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Zhang Q, Chen Q, Shaik S, Wang B. Flavin-N5OOH Functions as both a Powerful Nucleophile and a Base in the Superfamily of Flavoenzymes. Angew Chem Int Ed Engl 2024; 63:e202318629. [PMID: 38299700 DOI: 10.1002/anie.202318629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/02/2024]
Abstract
Flavoenzymes can mediate a large variety of oxidation reactions through the activation of oxygen. However, the O2 activation chemistry of flavin enzymes is not yet fully exploited. Normally, the O2 activation occurs at the C4a site of the flavin cofactor, yielding the flavin C4a-(hydro)hydroperoxyl species in monooxygenases or oxidases. Using extensive MD simulations, QM/MM calculations and QM calculations, our studies reveal the formation of the common nucleophilic species, Flavin-N5OOH, in two distinct flavoenzymes (RutA and EncM). Our studies show that Flavin-N5OOH acts as a powerful nucleophile that promotes C-N cleavage of uracil in RutA, and a powerful base in the deprotonation of substrates in EncM. We reason that Flavin-N5OOH can be a common reactive species in the superfamily of flavoenzymes, which accomplish generally selective general base catalysis and C-X (X=N, S, Cl, O) cleavage reactions that are otherwise challenging with solvated hydroxide ion base. These results expand our understanding of the chemistry and catalysis of flavoenzymes.
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Affiliation(s)
- Qiaoyu Zhang
- 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
| | - Qianqian Chen
- 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
| | - Sason Shaik
- Institute of Chemistry and the Lise Meitner-Minerva Center for Computational Quantum Chemistry, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
| | - Binju Wang
- 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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2
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Beal R, Valverde D, Gonçalvez PFB, Borin AC. Photophysics of tz Adenine and tz Guanine fluorescent nucleobases embedded into DNA and RNA. J Comput Chem 2023; 44:2246-2255. [PMID: 37486177 DOI: 10.1002/jcc.27194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 07/05/2023] [Accepted: 07/07/2023] [Indexed: 07/25/2023]
Abstract
UV-VIS photoinduced events of tz A and tz G embedded into DNA and RNA are described by combining the Extended Multi-State Second-Order Perturbation Theory (XMS-CASPT2) and electrostatic embedding molecular mechanics methods (QM/MM). Our results point out that the S1 1 (ππ* La ) state is the bright state in both environments. After the photoexcitation to the S1 1 (ππ* La ) state, the electronic population evolves barrierless towards its minimum, from where the excess of energy can be dissipated by fluorescence. As the minimum energy crossing point structure between the ground and first bright states lies in a high-energy region, the direct internal conversion to the ground state is an unviable mechanism. Other spectroscopic properties (for instance, absorption and Stokes shifts) and comparisons with photochemical properties of canonical nucleobases are also provided.
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Affiliation(s)
- Roiney Beal
- Grupo de Química Teórica e Computacional, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - Danillo Valverde
- Unité de Chimie Physique Théorique et Structurale, Namur Institute of Structured Matter, Université de Namur, Namur, Belgium
| | - Paulo F B Gonçalvez
- Grupo de Química Teórica e Computacional, Universidade Federal do Rio Grande do Sul-UFRGS, Porto Alegre, RS, Brazil
| | - Antonio Carlos Borin
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, SP, Brazil
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Paul A, Mishra S. Deciphering the role of the two metal-binding sites of DapE enzyme via metal substitution. Comput Biol Chem 2023; 103:107832. [PMID: 36805170 DOI: 10.1016/j.compbiolchem.2023.107832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 02/16/2023]
Abstract
DapE is a microbial metalloenzyme that hosts two Zn ions in its active site, although it shows catalytic activity with varying efficiency when the Zn ions in one or both of its metal-binding sites (MBS) are replaced by other transition-metal ions. The metal-ion promiscuity of DapE is believed to be a microbial strategy to overcome the homeostatic regulation of Zn ions by the mammalian host. Here, a hybrid QM/MM study is performed on a series of mixed-metal DapEs, where the Zn ion in the first MBS (MBS-1) is substituted by Mn, Co, Ni, and Cu ions, while the MBS-2 is occupied by Zn(II). The substrate binding affinity and the mechanism of catalytic action are estimated by optimizing the intermediates and the transition states with hybrid QM/MM method. Comparison of the binding affinity of the MBS-1 and MBS-2 substituted DapEs reveals that the MBS-1 substitution does not affect the substrate binding affinity in the mixed-metal DapEs, while a strong metal specificity was observed in MBS-2 substituted DapEs. On the contrary, the activation energy barriers show a high metal specificity at MBS-1 compared to MBS-2. Taken together, the QM/MM studies indicate that MBS-2 leads the substrate binding process, while MBS-1 steers the catalytic activity of the DapE enzyme.
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Affiliation(s)
- Atanuka Paul
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India
| | - Sabyashachi Mishra
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, India.
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Canyelles-Niño M, González-Lafont À, Lluch JM. Hydroperoxidation of Docosahexaenoic Acid by Human ALOX12 and pigALOX15-mini-LOX. Int J Mol Sci 2023; 24:ijms24076064. [PMID: 37047037 PMCID: PMC10094721 DOI: 10.3390/ijms24076064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/15/2023] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Human lipoxygenase 12 (hALOX12) catalyzes the conversion of docosahexaenoic acid (DHA) into mainly 14S-hydroperoxy-4Z,7Z,10Z,12E,16Z,19Z-docosahexaenoic acid (14S-H(p)DHA). This hydroperoxidation reaction is followed by an epoxidation and hydrolysis process that finally leads to maresin 1 (MaR1), a potent bioactive specialized pro-resolving mediator (SPM) in chronic inflammation resolution. By combining docking, molecular dynamics simulations, and quantum mechanics/molecular mechanics calculations, we have computed the potential energy profile of DHA hydroperoxidation in the active site of hALOX12. Our results describe the structural evolution of the molecular system at each step of this catalytic reaction pathway. Noteworthy, the required stereospecificity of the reaction leading to MaR1 is explained by the configurations adopted by DHA bound to hALOX12, along with the stereochemistry of the pentadienyl radical formed after the first step of the mechanism. In pig lipoxygenase 15 (pigALOX15-mini-LOX), our calculations suggest that 14S-H(p)DHA can be formed, but with a stereochemistry that is inadequate for MaR1 biosynthesis.
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Affiliation(s)
- Miquel Canyelles-Niño
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Arquebio SL, Carrer de Álava 51, 08005 Barcelona, Spain
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - José M Lluch
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Institut de Biotecnologia i Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
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Manna RN, Onuchic JN, Jana B. Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control. Proc Natl Acad Sci U S A 2023; 120:e2215170120. [PMID: 36574689 DOI: 10.1073/pnas.2215170120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Kinesin motor proteins perform several essential cellular functions powered by the adenosine triphosphate (ATP) hydrolysis reaction. Several single-point mutations in the kinesin motor protein KIF5A have been implicated to hereditary spastic paraplegia disease (HSP), a lethal neurodegenerative disease in humans. In earlier studies, we have shown that a series of HSP-related mutations can impair the kinesin's long-distance displacement or processivity by modulating the order-disorder transition of the linker connecting the heads to the coiled coil. On the other hand, the reduction of kinesin's ATP hydrolysis reaction rate by a distal asparagine-to-serine mutation is also known to cause HSP disease. However, the molecular mechanism of the ATP hydrolysis reaction in kinesin by this distal mutation is still not fully understood. Using classical molecular dynamics simulations combined with quantum mechanics/molecular mechanics calculations, the pre-organization geometry required for optimal hydrolysis in kinesin motor bound to α/β-tubulin is determined. This optimal geometry has only a single salt-bridge (of the possible two) between Arg203-Glu236, putting a reactive water molecule at a perfect position for hydrolysis. Such geometry is also needed to create the appropriate configuration for proton translocation during ATP hydrolysis. The distal asparagine-to-serine mutation is found to disrupt this optimal geometry. Therefore, the current study along with our previous one demonstrates how two different effects on kinesin dynamics (processivity and ATP hydrolysis), caused by a different set of genotypes, can give rise to the same phenotype leading to HSP disease.
