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Behera S, Balasubramanian S. Lipase A from Bacillus subtilis: Substrate Binding, Conformational Dynamics, and Signatures of a Lid. J Chem Inf Model 2023; 63:7545-7556. [PMID: 37989487 DOI: 10.1021/acs.jcim.3c01681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Protein-ligand binding studies are crucial for understanding the molecular basis of biological processes and for further advancing industrial biocatalysis and drug discovery. Using computational modeling and molecular dynamics simulations, we investigated the binding of a butyrate ester substrate to the lipase A (LipA) enzyme of Bacillus subtilis. Besides obtaining a close agreement of the binding free energy with the experimental value, the study reveals a remarkable reorganization of the catalytic triad upon substrate binding, leading to increased essential hydrogen bond populations. The investigation shows the distortion of the oxyanion hole in both the substrate-bound and unbound states of LipA and highlights the strengthening of the same in the tetrahedral intermediate complex. Principal component analysis of the unbound ensemble reveals the dominant motion in LipA to be the movement of Loop-1 (Tyr129-Arg142) between two states that cover and uncover the active site, mirroring that of a lid prevalent in several lipases. This lid-like motion of Loop-1 is also supported by its tendency to spontaneously open up at an oil-water interface. Overall, this study provides valuable insights into the impact of substrate binding on the structure, flexibility, and conformational dynamics of the LipA enzyme.
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Affiliation(s)
- Sudarshan Behera
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
| | - Sundaram Balasubramanian
- Chemistry and Physics of Materials Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560 064, India
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2
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Fu J, Chen S, Ni Z. Rational truncation, mutation, and halogenation of bradykinin neuropeptides as potent
ACEII
inhibitors by integrating molecular dynamics simulations, quantum mechanics calculations, and in vitro assays. J CHIN CHEM SOC-TAIP 2022. [DOI: 10.1002/jccs.202200242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Jun Fu
- Department of Neurology Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine Suzhou China
| | - Shenghui Chen
- Department of Neurology Suzhou Kowloon Hospital, Shanghai Jiao Tong University School of Medicine Suzhou China
| | - Zhong Ni
- Institute of Life Sciences Jiangsu University Zhenjiang China
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3
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Li D, Chen X, Chen Z, Lin X, Xu J, Wu Q. Directed evolution of lipase A from Bacillus subtilis for the preparation of enantiocomplementary sec-alcohols. GREEN SYNTHESIS AND CATALYSIS 2021. [DOI: 10.1016/j.gresc.2021.07.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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4
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Maldonado MR, Alnoch RC, de Almeida JM, Santos LAD, Andretta AT, Ropaín RDPC, de Souza EM, Mitchell DA, Krieger N. Key mutation sites for improvement of the enantioselectivity of lipases through protein engineering. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108047] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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5
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Toledo MV, Briand LE. Relevance and bio-catalytic strategies for the kinetic resolution of ketoprofen towards dexketoprofen. Crit Rev Biotechnol 2017; 38:778-800. [PMID: 29124963 DOI: 10.1080/07388551.2017.1399249] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
This review presents the most relevant investigations concerning the biocatalytic kinetic resolution of racemic ketoprofen to dexketoprofen for the last 22 years. The advantages related to the administration of the dex-enantiomer in terms of human health, the so called "chiral switch" in the pharmaceutical industry and the sustainability of biotransformations have been the driving forces to develop innovative technology to obtain dexketoprofen. In particular, the kinetic resolution of racemic ketoprofen through enantiomeric esterification and hydrolysis using lipases as biocatalysts are thoroughly revised and commented upon. In this context, the biocatalysts, acyl-acceptors (alcohols), reaction conditions, conversion, enantiomeric excess, and enantiomeric ratio among others are discussed. Moreover, the investigations concerning scaling up processes in order to obtain an optically pure enantiomer of the profen are presented. Finally, some guidelines about perspectives of the technology and research opportunities are given.
