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Yasutake Y, Konishi K, Muramatsu S, Yoshida K, Aburatani S, Sakasegawa SI, Tamura T. Bacterial triacylglycerol lipase is a potential cholesterol esterase: Identification of a key determinant for sterol-binding specificity. Int J Biol Macromol 2020; 167:578-586. [PMID: 33279561 DOI: 10.1016/j.ijbiomac.2020.11.184] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 11/09/2020] [Accepted: 11/26/2020] [Indexed: 11/18/2022]
Abstract
Cholesterol esterase (Che) from Burkholderia stabilis (BsChe) is a homolog of well-characterized and industrially relevant bacterial triacylglycerol lipases (Lips). BsChe is a rare bacterial Lip enzyme that exhibits practical Che activity and is currently used in clinical applications to determine total serum cholesterol levels. To investigate the sterol specificity of BsChe, we determined the X-ray structure of BsChe. We discovered a local structural change in the active-site cleft, which might be related to substrate binding and product release. We also performed molecular docking studies by using the X-ray models of BsChe and cholesterol linoleate (CLL), the most favorable substrate for BsChe. The results showed that the sterol moieties of reasonable CLL docking poses localized to a specific active-site cleft surface formed by Leu266 and Ile287, which are unconserved among Burkholderia Lip homologs. Site-directed mutagenesis identified these residues as essential for the Che activity of BsChe, and Leu or Ile substitution conferred marked Che activity to Burkholderia Lips. In particular, Burkholderia cepacia and Burkholderia ubonensis Lips with the V266L/L287I double mutation exhibited ~50-fold and 500-fold higher Che activities than those of the wild-type enzymes, respectively. These results provide new insights into the substrate-binding mechanisms and selectivities of bacterial Lips.
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Affiliation(s)
- Yoshiaki Yasutake
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan
| | - Kenji Konishi
- Asahi Kasei Pharma Corporation, Shizuoka 410-2321, Japan; Laboratory of Molecular Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | | | - Keitaro Yoshida
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan
| | - Sachiyo Aburatani
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan; Cellular and Molecular Biotechnology Research Institute, AIST, Tokyo 135-0064, Japan
| | | | - Tomohiro Tamura
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan; Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan; Laboratory of Molecular Environmental Microbiology, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan.
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Carboxylic Ester Hydrolases in Bacteria: Active Site, Structure, Function and Application. CRYSTALS 2019. [DOI: 10.3390/cryst9110597] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Carboxylic ester hydrolases (CEHs), which catalyze the hydrolysis of carboxylic esters to produce alcohol and acid, are identified in three domains of life. In the Protein Data Bank (PDB), 136 crystal structures of bacterial CEHs (424 PDB codes) from 52 genera and metagenome have been reported. In this review, we categorize these structures based on catalytic machinery, structure and substrate specificity to provide a comprehensive understanding of the bacterial CEHs. CEHs use Ser, Asp or water as a nucleophile to drive diverse catalytic machinery. The α/β/α sandwich architecture is most frequently found in CEHs, but 3-solenoid, β-barrel, up-down bundle, α/β/β/α 4-layer sandwich, 6 or 7 propeller and α/β barrel architectures are also found in these CEHs. Most are substrate-specific to various esters with types of head group and lengths of the acyl chain, but some CEHs exhibit peptidase or lactamase activities. CEHs are widely used in industrial applications, and are the objects of research in structure- or mutation-based protein engineering. Structural studies of CEHs are still necessary for understanding their biological roles, identifying their structure-based functions and structure-based engineering and their potential industrial applications.
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Bertolani SJ, Siegel JB. A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy. PLoS One 2019; 14:e0214126. [PMID: 30947258 PMCID: PMC6448891 DOI: 10.1371/journal.pone.0214126] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 03/07/2019] [Indexed: 01/06/2023] Open
Abstract
Enzymes play a critical role in a wide array of industrial, medical, and research applications and with the recent explosion of genomic sequencing, we now have sequences for millions of enzymes for which there is no known structure. In order to utilize modern computational design tools for constructing inhibitors or engineering novel catalysts, the ability to accurately model enzymes is critical. A popular approach for modeling enzymes are comparative modeling techniques which can often accurately predict the global structural features. However, achieving atomic accuracy of an active site remains a challenge and is an issue when trying to utilize the molecular details for designing inhibitors or enhanced catalysts. Here we explore integrating knowledge about the required geometric orientation of conserved catalytic residues into the comparative modeling process in order to improve modeling accuracy. In order to investigate the utility of adding this information, we first carefully construct a benchmark set of reference structures to use. Consistent with previous findings, our benchmark demonstrates that the geometry between catalytic residues across an enzyme family is conserved and does not tend to deviate by more than 0.5Å. We then find that by integrating these geometric constraints during modeling, we can double the number of atomic level accuracy models (<1Å RMSD to the crystal structure ligand) within our benchmarking dataset, even for targets with templates as low as 20-30% sequence identity. Catalytic residues within an enzyme family are highly conserved and can often be readily identified through comparative sequence analysis to a known structure within the enzyme family. Therefore utilizing this readily available information has the potential to significantly improve drug design and enzyme engineering efforts for which there is no known structure for the enzyme of interest.