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Matsunaga Y, Kamiya M, Oshima H, Jung J, Ito S, Sugita Y. Use of multistate Bennett acceptance ratio method for free-energy calculations from enhanced sampling and free-energy perturbation. Biophys Rev 2022; 14:1503-1512. [PMID: 36659993 PMCID: PMC9842838 DOI: 10.1007/s12551-022-01030-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 12/01/2022] [Indexed: 12/15/2022] Open
Abstract
Multistate Bennett acceptance ratio (MBAR) works as a method to analyze molecular dynamics (MD) simulation data after the simulations have been finished. It is widely used to estimate free-energy changes between different states and averaged properties at the states of interest. MBAR allows us to treat a wide range of states from those at different temperature/pressure to those with different model parameters. Due to the broad applicability, the MBAR equations are rather difficult to apply for free-energy calculations using different types of MD simulations including enhanced conformational sampling methods and free-energy perturbation. In this review, we first summarize the basic theory of the MBAR equations and categorize the representative usages into the following four: (i) perturbation, (ii) scaling, (iii) accumulation, and (iv) full potential energy. For each, we explain how to prepare input data using MD simulation trajectories for solving the MBAR equations. MBAR is also useful to estimate reliable free-energy differences using MD trajectories based on a semi-empirical quantum mechanics/molecular mechanics (QM/MM) model and ab initio QM/MM energy calculations on the MD snapshots. We also explain how to use the MBAR software in the GENESIS package, which we call mbar_analysis, for the four representative cases. The proposed estimations of free-energy changes and thermodynamic averages are effective and useful for various biomolecular systems.
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Affiliation(s)
- Yasuhiro Matsunaga
- grid.263023.60000 0001 0703 3735Graduate School of Science and Engineering, Saitama University, Saitama, Saitama 338-8570 Japan
| | - Motoshi Kamiya
- grid.467196.b0000 0001 2285 6123Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585 Japan
| | - Hiraku Oshima
- grid.508743.dLaboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047 Japan
| | - Jaewoon Jung
- grid.474693.bComputational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047 Japan
| | - Shingo Ito
- grid.7597.c0000000094465255Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
| | - Yuji Sugita
- grid.508743.dLaboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo 650-0047 Japan ,grid.474693.bComputational Biophysics Research Team, RIKEN Center for Computational Science, Kobe, Hyogo 650-0047 Japan ,grid.7597.c0000000094465255Theoretical Molecular Science Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198 Japan
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Kardam V, Kalita S, Dubey KD. Computations reveal a crucial role of an aromatic dyad in the catalytic function of plant cytochrome P450 mint superfamily. J Inorg Biochem 2022; 237:111990. [PMID: 36115330 DOI: 10.1016/j.jinorgbio.2022.111990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/27/2022] [Accepted: 08/31/2022] [Indexed: 01/18/2023]
Abstract
Enzymes are highly specific for their native functions, however with advances in bioengineering tools such as directed evolution, several enzymes are being repurposed for the secondary function of contemporary significance(Khersonsky and Tawfik, 2010 [1]). Due to the functional versatility, the Cytochrome P450 (CYP450) superfamily has become the ideal scaffold for such bioengineering. In the current study, using MD (molecular dynamics) simulations and hybrid QM/MM (Quantum mechanics/molecular mechanics) calculations, we have studied the mechanism of spontaneous emergence of a secondary function due to a single site mutation in two plant CYP450 enzymes from the mint family. The MD simulations of WT (wild type) CYP71D18 and CYP71D13 enzymes and their variants show a crucial gating mechanism by aromatic dyad formed by Phe121 and Phe363 which regulates the substrate recognition. The QM/MM calculations reveal that the hydroxylation reactions at C3 and C6 positions in WT CYP71D18 and CYP71D13 enzymes as well as their variants follow a hydrogen atom transfer (HAT) followed by a single electron transfer (SET) mechanism, which is different from the typical rebound mechanism shown by most of the CYP450 enzymes.
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Affiliation(s)
- Vandana Kardam
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Delhi-NCR, NH91, Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Surajit Kalita
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Delhi-NCR, NH91, Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Sciences, Shiv Nadar Institution of Eminence Delhi-NCR, NH91, Tehsil Dadri, Greater Noida, Uttar Pradesh 201314, India.
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Sosa Alfaro V, Waheed SO, Palomino H, Knorrscheidt A, Weissenborn M, Christov CZ, Lehnert N. YfeX - A New Platform for Carbene Transferase Development with High Intrinsic Reactivity. Chemistry 2022; 28:e202201474. [PMID: 35948517 PMCID: PMC9691539 DOI: 10.1002/chem.202201474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Indexed: 01/11/2023]
Abstract
Carbene transfer biocatalysis has evolved from basic science to an area with vast potential for the development of new industrial processes. In this study, we show that YfeX, naturally a peroxidase, has great potential for the development of new carbene transferases, due to its high intrinsic reactivity, especially for the N-H insertion reaction of aromatic and aliphatic primary and secondary amines. YfeX shows high stability against organic solvents (methanol and DMSO), greatly improving turnover of hydrophobic substrates. Interestingly, in styrene cyclopropanation, WT YfeX naturally shows high enantioselectivity, generating the trans product with 87 % selectivity for the (R,R) enantiomer. WT YfeX also catalyzes the Si-H insertion efficiently. Steric effects in the active site were further explored using the R232A variant. Quantum Mechanics/Molecular Mechanics (QM/MM) calculations reveal details on the mechanism of Si-H insertion. YfeX, and potentially other peroxidases, are exciting new targets for the development of improved carbene transferases.
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Affiliation(s)
- Victor Sosa Alfaro
- Department of Chemistry and Department of BiophysicsUniversity of MichiganAnn Arbor, Michigan48109–1055United States
| | - Sodiq O. Waheed
- Department of ChemistryMichigan Technological UniversityHoughton, Michigan49931United States
| | - Hannah Palomino
- Department of Chemistry and Department of BiophysicsUniversity of MichiganAnn Arbor, Michigan48109–1055United States
| | - Anja Knorrscheidt
- Institute of ChemistryMartin-Luther-University Halle-WittenbergKurt-Mothes-Str. 206120HalleGermany
| | - Martin Weissenborn
- Institute of ChemistryMartin-Luther-University Halle-WittenbergKurt-Mothes-Str. 206120HalleGermany
| | - Christo Z. Christov
- Department of ChemistryMichigan Technological UniversityHoughton, Michigan49931United States
| | - Nicolai Lehnert
- Department of Chemistry and Department of BiophysicsUniversity of MichiganAnn Arbor, Michigan48109–1055United States
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Tripathi A, Dutta Dubey K. Combined MD and QM/MM Calculations Reveal Allostery-Driven Promiscuity in Dipeptide Epimerases of Enolase Family. Chem Asian J 2022; 17:e202200528. [PMID: 35722826 DOI: 10.1002/asia.202200528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 06/19/2022] [Indexed: 11/10/2022]
Abstract
The adaptability of the active site to amplify the secondary function is supposed to be the fundamental cause of the promiscuity and the evolution of new functions in enzymes. In most cases, mutations occur close to the active site and/or in the catalytic site to change the active site plasticity to accommodate the non-native substrate. In the present study, using MD simulations and hybrid QM/MM calculations, we have shown a way to enhance the promiscuity, i. e., the allostery-driven promiscuity. Using a case study of the AEE enzyme where the capping loop recognizes the substrate, herein, we show that a single site mutation (D321G) far from the capping loop can induce a large conformational change in the capping loop to recognize different substrates for different functions. The QM/MM calculations for the WT and mutated enzyme provide a first validation of the mechanism of 1,1-proton transfer and dehydration by the AEE enzyme. Since AEE epimerase possesses a highly conserved TIM-barrel fold, we believe that our study provides a crucial lead to understanding the mechanism of emergence of secondary function which can be useful to repurpose ancient enzymes for modern usage.