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Affiliation(s)
- María Victoria Toledo
- a Centro de Investigación y Desarrollo en Ciencias Aplicadas-Dr. Jorge J. Ronco (CINDECA) , Universidad Nacional de La Plata, CONICET , La Plata , Buenos Aires , Argentina
| | - Laura Estefanía Briand
- a Centro de Investigación y Desarrollo en Ciencias Aplicadas-Dr. Jorge J. Ronco (CINDECA) , Universidad Nacional de La Plata, CONICET , La Plata , Buenos Aires , Argentina
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6
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Efficient resolution of profen ethyl ester racemates by engineered Yarrowia lipolytica Lip2p lipase. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.tetasy.2017.01.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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7
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Chen H, Jia J, Ni Z, Vastermark A, Wu B, Le Y, Jawad U. Orlistat response to missense mutations in lipoprotein lipase. Biotechnol Appl Biochem 2016; 64:464-470. [DOI: 10.1002/bab.1500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/14/2016] [Indexed: 11/09/2022]
Affiliation(s)
- Huayou Chen
- Institute of Life Sciences; Jiangsu University; Zhenjiang People's Republic of China
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering; Chinese Academy of Sciences; Beijing People's Republic of China
- Division of Biological Sciences; University of California at San Diego; La Jolla CA USA
| | - Jinru Jia
- Institute of Life Sciences; Jiangsu University; Zhenjiang People's Republic of China
| | - Zhong Ni
- Institute of Life Sciences; Jiangsu University; Zhenjiang People's Republic of China
| | - Ake Vastermark
- Division of Biological Sciences; University of California at San Diego; La Jolla CA USA
| | - Bangguo Wu
- Institute of Life Sciences; Jiangsu University; Zhenjiang People's Republic of China
| | - Yilin Le
- Institute of Life Sciences; Jiangsu University; Zhenjiang People's Republic of China
| | - Ullah Jawad
- Institute of Life Sciences; Jiangsu University; Zhenjiang People's Republic of China
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Zhang X, Ye J, Yu L, Shi X, Zhang M, Xu Q, Lautens M. Organoselenium-Catalyzed Baeyer-Villiger Oxidation of α,β-Unsaturated Ketones by Hydrogen Peroxide to Access Vinyl Esters. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201400957] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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9
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Ni Z, Chen H, Lin X, Jin R. Insight into molecular mechanism underlying the transesterification catalysed by penicillin G amidase (PGA) using a combination protocol of experimental assay and theoretical analysis. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2013.850500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Lu J, Zhang Z, Ni Z, Shen H, Tu Z, Liu H, Lu R, Shi H. The non-additive contribution of hydroxyl substituents to Akt kinase–apigenin affinity. MOLECULAR SIMULATION 2014. [DOI: 10.1080/08927022.2014.913099] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Chen H, Sun T, Chen H, Tian R, Zhang T, Chen Z, Ni Z. Structural and energetic insights into the selective interactions of monoacylglycerol lipase with its natural substrate and small-molecule inhibitors. Med Chem Res 2013. [DOI: 10.1007/s00044-013-0832-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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12
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Ni Z, Chen H, Qi X, Jin R. Why is Substrate Peptide Binding Unsusceptible to Multidrug-Resistant Mutations in HIV-1 Protease? A Structural and Energetic Analysis. Int J Pept Res Ther 2013. [DOI: 10.1007/s10989-013-9365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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13
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Lind MES, Himo F. Quantum chemistry as a tool in asymmetric biocatalysis: limonene epoxide hydrolase test case. Angew Chem Int Ed Engl 2013; 52:4563-7. [PMID: 23512539 PMCID: PMC3734700 DOI: 10.1002/anie.201300594] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Indexed: 12/24/2022]
Affiliation(s)
- Maria E S Lind
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, 10691 Stockholm, Sweden
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Lind MES, Himo F. Quantum Chemistry as a Tool in Asymmetric Biocatalysis: Limonene Epoxide Hydrolase Test Case. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201300594] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Kim S, Duc Ngo T, Kim KK, Kim TD. Characterization, crystallization and preliminary X-ray diffraction analysis of an (S)-specific esterase (pfEstA) from Pseudomonas fluorescens KCTC 1767: enantioselectivity for potential industrial applications. Acta Crystallogr Sect F Struct Biol Cryst Commun 2012; 68:1374-7. [PMID: 23143253 PMCID: PMC3515385 DOI: 10.1107/s1744309112040626] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 09/26/2012] [Indexed: 11/10/2022]
Abstract
The structures and reaction mechanisms of enantioselective hydrolases, which can be used in industrial applications such as biotransformations, are largely unknown. Here, the X-ray crystallographic study of a novel (S)-specific esterase (pfEstA) from Pseudomonas fluorescens KCTC 1767, which can be used in the production of (S)-ketoprofen, is described. Multiple sequence alignments with other hydrolases revealed that pfEstA contains a conserved Ser67 within the S-X-X-K motif as well as a highly conserved Tyr156. Recombinant protein containing an N-terminal His tag was expressed in Escherichia coli, purified to homogeneity and characterized using SDS-PAGE, MALDI-TOF MS and enantioselective analysis. pfEstA was crystallized using a solution consisting of 1 M sodium citrate, 0.1 M CHES pH 9.5, and X-ray diffraction data were collected to a resolution of 1.9 Å with an Rmerge of 7.9%. The crystals of pfEstA belonged to space group P2(1)2(1)2(1), with unit-cell parameters a=65.31, b=82.13, c=100.41 Å, α=β=γ=90°.
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Affiliation(s)
- Seulgi Kim
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
| | - Tri Duc Ngo
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746, Republic of Korea
| | - T. Doohun Kim
- Department of Molecular Science and Technology, Graduate School of Interdisciplinary Programs, Ajou University, Suwon 443-749, Republic of Korea
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Bassegoda A, Cesarini S, Diaz P. Lipase improvement: goals and strategies. Comput Struct Biotechnol J 2012; 2:e201209005. [PMID: 24688646 PMCID: PMC3962121 DOI: 10.5936/csbj.201209005] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/20/2012] [Accepted: 09/23/2012] [Indexed: 12/22/2022] Open
Affiliation(s)
- Arnau Bassegoda
- Department of Microbiology, University of Barcelona. Av. Diagonal 643, 08028-Barcelona. Spain
| | - Silvia Cesarini
- Department of Microbiology, University of Barcelona. Av. Diagonal 643, 08028-Barcelona. Spain
| | - Pilar Diaz
- Department of Microbiology, University of Barcelona. Av. Diagonal 643, 08028-Barcelona. Spain
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Insight into substituent effects in Cal-B catalyzed transesterification by combining experimental and theoretical approaches. J Mol Model 2012; 19:349-58. [DOI: 10.1007/s00894-012-1552-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Accepted: 07/25/2012] [Indexed: 10/28/2022]
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