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Affiliation(s)
- Steve J. Bertolani
- Department of Chemistry, University of California Davis, Davis, California, United States of America
| | - Justin B. Siegel
- Department of Chemistry, University of California Davis, Davis, California, United States of America
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, United States of America
- Genome Center, University of California Davis, Davis, California, United States of America
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Casas-Godoy L, Gasteazoro F, Duquesne S, Bordes F, Marty A, Sandoval G. Lipases: An Overview. Methods Mol Biol 2018; 1835:3-38. [PMID: 30109644 DOI: 10.1007/978-1-4939-8672-9_1] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Lipases are ubiquitous enzymes, widespread in nature. They were first isolated from bacteria in the early nineteenth century, and the associated research continuously increased due to the characteristics of these enzymes. This chapter reviews the main sources, structural properties, and industrial applications of these highly studied enzymes.
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Affiliation(s)
- Leticia Casas-Godoy
- Cátedras CONACYT-Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Guadalajara, Jalisco, Mexico.
| | - Francisco Gasteazoro
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Guadalajara, Jalisco, Mexico
| | - Sophie Duquesne
- Université de Toulouse, INSA, UPS, INP; LISBP, Toulouse, France.,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France.,CNRS, UMR5504, Toulouse, France
| | - Florence Bordes
- Université de Toulouse, INSA, UPS, INP; LISBP, Toulouse, France.,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France.,CNRS, UMR5504, Toulouse, France
| | - Alain Marty
- Université de Toulouse, INSA, UPS, INP; LISBP, Toulouse, France.,INRA, UMR792 Ingénierie des Systèmes Biologiques et des Procédés, Toulouse, France.,CNRS, UMR5504, Toulouse, France
| | - Georgina Sandoval
- Centro de Investigación y Asistencia en Tecnología y Diseño del Estado de Jalisco A.C. (CIATEJ), Guadalajara, Jalisco, Mexico
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Yaacob N, Ahmad Kamarudin NH, Leow ATC, Salleh AB, Raja Abd Rahman RNZ, Mohamad Ali MS. The Role of Solvent-Accessible Leu-208 of Cold-Active Pseudomonas fluorescens Strain AMS8 Lipase in Interfacial Activation, Substrate Accessibility and Low-Molecular Weight Esterification in the Presence of Toluene. Molecules 2017; 22:E1312. [PMID: 28805665 PMCID: PMC6152135 DOI: 10.3390/molecules22081312] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/31/2017] [Accepted: 08/04/2017] [Indexed: 11/23/2022] Open
Abstract
The alkaline cold-active lipase from Pseudomonas fluorescens AMS8 undergoes major structural changes when reacted with hydrophobic organic solvents. In toluene, the AMS8 lipase catalytic region is exposed by the moving hydrophobic lid 2 (Glu-148 to Gly-167). Solvent-accessible surface area analysis revealed that Leu-208, which is located next to the nucleophilic Ser-207 has a focal function in influencing substrate accessibility and flexibility of the catalytic pocket. Based on molecular dynamic simulations, it was found that Leu-208 strongly facilitates the lid 2 opening via its side-chain. The KM and Kcat/KM of L208A mutant were substrate dependent as it preferred a smaller-chain ester (pNP-caprylate) as compared to medium (pNP-laurate) or long-chain (pNP-palmitate) esters. In esterification of ethyl hexanoate, L208A promotes a higher ester conversion rate at 20 °C but not at 30 °C, as a 27% decline was observed. Interestingly, the wild-type (WT) lipase's conversion rate was found to increase with a higher temperature. WT lipase AMS8 esterification was higher in toluene as compared to L208A. Hence, the results showed that Leu-208 of AMS8 lipase plays an important role in steering a broad range of substrates into its active site region by regulating the flexibility of this region. Leu-208 is therefore predicted to be crucial for its role in interfacial activation and catalysis in toluene.