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Affiliation(s)
- Ankita Tripathi
- Department of Chemistry, School of Natural Science, Shiv Nadar University Delhi-NCR, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh, 201314, India
| | - Kshatresh Dutta Dubey
- Department of Chemistry, School of Natural Science, Shiv Nadar University Delhi-NCR, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh, 201314, India.,Center for Informatics, Department of Chemistry, School of Natural Science, Shiv Nadar University Delhi-NCR, NH91 Tehsil Dadri, Greater Noida, Uttar Pradesh, 201314, India
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Fu Y, Fan F, Wang B, Cao Z. Water-Regulated Mechanisms for Degradation of Pesticides Paraoxon and Parathion by Phosphotriesterase: Insight from QM/MM and MD Simulations. Chem Asian J 2022; 17:e202200439. [PMID: 35586954 DOI: 10.1002/asia.202200439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/12/2022] [Indexed: 11/06/2022]
Abstract
The enzymatic degradation of pesticides paraoxon (PON) and parathion (PIN) by phosphotriesterase (PTE) has been investigated by QM/MM calculations and MD simulations. In the PTE-PON complex, Zn α and Zn β in the active site are five- and six-coordinated, respectively, while both zinc ions are six coordinated with the Zn α -bound water molecule (WT1) for the PTE-PIN system. The hydrolytic reactions for PON and PIN are respectively driven by the nucleophilic attack of the bridging-OH - and the Zn α -bound water molecule on the phosphorus center of substrate, and the two-step hydrolytic process is predicted to be the rate-limiting step with the energy spans of 13.8 and 14.4 kcal/mol for PON and PIN, respectively. The computational studies reveal that the presence of the Zn α -bound water molecule depends on the structural feature of substrates characterized by P=O and P=S, which determines the hydrolytic mechanism and efficiency for the degradation of organophosphorus pesticides by PTE.
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Affiliation(s)
- Yuzhuang Fu
- Xiamen University, Department of Chemistry, CHINA
| | - Fangfang Fan
- Zhejiang University of Science and Technology, School of Biological and Chemical Engineering, CHINA
| | - Binju Wang
- Xiamen University, Department of Chemistry, CHINA
| | - Zexing Cao
- Xiamen University, Department of Chemistry, Si Ming Nan Lu, 361005, Xiamen, CHINA
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Canyelles-Niño M, González-Lafont À, Lluch JM. Theoretical Characterization of the Step-by-Step Mechanism of Conversion of Leukotriene A 4 to Leukotriene B 4 Catalysed by the Enzyme Leukotriene A 4 Hydrolase. Int J Mol Sci 2022; 23:ijms23063140. [PMID: 35328561 PMCID: PMC8954237 DOI: 10.3390/ijms23063140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/09/2022] [Accepted: 03/11/2022] [Indexed: 12/01/2022] Open
Abstract
LTA4H is a bifunctional zinc metalloenzyme that converts leukotriene A4 (LTA4) into leukotriene B4 (LTB4), one of the most potent chemotactic agents involved in acute and chronic inflammatory diseases. In this reaction, LTA4H acts as an epoxide hydrolase with a unique and fascinating mechanism, which includes the stereoselective attachment of one water molecule to the carbon backbone of LTA4 several methylene units away from the epoxide moiety. By combining Molecular Dynamics simulations and Quantum Mechanics/Molecular Mechanics calculations, we obtained a very detailed molecular picture of the different consecutive steps of that mechanism. By means of a rather unusual 1,7-nucleophilic substitution through a clear SN1 mechanism, the epoxide opens and the triene moiety of the substrate twists in such a way that the bond C6-C7 adopts its cis (Z) configuration, thus exposing the R face of C12 to the addition of a water molecule hydrogen-bonded to ASP375. Thus, the two stereochemical features that are required for the bioactivity of LTB4 appear to be closely related. The noncovalent π-π stacking interactions between the triene moiety and two tyrosines (TYR267 and, especially, TYR378) that wrap the triene system along the whole reaction explain the preference for the cis configuration inside LTA4H.
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Affiliation(s)
- Miquel Canyelles-Niño
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; (M.C.-N.); (À.G.-L.)
- Biochemize SL, Carrer de Zamora, 45, 08005 Barcelona, Barcelona, Spain
| | - Àngels González-Lafont
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; (M.C.-N.); (À.G.-L.)
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - José M. Lluch
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain; (M.C.-N.); (À.G.-L.)
- Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Correspondence:
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Varghese A, Chaturvedi SS, DiCastri B, Mehler E, Fields GB, Karabencheva-Christova TG. Effects of the Nature of the Metal Ion, Protein and Substrate on the Catalytic Center in Matrix Metalloproteinase-1: Insights from Multilevel MD, QM/MM and QM Studies. Chemphyschem 2021; 23:10.1002/cphc.202100680. [PMID: 35991515 PMCID: PMC9387770 DOI: 10.1002/cphc.202100680] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Indexed: 11/06/2022]
Abstract
Matrix metalloproteinase-1 (MMP-1) is a Zn(II) dependent endopeptidase involved in the degradation of collagen, the most abundant structural protein in the extracellular matrix of connective tissues and the human body. Herein we performed a multilevel computational analysis including molecular dynamics (MD), combined quantum mechanics/molecular mechanics (QM/MM), and quantum mechanics (QM) calculations to characterize the structure and geometry of the catalytic Zn(II) within the MMP-1 protein environment in comparison to crystallographic and spectroscopic data. The substrate's removal fine-tuned impact on the conformational dynamics and geometry of the catalytic Zn(II) center was also explored. Finally, the study examined the effect of substituting catalytic Zn(II) by Co(II) on the overall structure and dynamics of the MMP-1 THP complex and specifically on the geometry of the catalytic metal center. Overall our QM/MM and QM studies were in good agreement with the MM description of the Zn(II) centers in the MD simulations.
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Affiliation(s)
- Ann Varghese
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Shobhit S Chaturvedi
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Bella DiCastri
- Department of Chemistry, Michigan Technological University, Houghton, Michigan 49931
| | - Emerald Mehler
- Department of Chemical Engineering, Michigan Technological University, Houghton, Michigan 49931
| | - Gregg B Fields
- Department of Chemistry and Biochemistry and I-HEALTH, Florida Atlantic University, Jupiter, Florida 33458
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Jiang Y, Peng W, Li Z, You C, Zhao Y, Tang D, Wang B, Li S. Unexpected Reactions of α,β-Unsaturated Fatty Acids Provide Insight into the Mechanisms of CYP152 Peroxygenases. Angew Chem Int Ed Engl 2021; 60:24694-24701. [PMID: 34523786 DOI: 10.1002/anie.202111163] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/06/2021] [Indexed: 11/08/2022]
Abstract
CYP152 peroxygenases catalyze decarboxylation and hydroxylation of fatty acids using H2 O2 as cofactor. To understand the molecular basis for the chemo- and regioselectivity of these unique P450 enzymes, we analyze the activities of three CYP152 peroxygenases (OleTJE , P450SPα , P450BSβ ) towards cis- and trans-dodecenoic acids as substrate probes. The unexpected 6S-hydroxylation of the trans-isomer and 4R-hydroxylation of the cis-isomer by OleTJE , and molecular docking results suggest that the unprecedented selectivity is due to OleTJE 's preference of C2-C3 cis-configuration. In addition to the common epoxide products, undecanal is the unexpected major product of P450SPα and P450BSβ regardless of the cis/trans-configuration of substrates. The combined H2 18 O2 tracing experiments, MD simulations, and QM/MM calculations unravel an unusual mechanism for Compound I-mediated aldehyde formation in which the active site water derived from H2 O2 activation is involved in the generation of a four-membered ring lactone intermediate. These findings provide new insights into the unusual mechanisms of CYP152 peroxygenases.
