseases. A better understanding of the catalytic mechanism will help design novel and effective mechanism-based inhibitors of these enzymes. In this work, ab initio quantum mechanical/molecular mechanical studies are reported for the phosphoryl transfer reaction catalyzed by a cyclin-dependent kinase, CDK2. Our results suggest that an active-site Asp residue, rather than ATP as previously proposed, serves as the general base to activate the Ser nucleophile. The corresponding transition state features a dissociative, metaphosphate-like structure, stabilized by the Mg(2+) ion and several hydrogen bonds. The calculated free-energy barrier is consistent with experimental values. Implications of our results in this and other protein kinases are discussed.
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Affiliation(s)
- Gregory K Smith
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, USA
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Bellchambers GD, Manby FR. An approximate density-functional method using the Harris-Foulkes functional. J Chem Phys 2011; 135:084105. [DOI: 10.1063/1.3625433] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Johnson CM, Monzingo AF, Ke Z, Yoon DW, Linsky TW, Guo H, Robertus JD, Fast W. On the mechanism of dimethylarginine dimethylaminohydrolase inactivation by 4-halopyridines. J Am Chem Soc 2011; 133:10951-9. [PMID: 21630706 PMCID: PMC3135753 DOI: 10.1021/ja2033684] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Small molecules capable of selective covalent protein modification are of significant interest for the development of biological probes and therapeutics. We recently reported that 2-methyl-4-bromopyridine is a quiescent affinity label for the nitric oxide controlling enzyme dimethylarginine dimethylaminohydrolase (DDAH) (Johnson, C. M.; Linsky, T. W.; Yoon, D. W.; Person, M. D.; Fast, W. J. Am. Chem. Soc. 2011, 133, 1553-1562). Discovery of this novel protein modifier raised the possibility that the 4-halopyridine motif may be suitable for wider application. Therefore, the inactivation mechanism of the related compound 2-hydroxymethyl-4-chloropyridine is probed here in more detail. Solution studies support an inactivation mechanism in which the active site Asp66 residue stabilizes the pyridinium form of the inactivator, which has enhanced reactivity toward the active site Cys, resulting in covalent bond formation, loss of the halide, and irreversible inactivation. A 2.18 Å resolution X-ray crystal structure of the inactivated complex elucidates the orientation of the inactivator and its covalent attachment to the active site Cys, but the structural model does not show an interaction between the inactivator and Asp66. Molecular modeling is used to investigate inactivator binding, reaction, and also a final pyridinium deprotonation step that accounts for the apparent differences between the solution-based and structural studies with respect to the role of Asp66. This work integrates multiple approaches to elucidate the inactivation mechanism of a novel 4-halopyridine "warhead," emphasizing the strategy of using pyridinium formation as a "switch" to enhance reactivity when bound to the target protein.
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Affiliation(s)
| | | | | | | | | | - Hua Guo
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
| | - Jon D. Robertus
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
| | - Walter Fast
- To whom correspondence should be addressed. W.F.: College of Pharmacy, PHAR-MED CHEM, 1 University Station; C0850, Austin, Texas 78712; Phone: (512) 232-4000; Fax: (512) 232-2606; ; J.D.R.: Department of Chemistry and Biochemistry, University of Texas, Austin, TX 78712. Phone: (512) 471-3175. Fax: (512) 471-6135. , and H.G.: Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, NM 87131;
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