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Affiliation(s)
- Norhayati Yaacob
- Enzyme Technology/Molecular Biomedicine Laboratory, Enzyme and Microbial Technology Research Centre, Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, University Putra Malaysia, 43400 Serdang, Malaysia.
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Department of Cell Biology and Molecule, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Centre, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Centre, Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
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Khan FI, Lan D, Durrani R, Huan W, Zhao Z, Wang Y. The Lid Domain in Lipases: Structural and Functional Determinant of Enzymatic Properties. Front Bioeng Biotechnol 2017; 5:16. [PMID: 28337436 PMCID: PMC5343024 DOI: 10.3389/fbioe.2017.00016] [Citation(s) in RCA: 209] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Lipases are important industrial enzymes. Most of the lipases operate at lipid–water interfaces enabled by a mobile lid domain located over the active site. Lid protects the active site and hence responsible for catalytic activity. In pure aqueous media, the lid is predominantly closed, whereas in the presence of a hydrophobic layer, it is partially opened. Hence, the lid controls the enzyme activity. In the present review, we have classified lipases into different groups based on the structure of lid domains. It has been observed that thermostable lipases contain larger lid domains with two or more helices, whereas mesophilic lipases tend to have smaller lids in the form of a loop or a helix. Recent developments in lipase engineering addressing the lid regions are critically reviewed here. After on, the dramatic changes in substrate selectivity, activity, and thermostability have been reported. Furthermore, improved computational models can now rationalize these observations by relating it to the mobility of the lid domain. In this contribution, we summarized and critically evaluated the most recent developments in experimental and computational research on lipase lids.
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Affiliation(s)
- Faez Iqbal Khan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China; School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
| | - Rabia Durrani
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Weiqian Huan
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Zexin Zhao
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
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Shen YF, Chen GH, Lin SH, Lin G. S-endo-2-Norbornyl-N-n-butylcarbamate as a PotentialPseudomonasLipase Inhibitor to Probe the Enantioselectivity of the Enzyme by Kinetic and Molecular Docking Evaluation. J CHIN CHEM SOC-TAIP 2016. [DOI: 10.1002/jccs.201600005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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8
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Rauwerdink A, Kazlauskas RJ. How the Same Core Catalytic Machinery Catalyzes 17 Different Reactions: the Serine-Histidine-Aspartate Catalytic Triad of α/β-Hydrolase Fold Enzymes. ACS Catal 2015; 5:6153-6176. [PMID: 28580193 DOI: 10.1021/acscatal.5b01539] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes within a family often catalyze different reactions. In some cases, this variety stems from different catalytic machinery, but in other cases the machinery is identical; nevertheless, the enzymes catalyze different reactions. In this review, we examine the subset of α/β-hydrolase fold enzymes that contain the serine-histidine-aspartate catalytic triad. In spite of having the same protein fold and the same core catalytic machinery, these enzymes catalyze seventeen different reaction mechanisms. The most common reactions are hydrolysis of C-O, C-N and C-C bonds (Enzyme Classification (EC) group 3), but other enzymes are oxidoreductases (EC group 1), acyl transferases (EC group 2), lyases (EC group 4) or isomerases (EC group 5). Hydrolysis reactions often follow the canonical esterase mechanism, but eight variations occur where either the formation or cleavage of the acyl enzyme intermediate differs. The remaining eight mechanisms are lyase-type elimination reactions, which do not have an acyl enzyme intermediate and, in four cases, do not even require the catalytic serine. This diversity of mechanisms from the same catalytic triad stems from the ability of the enzymes to bind different substrates, from the requirements for different chemical steps imposed by these new substrates and, only in about half of the cases, from additional hydrogen bond partners or additional general acids/bases in the active site. This detailed analysis shows that binding differences and non-catalytic residues create new mechanisms and are essential for understanding and designing efficient enzymes.