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Affiliation(s)
- Yuanyuan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China.,Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Peng
- 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
| | - Zhong Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China.,Shandong Provincial Key Laboratory of Synthetic Biology, CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, No. 189 Songling Road, Qingdao, Shandong, 266101, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Cai You
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Yue Zhao
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, China
| | - Dandan Tang
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China
| | - Binju Wang
- 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
| | - Shengying Li
- State Key Laboratory of Microbial Technology, Shandong University, No. 72 Binhai Road, Qingdao, Shandong, 266237, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, 266237, China
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14
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Ramanan R, Waheed SO, Schofield CJ, Christov CZ. What Is the Catalytic Mechanism of Enzymatic Histone N-Methyl Arginine Demethylation and Can It Be Influenced by an External Electric Field? Chemistry 2021; 27:11827-11836. [PMID: 33989435 DOI: 10.1002/chem.202101174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Indexed: 11/11/2022]
Abstract
Arginine methylation is an important mechanism of epigenetic regulation. Some Fe(II) and 2-oxoglutarate dependent Jumonji-C (JmjC) Nϵ-methyl lysine histone demethylases also have N-methyl arginine demethylase activity. We report combined molecular dynamic (MD) and Quantum Mechanical/Molecular Mechanical (QM/MM) studies on the mechanism of N-methyl arginine demethylation by human KDM4E and compare the results with those reported for N-methyl lysine demethylation by KDM4A. At the KDM4E active site, Glu191, Asn291, and Ser197 form a conserved scaffold that restricts substrate dynamics; substrate binding is also mediated by an out of active site hydrogen-bond between the substrate Ser1 and Tyr178. The calculations imply that in either C-H or N-H potential bond cleaving pathways for hydrogen atom transfer (HAT) during N-methyl arginine demethylation, electron transfer occurs via a σ-channel; the transition state for the N-H pathway is ∼10 kcal/mol higher than for the C-H pathway due to the higher bond dissociation energy of the N-H bond. The results of applying external electric fields (EEFs) reveal EEFs with positive field strengths parallel to the Fe=O bond have a significant barrier-lowering effect on the C-H pathway, by contrast, such EEFs inhibit the N-H activation rate. The overall results imply that KDM4 catalyzed N-methyl arginine demethylation and N-methyl lysine demethylation occur via similar C-H abstraction and rebound mechanisms leading to methyl group hydroxylation, though there are differences in the interactions leading to productive binding of intermediates.
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Affiliation(s)
- Rajeev Ramanan
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA.,Present address: Department of Chemistry, National Institute of Technology, Rourkela, Odisha, 769001, India
| | - Sodiq O Waheed
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
| | - Christopher J Schofield
- The Department of Chemistry and the Ineos Oxford Institute for, Antimicrobial Research, The Chemistry Research Laboratory, University of Oxford, Mansfield Road, OX1 5JJ, Oxford, UK
| | - Christo Z Christov
- Department of Chemistry, Michigan Technological University, Houghton, Michigan, 49931, USA
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15
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Wang R, Tao W, Liu L, Li C, Bai L, Zhao YL, Shi T. Insights into specificity and catalytic mechanism of amphotericin B/nystatin thioesterase. Proteins 2021; 89:558-568. [PMID: 33389775 DOI: 10.1002/prot.26041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/22/2020] [Accepted: 12/27/2020] [Indexed: 11/12/2022]
Abstract
Polyene polyketides amphotericin B (AMB) and nystatin (NYS) are important antifungal drugs. Thioesterases (TEs), located at the last module of PKS, control the release of polyketides by cyclization or hydrolysis. Intrigued by the tiny structural difference between AMB and NYS, as well as the high sequence identity between AMB TE and NYS TE, we constructed four systems to study the structural characteristics, catalytic mechanism, and product release of AMB TE and NYS TE with combined MD simulations and quantum mechanics/molecular mechanics calculations. The results indicated that compared with AMB TE, NYS TE shows higher specificity on its natural substrate and R26 as well as D186 were proposed to a key role in substrate recognition. The energy barrier of macrocyclization in AMB-TE-Amb and AMB-TE-Nys systems were calculated to be 14.0 and 22.7 kcal/mol, while in NYS-TE-Nys and NYS-TE-Amb systems, their energy barriers were 17.5 and 25.7 kcal/mol, suggesting the cyclization with their natural substrates were more favorable than that with exchanged substrates. At last, the binding free energy obtained with the MM-PBSA.py program suggested that it was easier for natural products to leave TE enzymes after cyclization. And key residues to the departure of polyketide product from the active site were highlighted. We provided a catalytic overview of AMB TE and NYS TE including substrate recognition, catalytic mechanism and product release. These will improve the comprehension of polyene polyketide TEs and benefit for broadening the substrate flexibility of polyketide TEs.
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Affiliation(s)
- Rufan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wentao Tao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lei Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen Li
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Linquan Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yi-Lei Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Shi
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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16
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Phintha A, Prakinee K, Jaruwat A, Lawan N, Visitsatthawong S, Kantiwiriyawanitch C, Songsungthong W, Trisrivirat D, Chenprakhon P, Mulholland A, van Pée KH, Chitnumsub P, Chaiyen P. Dissecting the low catalytic capability of flavin-dependent halogenases. J Biol Chem 2021; 296:100068. [PMID: 33465708 PMCID: PMC7948982 DOI: 10.1074/jbc.ra120.016004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/11/2020] [Accepted: 11/13/2020] [Indexed: 12/11/2022] Open
Abstract
Although flavin-dependent halogenases (FDHs) are attractive biocatalysts, their practical applications are limited because of their low catalytic efficiency. Here, we investigated the reaction mechanisms and structures of tryptophan 6-halogenase (Thal) from Streptomyces albogriseolus using stopped-flow, rapid-quench flow, quantum/mechanics molecular mechanics calculations, crystallography, and detection of intermediate (hypohalous acid [HOX]) liberation. We found that the key flavin intermediate, C4a-hydroperoxyflavin (C4aOOH-FAD), formed by Thal and other FDHs (tryptophan 7-halogenase [PrnA] and tryptophan 5-halogenase [PyrH]), can react with I-, Br-, and Cl- but not F- to form C4a-hydroxyflavin and HOX. Our experiments revealed that I- reacts with C4aOOH-FAD the fastest with the lowest energy barrier and have shown for the first time that a significant amount of the HOX formed leaks out as free HOX. This leakage is probably a major cause of low product coupling ratios in all FDHs. Site-saturation mutagenesis of Lys79 showed that changing Lys79 to any other amino acid resulted in an inactive enzyme. However, the levels of liberated HOX of these variants are all similar, implying that Lys79 probably does not form a chloramine or bromamine intermediate as previously proposed. Computational calculations revealed that Lys79 has an abnormally lower pKa compared with other Lys residues, implying that the catalytic Lys may act as a proton donor in catalysis. Analysis of new X-ray structures of Thal also explains why premixing of FDHs with reduced flavin adenine dinucleotide generally results in abolishment of C4aOOH-FAD formation. These findings reveal the hidden factors restricting FDHs capability which should be useful for future development of FDHs applications.
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Affiliation(s)
- Aisaraphon Phintha
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Kridsadakorn Prakinee
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Aritsara Jaruwat
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Narin Lawan
- Department of Chemistry, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Surawit Visitsatthawong
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Chadaporn Kantiwiriyawanitch
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Warangkhana Songsungthong
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand
| | - Duangthip Trisrivirat
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand
| | - Pirom Chenprakhon
- Institute for Innovative Learning, Mahidol University, Nakhon Pathom, Thailand
| | - Adrian Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol, UK
| | - Karl-Heinz van Pée
- General Biochemistry, Faculty of Chemistry and Food Chemistry, Technical University of Dresden, Dresden, Germany
| | - Penchit Chitnumsub
- Biomolecular Analysis and Application Research Team, National Center for Genetic Engineering and Biotechnology, Klong Luang, Pathumthani, Thailand.
| | - Pimchai Chaiyen
- Department of Biochemistry and Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand; School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong, Thailand.
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17
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Hernández-Rodríguez EW, Escorcia AM, van der Kamp MW, Montero-Alejo AL, Caballero J. Multi-scale simulation reveals that an amino acid substitution increases photosensitizing reaction inputs in Rhodopsins. J Comput Chem 2020; 41:2278-2295. [PMID: 32757375 DOI: 10.1002/jcc.26392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 06/27/2020] [Accepted: 07/04/2020] [Indexed: 11/11/2022]
Abstract
Evaluating the availability of molecular oxygen (O2 ) and energy of excited states in the retinal binding site of rhodopsin is a crucial challenging first step to understand photosensitizing reactions in wild-type (WT) and mutant rhodopsins by absorbing visible light. In the present work, energies of the ground and excited states related to 11-cis-retinal and the O2 accessibility to the β-ionone ring are evaluated inside WT and human M207R mutant rhodopsins. Putative O2 pathways within rhodopsins are identified by using molecular dynamics simulations, Voronoi-diagram analysis, and implicit ligand sampling while retinal energetic properties are investigated through density functional theory, and quantum mechanical/molecular mechanical methods. Here, the predictions reveal that an amino acid substitution can lead to enough energy and O2 accessibility in the core hosting retinal of mutant rhodopsins to favor the photosensitized singlet oxygen generation, which can be useful in understanding retinal degeneration mechanisms and in designing blue-lighting-absorbing proteic photosensitizers.
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Affiliation(s)
- Erix W Hernández-Rodríguez
- Laboratorio de Bioinformática y Química Computacional, Escuela de Química y Farmacia, Facultad de Medicina, Universidad Católica del Maule, Talca, Chile
| | - Andrés M Escorcia
- School of Biochemistry, University of Bristol, University Walk, Bristol, UK
| | | | - Ana L Montero-Alejo
- Departamento de Física, Facultad de Ciencias Naturales, Matemática y del Medio Ambiente (FCNMM), Universidad Tecnológica Metropolitana, Santiago, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Talca, Chile
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18
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Šebesta F, Šebera J, Sychrovský V, Tanaka Y, Burda JV. QM and QM/MM umbrella sampling MD study of the formation of Hg(II)-thymine bond: Model for evaluation of the reaction energy profiles in solutions with constant pH. J Comput Chem 2020; 41:1509-1520. [PMID: 32208552 DOI: 10.1002/jcc.26194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/24/2020] [Accepted: 02/28/2020] [Indexed: 01/01/2023]
Abstract
The formation of the Hg-N3(T) bond between the 1-methylthymine (T) molecule and the hydrated Hg2+ cation was explored with the combined quantum mechanics/molecular mechanics (QM/MM) method including Free Energy Perturbation corrections. The thermodynamic properties were determined in the whole pH range, when these systems were explicitly investigated and considered as the QM part: (1) T + [Hg(H2 O)6 ]2+ , (2) T + [Hg(H2 O)5 (OH)]+ , (3) T + Hg(H2 O)4 (OH)2 , and (4) N3-deprotonated T + Hg(H2 O)4 (OH)2 . The MM part contained only solvent molecules and counterions. As a result, the dependence of Gibbs-Alberty reaction free energy on pH was obtained along the reaction coordinate. We found that an endoergic reaction in acidic condition up to pH < 4-5 becomes exoergic for a higher pH corresponding to neutral and basic solutions. The migration of the Hg2+ cation between N3 and O4/2 positions in dependence on pH is discussed as well. For the verification, DFT calculations of stationary points were performed confirming the qualitative trends of QM/MM MD simulations and NMR parameters were determined for them.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
| | - Jakub Šebera
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Yoshiyuki Tanaka
- Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Japan
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic
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Stensitzki T, Adam S, Schlesinger R, Schapiro I, Heyne K. Ultrafast Backbone Protonation in Channelrhodopsin-1 Captured by Polarization Resolved Fs Vis-pump-IR-Probe Spectroscopy and Computational Methods. Molecules 2020; 25:E848. [PMID: 32075128 DOI: 10.3390/molecules25040848] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/03/2020] [Accepted: 02/12/2020] [Indexed: 12/19/2022] Open
Abstract
Channelrhodopsins (ChR) are light-gated ion-channels heavily used in optogenetics. Upon light excitation an ultrafast all-trans to 13-cis isomerization of the retinal chromophore takes place. It is still uncertain by what means this reaction leads to further protein changes and channel conductivity. Channelrhodopsin-1 in Chlamydomonas augustae exhibits a 100 fs photoisomerization and a protonated counterion complex. By polarization resolved ultrafast spectroscopy in the mid-IR we show that the initial reaction of the retinal is accompanied by changes in the protein backbone and ultrafast protonation changes at the counterion complex comprising Asp299 and Glu169. In combination with homology modelling and quantum mechanics/molecular mechanics (QM/MM) geometry optimization we assign the protonation dynamics to ultrafast deprotonation of Glu169, and transient protonation of the Glu169 backbone, followed by a proton transfer from the backbone to the carboxylate group of Asp299 on a timescale of tens of picoseconds. The second proton transfer is not related to retinal dynamics and reflects pure protein changes in the first photoproduct. We assume these protein dynamics to be the first steps in a cascade of protein-wide changes resulting in channel conductivity.
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20
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Wang J, Yao H, Lu T, Dong J, Xu B, Liu Y, Liu C, Zhou L, Shi T. Spectroscopic, kinetic, and theoretical analyses of oxidation of dl-ethionine by Pt(IV) anticancer model compounds. Spectrochim Acta A Mol Biomol Spectrosc 2019; 223:117328. [PMID: 31295632 DOI: 10.1016/j.saa.2019.117328] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 06/18/2019] [Accepted: 06/28/2019] [Indexed: 06/09/2023]
Abstract
Ethionine is an S-ethyl analog of methionine (Met) having a small change in structure. But it is a chemical carcinogen and an antagonist of Met, thus displaying a disparate biological profile. The oxidations of ethionine by biologically important oxidants have not been exploited. Oxidations of dl-ethionine by Pt(IV) anticancer model complexes trans-[PtX2(CN4)]2- (X = Cl or Br) were thus analyzed by time-resolved and stopped-flow spectral techniques. Overall second-order kinetics was established, being first-order in [Pt(IV)] and [Ethionine]tot (the total concentration of ethionine); the observed second-order rate constant k' versus pH profiles were obtained. A stoichiometry of Δ[Pt(IV)]:Δ[Ethionine]tot = 1:1 was unraveled, indicating that ethionine was oxidized to ethionine-sulfoxide which was confirmed by NMR spectroscopic and high-resolution mass spectral analyses. In the proposed reaction mechanism which is similar to that for the oxidation of Met by the same Pt(IV) compounds, the rate-determining steps are rationalized in terms of a bridge formation between one of the coordinated halides in [PtX2(CN4)]2- and the sulfur atom in ethionine, followed by an X+ transfer. Moreover, a large rate enhancement for the reaction of ethionine with [PtBr2(CN4)]2- compared with [PtCl2(CN4)]2- strongly supports an X+ transfer mechanism. Furthermore, a combined quantum-mechanical/molecular-mechanical (QM/MM) method was utilized to simulate a Cl+ transfer mechanism from trans-[PtCl2(CN)4]2- to ethionine. The simulations unraveled the energetically stable structures of reactants and products, which favor the Cl+ transfer process. Rate constants of the rate-determining steps have been derived. Ratios of k (ethionine)/k (Met) are between 2.2 and 2.6 obtained for the three protolytic species of ethionine and Met; the enhanced reactivity might be partially responsible for the disparate biological profiles.
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Affiliation(s)
- Jinhu Wang
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang 277160, Shandong Province, People's Republic of China
| | - Haiping Yao
- College of Chemistry and Environmental Science, MOE Key Laboratory of Medicinal Chemistry and Molecular Diagnostics, Hebei University, Baoding 071002, Hebei Province, People's Republic of China
| | - Taotao Lu
- College of Chemistry and Environmental Science, MOE Key Laboratory of Medicinal Chemistry and Molecular Diagnostics, Hebei University, Baoding 071002, Hebei Province, People's Republic of China
| | - Jingran Dong
- College of Chemistry and Environmental Science, MOE Key Laboratory of Medicinal Chemistry and Molecular Diagnostics, Hebei University, Baoding 071002, Hebei Province, People's Republic of China
| | - Benyan Xu
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang 277160, Shandong Province, People's Republic of China
| | - Yang Liu
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang 277160, Shandong Province, People's Republic of China
| | - Chunli Liu
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang 277160, Shandong Province, People's Republic of China.
| | - Li Zhou
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang 277160, Shandong Province, People's Republic of China.
| | - Tiesheng Shi
- College of Chemistry, Chemical Engineering and Materials Science, Zaozhuang University, Zaozhuang 277160, Shandong Province, People's Republic of China; College of Chemistry and Environmental Science, MOE Key Laboratory of Medicinal Chemistry and Molecular Diagnostics, Hebei University, Baoding 071002, Hebei Province, People's Republic of China.