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Affiliation(s)
- Alissa Rauwerdink
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
| | - Romas J. Kazlauskas
- Department of Biochemistry, Molecular Biology & Biophysics and The Biotechnology Institute, University of Minnesota, Saint Paul, Minnesota 55108, United States
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10
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Purification and characterization of lipase from Burkholderia sp. EQ3 isolated from wastewater from a canned fish factory and its application for the synthesis of wax esters. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.02.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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11
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Eum H, Kazlauskas RJ, Ha HJ. Molecular Basis for the Enantio- and Diastereoselectivity ofBurkholderia cepaciaLipase toward γ-Butyrolactone Primary Alcohols. Adv Synth Catal 2014. [DOI: 10.1002/adsc.201400510] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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12
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Lin MC, Lai GW, Lin CS, Lin G. Activation Mechanisms forPseudomonas SpeciesLipase by Cardiovascular Drugsin Vitro. J CHIN CHEM SOC-TAIP 2013. [DOI: 10.1002/jccs.200700226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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13
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Lipase from Pseudomonas stutzeri: Purification, homology modelling and rational explanation of the substrate binding mode. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.11.005] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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14
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Shimotori Y, Tsutano K, Soga K, Osawa Y, Aoyama M, Miyakoshi T. Synthesis of glycosyl ferulate derivatives by amine-promoted glycosylation with regioselective hydrolysis using Novozym 435 and evaluation of their antioxidant properties. Carbohydr Res 2012; 359:11-7. [DOI: 10.1016/j.carres.2012.06.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2012] [Revised: 06/28/2012] [Accepted: 06/29/2012] [Indexed: 12/01/2022]
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15
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Shen YF, Lin G. Kinetics and Protein-Inhibitor Docking Studies of Enantiomers of exo-2-Norbornyl-N-n-butylcarbamates as Pseudomonas Lipase Inhibitors to Probe the Enantioselectivity of the Enzyme. J CHIN CHEM SOC-TAIP 2012. [DOI: 10.1002/jccs.201100252] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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16
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Abstract
Lipases are ubiquitous enzymes, widespread in nature. They were first isolated from bacteria in the early nineteenth century and the associated research continuously increased due to the particular characteristics of these enzymes. This chapter reviews the main sources, structural properties, and industrial applications of these highly studied enzymes.
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Affiliation(s)
- Leticia Casas-Godoy
- Equipe de Catalyse et Ingénierie Moléculaire Enzymatique, Laboratoire d'Ingénierie des Systèmes Biologiques et Procédés, Université de Toulouse, INSA, UPS, INP, LISBP, Toulouse, France
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Shimotori Y, Aoyama M, Tsukasa H, Miyakoshi T. Enantioselective Synthesis of ε-Lactones by Lipase-Catalyzed Resolution. HETEROCYCLES 2012. [DOI: 10.3987/com-12-12426] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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18
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Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study. Acta Biotheor 2011; 59:291-312. [PMID: 21710316 DOI: 10.1007/s10441-011-9137-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 06/11/2011] [Indexed: 12/07/2022]
Abstract
Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.
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Ferrario V, Ebert C, Knapic L, Fattor D, Basso A, Spizzo P, Gardossi L. Conformational Changes of Lipases in Aqueous Media: A Comparative Computational Study and Experimental Implications. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100397] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Barbe S, Cortés J, Siméon T, Monsan P, Remaud-Siméon M, André I. A mixed molecular modeling-robotics approach to investigate lipase large molecular motions. Proteins 2011; 79:2517-29. [DOI: 10.1002/prot.23075] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/18/2011] [Accepted: 04/19/2011] [Indexed: 11/07/2022]
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Solanki K, Gupta MN. A chemically modified lipase preparation for catalyzing the transesterification reaction in even highly polar organic solvents. Bioorg Med Chem Lett 2011; 21:2934-6. [DOI: 10.1016/j.bmcl.2011.03.059] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2011] [Revised: 03/11/2011] [Accepted: 03/16/2011] [Indexed: 10/18/2022]
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22
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GarcÃa-Urdiales E, Busto E, RÃos-LombardÃa N, Gotor-Fernández V, Gotor V. Computational Study of the Lipase-Mediated Desymmetrisation of 2-Substituted-Propane-1,3-Diamines. Chembiochem 2009; 10:2875-83. [DOI: 10.1002/cbic.200900412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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23