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21
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Zhang Y, Zhang H, Zheng Q. How Chorismatases Regulate Distinct Reaction Channels in a Single Conserved Active Pocket: Mechanistic Analysis with QM/MM (ONIOM) Investigations. Chemistry 2019; 25:1326-1336. [PMID: 30395358 DOI: 10.1002/chem.201804622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Indexed: 01/12/2023]
Abstract
The FkbO and Hyg5 subfamilies of chorismatases share the same active-site architectures, but perform distinct reaction mechanisms, that is, FkbO employs a hydrolysis reaction whereas Hyg5 proceeds through an intramolecular mechanism. Despite extensive research efforts, the detailed mechanism of the product selectivity in chorismatases need to be further unmasked. In this study, the effects of the A/G residue group (A244FkbO /G240Hyg5 ) and the V/Q residue group (V209FkbO /Q201Hyg5 ) on the catalytic mechanisms are investigated by employing molecular dynamics simulations and hybrid quantum mechanical/molecular mechanical (QM/MM) calculations of the two wild-type models (FkbO/CHO and Hyg5/CHO; CHO=chorismate) and four mutants models (A244G-FkbO/CHO and G240A-Hyg5/CHO; V209Q-FkbO/CHO and Q201V-Hyg5/CHO). Our results showed that the A/G residue group mentioned by previous works would cause changes in the binding states of the substrate and the orientation of the catalytic glutamate, but only these changes affect the product selectivity in chorismatases limitedly. Interestingly, the distal V/Q residue group, which determines the internal water self-regulating ability at the active site, has significant impact on the selectivity of the catalytic mechanisms. The V/Q residue group is suggested to be an important factor to control the catalytic activities in chorismatases. The results are consistent with biochemical and structural experiments, providing novel insight into the mechanism of product selectivity in chorismatases.
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Affiliation(s)
- Yulai Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of, Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, P.R. China
| | - Hongxing Zhang
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of, Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, P.R. China
| | - Qingchuan Zheng
- Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, International Joint Research Laboratory of, Nano-Micro Architecture Chemistry, Jilin University, Changchun, 130023, P.R. China.,Key Laboratory for Molecular Enzymology and Engineering of the Ministry, of Education, Jilin University, Changchun, 130023, P.R. China
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22
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Abstract
In this work, we propose an improved QM/MM-based strategy to determine condensed-phase polarizabilities and we use this approach to optimize a new and simple polarizable four-site water model for classical molecular simulation. For the determination of the model value for the polarizability from QM/MM, we show that our proposed consensus-fitting strategy significantly reduces the uncertainty in calculated polarizabilities in cases where the size of the local external electric field is small. By fitting electrostatic, polarization and dispersion properties of our water model based on quantum and/or combined QM/MM calculations, only a single model parameter (describing exchange repulsion) is left for empirical calibration. The resulting model performs well in describing relevant pure-liquid thermodynamic and transport properties, which illustrates the merit of our approach to minimize the number of free variables in our model.
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Affiliation(s)
- Koen M Visscher
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, De Boelelaan 1108, 1081 HV Amsterdam, The Netherlands.
| | - William C Swope
- IBM Almaden Research Center, 650 Harry Road, San Jose, CA 95120, USA.
| | - Daan P Geerke
- AIMMS Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical Sciences, Faculty of Science, De Boelelaan 1108, 1081 HV Amsterdam, The Netherlands.
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Gurevic I, Islam Z, Świderek K, Trepka K, Ghosh AK, Moliner V, Kohen A. Experimental and Computational Studies Delineate the Role of Asparagine 177 in Hydride Transfer for E. coli Thymidylate Synthase. ACS Catal 2018; 8:10241-10253. [PMID: 31275729 DOI: 10.1021/acscatal.8b02554] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Thymidylate synthase (TSase), an enzyme responsible for the de novo biosynthesis of 2'-deoxythymidine 5'-monophosphate (thymidylate, dTMP) necessary for DNA synthesis, has been a drug target for decades. TSase is a highly conserved enzyme across species ranging from very primitive organisms to mammals. Among the many conserved active site residues, an asparagine (N177, using Escherichia coli residues numbering) appears to make direct hydrogen bonds with both the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate and its pyrimidine ring's N3. Recent studies have reassessed the TSase catalytic mechanism, focusing on the degree of negative charge accumulation at the O4 carbonyl of the substrate during two critical H-transfers - a proton abstraction and a hydride transfer. To obtain insights into the role of this conserved N177 on the hydride transfer, we examined its aspartic acid (D) and serine (S) mutants - each of which is expected to alter hydrogen bonding and charge stabilization around the C4=O4 carbonyl of the 2'-deoxyuridine 5'-monophosphate (uridylate, dUMP) substrate. Steady-state kinetics, substrate binding order studies and temperature-dependency analysis of intrinsic KIEs for the hydride transfer step of the TSase catalytic cycle suggest the active site of N177D is not precisely organized for that step. A smaller disruption was observed for N177S, which could be rationalized by partial compensation by water molecules and rearrangement of other residues toward preparation of the system for the hydride transfer under study. These experimental findings are qualitatively mirrored by QM/MM computational simulations, thereby shedding light on the sequence and synchronicity of steps in the TSase-catalyzed reaction. This information could potentially inform the design of mechanism-based drugs targeting this enzyme.
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Affiliation(s)
- Ilya Gurevic
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Zahidul Islam
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Katarzyna Świderek
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Kai Trepka
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Ananda K. Ghosh
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
| | - Vicent Moliner
- Departament de Química Física i Analítica, Universitat Jaume I, 12071 Castelló, Spain
| | - Amnon Kohen
- Department of Chemistry, College of Liberal Arts & Sciences, University of Iowa, Iowa City, Iowa 52242-1727, United States
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Kholodar SA, Ghosh AK, Świderek K, Moliner V, Kohen A. Parallel reaction pathways and noncovalent intermediates in thymidylate synthase revealed by experimental and computational tools. Proc Natl Acad Sci U S A 2018; 115:10311-4. [PMID: 30249644 DOI: 10.1073/pnas.1811059115] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Thymidylate synthase was one of the most studied enzymes due to its critical role in molecular pathogenesis of cancer. Nevertheless, many atomistic details of its chemical mechanism remain unknown or debated, thereby imposing limits on design of novel mechanism-based anticancer therapeutics. Here, we report unprecedented isolation and characterization of a previously proposed intact noncovalent bisubstrate intermediate formed in the reaction catalyzed by thymidylate synthase. Free-energy surfaces of the bisubstrate intermediates interconversions computed with quantum mechanics/molecular mechanics (QM/MM) methods and experimental assessment of the corresponding kinetics indicate that the species is the most abundant productive intermediate along the reaction coordinate, whereas accumulation of the covalent bisubstrate species largely occurs in a parallel nonproductive pathway. Our findings not only substantiate relevance of the previously proposed noncovalent intermediate but also support potential implications of the overstabilized covalent intermediate in drug design targeting DNA biosynthesis.
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Szatkowski L, Manna RN, Grzybkowska A, Kamiński R, Dybala-Defratyka A, Paneth P. Measurement and Prediction of Chlorine Kinetic Isotope Effects in Enzymatic Systems. Methods Enzymol 2017; 596:179-215. [PMID: 28911771 DOI: 10.1016/bs.mie.2017.07.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Abstract
Approaches to determine chlorine kinetic isotope effects (Cl-KIEs) on enzymatic dehalogenations are discussed and illustrated by representative examples. Three aspects are considered. First methodology for experimental measurement of Cl-KIEs, with stress being on FAB-IRMS technique developed in our laboratory, is described. Subsequently, we concentrate our discussion on the consequences of reaction complexity in the interpretation of experimental values, a problem especially important in cases of polychlorinated reactants. The most fruitful studies of enzymatic dehalogenations by Cl-KIEs require their theoretical evaluation, hence the computational focus of the second part of this chapter.