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Insights into lid movements ofBurkholderia cepacialipase inferred from molecular dynamics simulations. Proteins 2009; 77:509-23. [DOI: 10.1002/prot.22462] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Majumder AB, Mondal K, Singh TP, Gupta MN. Designing cross-linked lipase aggregates for optimum performance as biocatalysts. BIOCATAL BIOTRANSFOR 2009. [DOI: 10.1080/10242420701685601] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Trodler P, Schmid RD, Pleiss J. Modeling of solvent-dependent conformational transitions in Burkholderia cepacia lipase. BMC STRUCTURAL BIOLOGY 2009; 9:38. [PMID: 19476626 PMCID: PMC2695465 DOI: 10.1186/1472-6807-9-38] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2008] [Accepted: 05/28/2009] [Indexed: 11/10/2022]
Abstract
BACKGROUND The characteristic of most lipases is the interfacial activation at a lipid interface or in non-polar solvents. Interfacial activation is linked to a large conformational change of a lid, from a closed to an open conformation which makes the active site accessible for substrates. While for many lipases crystal structures of the closed and open conformation have been determined, the pathway of the conformational transition and possible bottlenecks are unknown. Therefore, molecular dynamics simulations of a closed homology model and an open crystal structure of Burkholderia cepacia lipase in water and toluene were performed to investigate the influence of solvents on structure, dynamics, and the conformational transition of the lid. RESULTS The conformational transition of B. cepacia lipase was dependent on the solvent. In simulations of closed B. cepacia lipase in water no conformational transition was observed, while in three independent simulations of the closed lipase in toluene the lid gradually opened during the first 10-15 ns. The pathway of conformational transition was accessible and a barrier was identified, where a helix prevented the lid from opening to the completely open conformation. The open structure in toluene was stabilized by the formation of hydrogen bonds.In simulations of open lipase in water, the lid closed slowly during 30 ns nearly reaching its position in the closed crystal structure, while a further lid opening compared to the crystal structure was observed in toluene. While the helical structure of the lid was intact during opening in toluene, it partially unfolded upon closing in water. The closing of the lid in water was also observed, when with eight intermediate structures between the closed and the open conformation as derived from the simulations in toluene were taken as starting structures. A hydrophobic beta-hairpin was moving away from the lid in all simulations in water, which was not observed in simulations in toluene. The conformational transition of the lid was not correlated to the motions of the beta-hairpin structure. CONCLUSION Conformational transitions between the experimentally observed closed and open conformation of the lid were observed by multiple molecular dynamics simulations of B. cepacia lipase. Transitions in both directions occurred without applying restraints or external forces. The opening and closing were driven by the solvent and independent of a bound substrate molecule.
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Affiliation(s)
- Peter Trodler
- Institute of Technical Biochemistry, University of Stuttgart, Allmandring 31, D-70569 Stuttgart, Germany.
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Luić M, Stefanić Z, Ceilinger I, Hodoscek M, Janezic D, Lenac T, Asler IL, Sepac D, Tomić S. Combined X-ray diffraction and QM/MM study of the Burkholderia cepacia lipase-catalyzed secondary alcohol esterification. J Phys Chem B 2008; 112:4876-83. [PMID: 18386861 DOI: 10.1021/jp077717u] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To understand the origin of high enantioselectivity of Burkholderia cepacia lipase (BCL) toward secondary alcohol, (R,S)-1-phenoxy-2-hydroxybutane (1), and its ester (E1), we determined the crystal structure of BCL complexed with phosphonate analogue of S-E1 and accomplished a series of MM, MC, and QM/MM studies. We have found that the inhibitor in the S configuration binds into the BCL active site in the same manner as the R isomer, with an important difference: while in case of the R-inhibitor the H-bond between its alcohol oxygen and catalytic His286 can be formed, in the case of the S-inhibitor this is not possible. Molecular modeling for both E1 enantiomers revealed orientations in which all hydrogen bonds characteristic of productive binding are formed. To check the possibility of chemical transformation, four different orientations of the substrate (two for each enantiomer) were chosen, and a series of ab initio QM/MM calculations were accomplished. Starting from the covalent complex, we modeled the ester (E1) hydrolysis and the alcohol (1) esterification. The calculations revealed that ester release is possible starting with all four covalent complexes. Alcohol release from the BCL-E1 complex in which the S-substrate is bound in the same manner as the S-inhibitor in the crystal structure however is not possible. These results show that the crystallographically determined binding modes should be taken with caution when modeling chemical reactions.
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Affiliation(s)
- Marija Luić
- Rudjer Bosković Institute, Bijenicka 54, HR-10000 Zagreb, Croatia, Belupo dd, Danica 5, HR-48000 Koprivnica, Croatia.
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27
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Jing Q, Kazlauskas RJ. Determination of absolute configuration of secondary alcohols using lipase-catalyzed kinetic resolutions. Chirality 2008; 20:724-35. [DOI: 10.1002/chir.20543] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Lin MC, Hwang MT, Chang HG, Lin CS, Lin G. Benzene-di-N-substituted carbamates as conformationally constrained analogs ofPseudomonas lipase substrates. EUR J LIPID SCI TECH 2007. [DOI: 10.1002/ejlt.200700073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Petkowski JJ, Chruszcz M, Zimmerman MD, Zheng H, Skarina T, Onopriyenko O, Cymborowski MT, Koclega KD, Savchenko A, Edwards A, Minor W. Crystal structures of TM0549 and NE1324--two orthologs of E. coli AHAS isozyme III small regulatory subunit. Protein Sci 2007; 16:1360-7. [PMID: 17586771 PMCID: PMC2206681 DOI: 10.1110/ps.072793807] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2007] [Revised: 04/09/2007] [Accepted: 04/16/2007] [Indexed: 10/23/2022]
Abstract
Crystal structures of two orthologs of the regulatory subunit of acetohydroxyacid synthase III (AHAS, EC 2.2.1.6) from Thermotoga maritima (TM0549) and Nitrosomonas europea (NE1324) were determined by single-wavelength anomalous diffraction methods with the use of selenomethionine derivatives at 2.3 A and 2.5 A, respectively. TM0549 and NE1324 share the same fold, and in both proteins the polypeptide chain contains two separate domains of a similar size. Each protein contains a C-terminal domain with ferredoxin-type fold and an N-terminal ACT domain, of which the latter is characteristic for several proteins involved in amino acid metabolism. The ferredoxin domain is stabilized by a calcium ion in the crystal structure of NE1324 and by a Mg(H2O)(6)2+ ion in TM0549. Both TM0549 and NE1324 form dimeric assemblies in the crystal lattice.
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Affiliation(s)
- Janusz J Petkowski
- Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville 22908, USA
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Reetz MT, Carballeira JD, Peyralans J, Höbenreich H, Maichele A, Vogel A. Expanding the substrate scope of enzymes: combining mutations obtained by CASTing. Chemistry 2007; 12:6031-8. [PMID: 16789057 DOI: 10.1002/chem.200600459] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In a previous paper, the combinatorial active-site saturation test (CAST) was introduced as an effective strategy for the directed evolution of enzymes toward broader substrate acceptance. CASTing comprises the systematic design and screening of focused libraries around the complete binding pocket, but it is only the first step of an evolutionary process because only the initial libraries of mutants are considered. In the present study, a simple method is presented for further optimization of initial hits by combining the mutational changes obtained from two different libraries. Combined lipase mutants were screened for hydrolytic activity against six notoriously difficult substrates (bulky carboxylic acid esters) and improved mutants showing significantly higher activity were identified. The enantioselectivity of the mutants in the hydrolytic kinetic resolution of two substrates was also studied, with the best mutant-substrate combination resulting in a selectivity factor of E=49. Finally, the catalytic profile of the evolved mutants in the hydrolysis of simple nonbranched carboxylic acid esters, ranging from acetate to palmitate, was studied for theoretical reasons.
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Affiliation(s)
- Manfred T Reetz
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim/Ruhr, Germany.
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31
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Lin MC, Lu CP, Cheng YR, Lin YF, Lin CS, Lin G. Inhibition or activation of Pseudomonas species lipase by 1,2-ethylene-di-N-alkylcarbamates in detergents. Chem Phys Lipids 2007; 146:85-93. [PMID: 17274971 DOI: 10.1016/j.chemphyslip.2006.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2006] [Revised: 12/06/2006] [Accepted: 12/22/2006] [Indexed: 11/17/2022]
Abstract
1,2-Ethylene-di-N-n-propylcarbamate (1) is characterized as an essential activator of Pseudomonas species lipase while 1,2-ethylene-di-N-n-butyl-, t-butyl-, n-heptyl-, and n-octyl-carbamates (2-5) are characterized as the pseudo substrate inhibitors of the enzyme in the presence of the detergent taurocholate or triton X-100. The inhibition and activation reactions are more sensitive in taurocholate than in triton X-100. From CD studies, the enzyme changes conformations in the presence of the detergent and further alters conformations by addition of the carbamate activator or inhibitor into the enzyme-detergent adduct. Therefore, this study suggests that the conformational change of lipase during interfacial activation is a continuous process to expose the active site of the enzyme to substrate. From 600 MHz (1)H NMR studies, the conformations of the alpha- and beta-methylene moieties of the activator 1,2-ethylene-di-N-n-propylcarbamate in the presence of substrate change after adding taurocholate into the mixture, and the conformations of the beta-methylene moieties of the inhibitor 1,2-ethylene-di-N-n-butylcarbamate in the presence of substrate alter after adding taurocholate into the mixture.