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Haudecoeur R, Carotti M, Gouron A, Maresca M, Buitrago E, Hardré R, Bergantino E, Jamet H, Belle C, Réglier M, Bubacco L, Boumendjel A. 2-Hydroxypyridine- N-oxide-Embedded Aurones as Potent Human Tyrosinase Inhibitors. ACS Med Chem Lett 2017; 8:55-60. [PMID: 28105275 DOI: 10.1021/acsmedchemlett.6b00369] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 11/17/2016] [Indexed: 01/31/2023] Open
Abstract
With the aim to develop effective and selective human tyrosinase inhibitors, we investigated aurone derivatives whose B-ring was replaced by a non-oxidizable 2-hydroxypyridine-N-oxide (HOPNO) moiety. These aurones were synthesized and evaluated as inhibitors of purified human tyrosinase. Excellent inhibition activity was revealed and rationalized by theoretical calculations. The aurone backbone was especially found to play a crucial role, as the HOPNO moiety alone provided very modest activity on human tyrosinase. Furthermore, the in vitro activity was confirmed by measuring the melanogenesis suppression ability of the compounds in melanoma cell lysates and whole cells. Our study reveals that HOPNO-embedded 6-hydroxyaurone is to date the most effective inhibitor of isolated human tyrosinase. Owing to its low toxicity and its high inhibition activity, it could represent a milestone on the path toward new valuable agents in dermocosmetics, as well as in medical fields where it was recently suggested that tyrosinase could play key roles.
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Affiliation(s)
- Romain Haudecoeur
- Univ. Grenoble-Alpes/CNRS, DPM UMR 5063, CS 40700, 38058 Grenoble, France
| | - Marcello Carotti
- Department
of Biology, University of Padova, Via Ugo Bassi 58b, Padova 35121, Italy
| | - Aurélie Gouron
- Univ. Grenoble-Alpes/CNRS, DCM UMR 5250, CS 40700, 38058 Grenoble, France
| | - Marc Maresca
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Elina Buitrago
- Univ. Grenoble-Alpes/CNRS, DPM UMR 5063, CS 40700, 38058 Grenoble, France
- Univ. Grenoble-Alpes/CNRS, DCM UMR 5250, CS 40700, 38058 Grenoble, France
| | - Renaud Hardré
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | | | - Hélène Jamet
- Univ. Grenoble-Alpes/CNRS, DCM UMR 5250, CS 40700, 38058 Grenoble, France
| | - Catherine Belle
- Univ. Grenoble-Alpes/CNRS, DCM UMR 5250, CS 40700, 38058 Grenoble, France
| | - Marius Réglier
- Aix Marseille Univ, CNRS, Centrale Marseille, iSm2, Marseille, France
| | - Luigi Bubacco
- Department
of Biology, University of Padova, Via Ugo Bassi 58b, Padova 35121, Italy
| | - Ahcène Boumendjel
- Univ. Grenoble-Alpes/CNRS, DPM UMR 5063, CS 40700, 38058 Grenoble, France
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Mann D, Teuber C, Tennigkeit SA, Schröter G, Gerwert K, Kötting C. Mechanism of the intrinsic arginine finger in heterotrimeric G proteins. Proc Natl Acad Sci U S A 2016; 113:E8041-50. [PMID: 27911799 DOI: 10.1073/pnas.1612394113] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterotrimeric G proteins are crucial molecular switches that maintain a large number of physiological processes in cells. The signal is encoded into surface alterations of the Gα subunit that carries GTP in its active state and GDP in its inactive state. The ability of the Gα subunit to hydrolyze GTP is essential for signal termination. Regulator of G protein signaling (RGS) proteins accelerates this process. A key player in this catalyzed reaction is an arginine residue, Arg178 in Gαi1, which is already an intrinsic part of the catalytic center in Gα in contrast to small GTPases, at which the corresponding GTPase-activating protein (GAP) provides the arginine "finger." We applied time-resolved FTIR spectroscopy in combination with isotopic labeling and site-directed mutagenesis to reveal the molecular mechanism, especially of the role of Arg178 in the intrinsic Gαi1 mechanism and the RGS4-catalyzed mechanism. Complementary biomolecular simulations (molecular mechanics with molecular dynamics and coupled quantum mechanics/molecular mechanics) were performed. Our findings show that Arg178 is bound to γ-GTP for the intrinsic Gαi1 mechanism and pushed toward a bidentate α-γ-GTP coordination for the Gαi1·RGS4 mechanism. This movement induces a charge shift toward β-GTP, increases the planarity of γ-GTP, and thereby catalyzes the hydrolysis.
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28
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Sezer M, Woelke AL, Knapp EW, Schlesinger R, Mroginski MA, Weidinger IM. Redox induced protonation of heme propionates in cytochrome c oxidase: Insights from surface enhanced resonance Raman spectroscopy and QM/MM calculations. Biochim Biophys Acta Bioenerg 2017; 1858:103-8. [PMID: 27810193 DOI: 10.1016/j.bbabio.2016.10.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2016] [Revised: 10/18/2016] [Accepted: 10/28/2016] [Indexed: 12/16/2022]
Abstract
Understanding the coupling between heme reduction and proton translocation in cytochrome c oxidase (CcO) is still an open problem. The propionic acids of heme a3 have been proposed to act as a proton loading site (PLS) in the proton pumping pathway, yet this proposal could not be verified by experimental data so far. We have set up an experiment where the redox states of the two hemes in CcO can be controlled via external electrical potential. Surface enhanced resonance Raman (SERR) spectroscopy was applied to simultaneously monitor the redox state of the hemes and the protonation state of the heme propionates. Simulated spectra based on QM/MM calculations were used to assign the resonant enhanced CH2 twisting modes of the propionates to the protonation state of the individual heme a and heme a3 propionates respectively. The comparison between calculated and measured H2OD2O difference spectra allowed a sound band assignment. In the fully reduced enzyme at least three of the four heme propionates were found to be protonated whereas in the presence of a reduced heme a and an oxidized heme a3 only protonation of one heme a3 propionates was observed. Our data supports the postulated scenario where the heme a3 propionates are involved in the proton pathway.
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29
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Khrenova MG, Grigorenko BL, Nemukhin AV. Theoretical vibrational spectroscopy of intermediates and the reaction mechanism of the guanosine triphosphate hydrolysis by the protein complex Ras-GAP. Spectrochim Acta A Mol Biomol Spectrosc 2016; 166:68-72. [PMID: 27214270 DOI: 10.1016/j.saa.2016.04.056] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2015] [Revised: 04/17/2016] [Accepted: 04/27/2016] [Indexed: 06/05/2023]
Abstract
The structures and vibrational spectra of the reacting species upon guanosine triphosphate (GTP) hydrolysis to guanosine diphosphate and inorganic phosphate (Pi) trapped inside the protein complex Ras-GAP were analyzed following the results of QM/MM simulations. The frequencies of the phosphate vibrations referring to the reactants and to Pi were compared to those observed in the experimental FTIR studies. A good correlation between the theoretical and experimental vibrational data provides a strong support to the reaction mechanism of GTP hydrolysis by the Ras-GAP enzyme system revealed by the recent QM/MM modeling. Evolution of the vibrational bands associated with the inorganic phosphate Pi during the elementary stages of GTP hydrolysis is predicted.
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Affiliation(s)
- Maria G Khrenova
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russia
| | - Bella L Grigorenko
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russia; N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119334, Russia
| | - Alexander V Nemukhin
- Chemistry Department, M.V. Lomonosov Moscow State University, 1-3 Leninskie Gory, Moscow 119991, Russia; N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, 4 Kosygin Street, Moscow 119334, Russia.
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30
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Cortopassi WA, Simion R, Honsby CE, França TCC, Paton RS. Dioxygen Binding in the Active Site of Histone Demethylase JMJD2A and the Role of the Protein Environment. Chemistry 2015; 21:18983-92. [PMID: 26577067 DOI: 10.1002/chem.201502983] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Indexed: 12/17/2022]
Abstract
JMJD2A catalyses the demethylation of di- and trimethylated lysine residues in histone tails and is a target for the development of new anticancer medicines. Mechanistic details of demethylation are yet to be elucidated and are important for the understanding of epigenetic processes. We have evaluated the initial step of histone demethylation by JMJD2A and demonstrate the dramatic effect of the protein environment upon oxygen binding using quantum mechanics/molecular mechanics (QM/MM) calculations. The changes in electronic structure have been studied for possible spin states and different conformations of O2 , using a combination of quantum and classical simulations. O2 binding to this histone demethylase is computed to occur preferentially as an end-on superoxo radical bound to a high-spin ferric centre, yielding an overall quintet ground state. The favourability of binding is strongly influenced by the surrounding protein: we have quantified this effect using an energy decomposition scheme into electrostatic and dispersion contributions. His182 and the methylated lysine assist while Glu184 and the oxoglutarate cofactor are deleterious for O2 binding. Charge separation in the superoxo-intermediate benefits from the electrostatic stabilization provided by the surrounding residues, stabilizing the binding process significantly. This work demonstrates the importance of the extended protein environment in oxygen binding, and the role of energy decomposition in understanding the physical origin of binding/recognition.
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Affiliation(s)
- Wilian A Cortopassi
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) paton.chem.ox.ac.uk.,Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Robert Simion
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) paton.chem.ox.ac.uk.,Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Charles E Honsby
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) paton.chem.ox.ac.uk.,Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK)
| | - Tanos C C França
- Department of Chemical Engineering, Military Institute of Engineering, 80 Praça General Tibúrcio, Urca, 22290 270, Rio de Janeiro (Brazil).,Center for Basic and Applied Research, Faculty of Informatics and Management, University of Hradec Kralove, Hradec Kralove (Czech Republic)
| | - Robert S Paton
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA (UK) paton.chem.ox.ac.uk. .,Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ (UK).
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Abstract
Thymidylate synthase (TSase) catalyzes the de novo biosynthesis of thymidylate, a precursor for DNA, and is thus an important target for chemotherapeutics and antibiotics. Two sequential C-H bond cleavages catalyzed by TSase are of particular interest: a reversible proton abstraction from the 2'-deoxy-uridylate substrate, followed by an irreversible hydride transfer forming the thymidylate product. QM/MM calculations of the former predicted a mechanism where the abstraction of the proton leads to formation of a novel nucleotide-folate intermediate that is not covalently bound to the enzyme (Wang, Z.; Ferrer, S.; Moliner, V.; Kohen, A. Biochemistry2013, 52, 2348-2358). Existence of such intermediate would hold promise as a target for a new class of drugs. Calculations of the subsequent hydride transfer predicted a concerted H-transfer and elimination of the enzymatic cysteine (Kanaan, N.; Ferrer, S.; Marti, S.; Garcia-Viloca, M.; Kohen, A.; Moliner, V. J. Am. Chem. Soc.2011, 133, 6692-6702). A key to both C-H activations is a highly conserved arginine (R166) that stabilizes the transition state of both H-transfers. Here we test these predictions by studying the R166 to lysine mutant of E. coli TSase (R166K) using intrinsic kinetic isotope effects (KIEs) and their temperature dependence to assess effects of the mutation on both chemical steps. The findings confirmed the predictions made by the QM/MM calculations, implicate R166 as an integral component of both reaction coordinates, and thus provide critical support to the nucleotide-folate intermediate as a new target for rational drug design.
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Affiliation(s)
- Zahidul Islam
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52242, U.S.A
| | | | - Ananda K. Ghosh
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52242, U.S.A
| | - Amnon Kohen
- The Department of Chemistry, The University of Iowa, Iowa City, IA 52242, U.S.A
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32
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Palló A, Oláh J, Gráczer E, Merli A, Závodszky P, Weiss MS, Vas M. Structural and energetic basis of isopropylmalate dehydrogenase enzyme catalysis. FEBS J 2014; 281:5063-76. [PMID: 25211160 DOI: 10.1111/febs.13044] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Revised: 09/06/2014] [Accepted: 09/08/2014] [Indexed: 01/17/2023]
Abstract
UNLABELLED The three-dimensional structure of the enzyme 3-isopropylmalate dehydrogenase from the bacterium Thermus thermophilus in complex with Mn(2+) , its substrate isopropylmalate and its co-factor product NADH at 2.0 Å resolution features a fully closed conformation of the enzyme. Upon closure of the two domains, the substrate and the co-factor are brought into precise relative orientation and close proximity, with a distance between the C2 atom of the substrate and the C4N atom of the pyridine ring of the co-factor of approximately 3.0 Å. The structure further shows binding of a K(+) ion close to the active site, and provides an explanation for its known activating effect. Hence, this structure is an excellent mimic for the enzymatically competent complex. Using high-level QM/MM calculations, it may be demonstrated that, in the observed arrangement of the reactants, transfer of a hydride from the C2 atom of 3-isopropylmalate to the C4N atom of the pyridine ring of NAD(+) is easily possible, with an activation energy of approximately 15 kcal·mol(-1) . The activation energy increases by approximately 4-6 kcal·mol(-1) when the K(+) ion is omitted from the calculations. In the most plausible scenario, prior to hydride transfer the ε-amino group of Lys185 acts as a general base in the reaction, aiding the deprotonation reaction of 3-isopropylmalate prior to hydride transfer by employing a low-barrier proton shuttle mechanism involving a water molecule. DATABASE Structural data have been submitted to the Protein Data Bank under accession number 4F7I.
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Affiliation(s)
- Anna Palló
- Institute of Organic Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
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Suardíaz R, Masgrau L, Lluch JM, González-Lafont À. Introducing mutations to modify the C13/C9 ratio in linoleic acid oxygenations catalyzed by rabbit 15-lipoxygenase: a QM/MM and MD study. Chemphyschem 2014; 15:4049-54. [PMID: 25186660 DOI: 10.1002/cphc.201402471] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 07/31/2014] [Indexed: 12/22/2022]
Abstract
Lipoxygenases (LOs) are a family of nonheme iron-containing enzymes that catalyze the hydroperoxidation of several polyunsaturated fatty acids with a huge regio- and stereospecificity. Mammalian 15-LO-1 yields almost exclusively oxygenation at the C13 position of the linoleic acid (LA), its preferred substrate. This is very important because metabolites derived from oxidation in distinct positions produce opposite physiological effects. We have combined here quantum mechanics/molecular mechanics calculations with molecular dynamics simulations to show how a suitable mutation of the rabbit 15-LO-1 enzyme can produce a significant amount of products derived from oxygenation at the C9 position of LA. In effect, the Leu597Val or Leu597Ala mutants are predicted to lead to a diminution of the oxygenation C13/C9 ratio in LA as huge as five orders of magnitude. This shows that the conserved residue Leu597 actually drives the regiospecific hydroperoxidation of LA catalyzed by 15-LO-1 enzyme.
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Affiliation(s)
- Reynier Suardíaz
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona (Spain); Institut de Biotecnologia i de Biomedicina (IBB), Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona (Spain)
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Somboon T, Ochiai J, Treesuwan W, Gleeson MP, Hannongbua S, Mori S. Mechanistic insights into the catalytic reaction of plant allene oxide synthase (pAOS) via QM and QM/MM calculations. J Mol Graph Model 2014; 52:20-9. [PMID: 24984079 DOI: 10.1016/j.jmgm.2014.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Revised: 05/29/2014] [Accepted: 05/30/2014] [Indexed: 11/26/2022]
Abstract
QM cluster and QM/MM protein models have been employed to understand aspects of the reaction mechanism of plant allene oxide synthase (pAOS). In this study we have investigated two reaction mechanisms for pAOS. The standard pAOS mechanism was contrasted with an alternative involving an additional active site molecule which has been shown to facilitate proton coupled electron transfer (PCET) in related systems. Firstly, we found that the results from QM/MM protein model are comparable with those from the QM cluster model, presumably due to the large active site used. Furthermore, the results from the QM cluster model show that the Fe(III) and Fe(IV) pathways for the standard mechanism have similar energetic and structural properties, indicating that the reaction mechanism may well proceed via both pathways. However, while the PCET process is facilitated by an additional active site bound water in other related families, in pAOS it is not, suggesting this type of process is not general to all closely related family members.
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Affiliation(s)
- Tuanjai Somboon
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Jun Ochiai
- Faculty of Science, Ibaraki University, Ibaraki 310-8512, Japan
| | - Witcha Treesuwan
- Institute of Food Research and Product Development, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - M Paul Gleeson
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok 10900, Thailand; Center of Nanotechnology KU, Kasetsart University, Chatuchak, Bangkok 10900 Thailand.
| | - Seiji Mori
- Faculty of Science, Ibaraki University, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, Tokai, Ibaraki 319-1106, Japan.
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