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Affiliation(s)
- Ming-Cheng Lin
- Institute of Medicine, Department of Cardiology, Chung Shan Medical University Hospital, Taichung 402, Taiwan
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32
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Liljeblad A, Kanerva LT. Biocatalysis as a profound tool in the preparation of highly enantiopure β-amino acids. Tetrahedron 2006. [DOI: 10.1016/j.tet.2006.03.109] [Citation(s) in RCA: 155] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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33
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González-Sabín J, Lavandera I, Rebolledo F, Gotor V. Redesigning the mechanism of the lipase-catalysed aminolysis of esters. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.tetasy.2006.04.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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34
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Tomić S, Ramek M. Quantum mechanical study of Burkholderia cepacia lipase enantioselectivity. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.molcatb.2005.12.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Chiou SY, Cheng YR, Lu CP, Lin YF, Lin LY, Lin G. Kinetics and quantitative structure-activity relationships for pseudomonas
sp. Lipase-catalyzed hydrolysis of both monoesters and diesters of ethylene glycol. J AM OIL CHEM SOC 2006. [DOI: 10.1007/s11746-006-1194-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Shyh-Ying Chiou
- ; Institute of Medicine and Department of Neurosurgery; Chung Shan Medical University; Taichung 402 Taiwan
| | - Yu-Ru Cheng
- ; Department of Chemistry; National Chung-Hsing University; Taiching 402 Taiwan
| | - Chun-Ping Lu
- ; Institute of Biochemistry; National Chung-Hsing University; Taichung 402 Taiwan
| | - Yan-Fu Lin
- ; Department of Chemistry; National Chung-Hsing University; Taiching 402 Taiwan
| | - Long-Yau Lin
- ; Institute of Medicine and Department of Neurosurgery; Chung Shan Medical University; Taichung 402 Taiwan
| | - Gialih Lin
- ; Department of Chemistry; National Chung-Hsing University; Taiching 402 Taiwan
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Mezzetti A, Schrag JD, Cheong CS, Kazlauskas RJ. Mirror-Image Packing in Enantiomer Discrimination. ACTA ACUST UNITED AC 2005; 12:427-37. [PMID: 15850979 DOI: 10.1016/j.chembiol.2005.01.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2004] [Revised: 12/30/2004] [Accepted: 01/28/2005] [Indexed: 11/22/2022]
Abstract
Synthetic chemists often exploit the high enantioselectivity of lipases to prepare pure enantiomers of primary alcohols, but the molecular basis for this enantioselectivity is unknown. The crystal structures of two phosphonate transition-state analogs bound to Burkholderia cepacia lipase reveal this molecular basis for a typical primary alcohol: 2-methyl-3-phenyl-1-propanol. The enantiomeric alcohol moieties adopt surprisingly similar orientations, with only subtle differences that make it difficult to predict how to alter enantioselectivity. These structures, along with a survey of previous structures of enzyme bound enantiomers, reveal that binding of enantiomers does not involve an exchange of two substituent positions as most researchers assumed. Instead, the enantiomers adopt mirror-image packing, where three of the four substituents at the stereocenter lie in similar positions. The fourth substituent, hydrogen, points in opposite directions.
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Affiliation(s)
- Alessandra Mezzetti
- Department of Chemistry, McGill University, Montréal, Québec H3A 2K6, Canada
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37
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A study of the enantiopreference of lipase PS (Pseudomonas cepacia) towards diastereomeric dihydro-5-alkyl-4-hydroxymethyl-2(3H)-furanones. ACTA ACUST UNITED AC 2005. [DOI: 10.1016/j.tetasy.2005.01.036] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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38
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Takano Y, Houk KN. Conformational Preferences in the Transition States and Tetrahedral Intermediates of Transacylations. Relationships to Enzyme-Bound Conformations of Phosphonate Inhibitors of Lipases and Esterases. J Phys Chem A 2004. [DOI: 10.1021/jp045889a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Yu Takano
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
| | - K. N. Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569
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39
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Skouridou V, Chrysina ED, Stamatis H, Oikonomakos NG, Kolisis FN. Kinetic and modelling studies on the lipase catalysed enantioselective esterification of (±)-perillyl alcohol. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.molcatb.2004.02.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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40
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Kim CH, Lee JH, Heo JH, Kwon OS, Kang HA, Rhee SK. Cloning and expression of a novel esterase gene cpoA from Burkholderia cepacia. J Appl Microbiol 2004; 96:1306-16. [PMID: 15139923 DOI: 10.1111/j.1365-2672.2004.02262.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AIMS To screen and clone a novel enzyme with specific activity for the resolution of (R)-beta-acetylmercaptoisobutyrate (RAM) from (R,S)-beta-acetylmercaptoisobutyrate [(R,S)-ester]. METHODS AND RESULTS A micro-organism that produces a novel esterase was isolated and identified as the bacterium Burkholderia cepacia by using the analysis of cellular fatty acids, Biolog automated microbial identification/characterization system, and 16S rRNA gene sequence analysis. A novel esterase gene was cloned from the chromosomal DNA of B. cepacia and was designated as cpoA. The cpoA encodes a polypeptide of 273 amino acids which shows a strong sequence homology with many bacterial nonhaeme chloroperoxidases. In addition, a typical serine-hydrolase motif, Gly-X-Ser-X-Gly, and the highly conserved catalytic triad, Ser95, Asp224, and His253, were identified in the deduced amino acid sequence of cpoA by multiple sequence alignment. CONCLUSION The cpoA cloned from B. cepacia encodes a novel esterase which is highly related to the nonhaeme chloroperoxidases. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first report that describes the isolation and cloning of a serine esterase gene from B. cepacia, which is useful in the chiral resolution of (R,S)-ester. The cloned gene will allow additional research on the bifunctionality of the enzyme with esterase and chloroperoxidase activity at the structural and functional levels.
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Affiliation(s)
- C H Kim
- Laboratory of Metabolic Engineering, Korea Research Institute of Bioscience and Biotechnology, Oun-dong, Yusong, Daejeon, Korea
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41
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Tomić S, Bertoša B, Kojić-Prodić B, Kolosvary I. Stereoselectivity of Burkholderia cepacia lipase towards secondary alcohols: molecular modelling and 3D QSAR approach. ACTA ACUST UNITED AC 2004. [DOI: 10.1016/j.tetasy.2004.02.016] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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42
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Bocola M, Otte N, Jaeger KE, Reetz MT, Thiel W. Learning from Directed Evolution: Theoretical Investigations into Cooperative Mutations in Lipase Enantioselectivity. Chembiochem 2004; 5:214-23. [PMID: 14760743 DOI: 10.1002/cbic.200300731] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Molecular modeling with classical force-fields has been used to study the reactant complex and the tetrahedral intermediate in lipase-catalyzed ester hydrolysis in 20 enzyme/substrate combinations. The R and S enantiomers of alpha-methyldecanoic acid ester served as substrates for the wild-type lipase from Pseudomonas aeruginosa and nine selected mutants. After suitable preparation of initial structures from an available wild-type crystal structure, each system was subjected to 1 ns CHARMM force-field molecular dynamics simulations. The resulting geometric and energetic changes allow interpretation of some experimentally observed effects of mutations, particularly with regard to the "hot spots" at residues 155 and 162. The replacement S155F enhances S enantiopreference through a steric relay involving Leu162. The double mutation S53P + L162G improves S enantioselectivity by creating a new binding pocket for the S enantiomer with an additional stabilizing hydrogen bond to His83. The simulations provide insight into remote and cooperative effects of mutations.
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Affiliation(s)
- Marco Bocola
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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43
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Highly enantioselective kinetic resolution of primary alcohols of the type Ph-X-CH(CH3)-CH2OH by Pseudomonas cepacia lipase: effect of acyl chain length and solvent. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/j.tetasy.2003.09.049] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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44
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Guieysse D, Salagnad C, Monsan P, Remaud-Simeon M, Tran V. Towards a novel explanation of Pseudomonas cepacia lipase enantioselectivity via molecular modelling of the enantiomer trajectory into the active site. ACTA ACUST UNITED AC 2003. [DOI: 10.1016/s0957-4166(03)00374-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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45
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Tomić S, Kojić-Prodić B. A quantitative model for predicting enzyme enantioselectivity: application to Burkholderia cepacia lipase and 3-(aryloxy)-1,2-propanediol derivatives. J Mol Graph Model 2002; 21:241-52. [PMID: 12463642 DOI: 10.1016/s1093-3263(02)00148-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We describe a new approach for predicting the enantioselectivity of enzymes towards racemic compounds. It is based on comparative binding energy (COMBINE) analysis. The approach is used to rationalise the enantioselectivity of Burkholderia cepacia lipase (BCL) towards thirteen racemic 3-(aryloxy)-1,2-propanediols in the process of acylation. According to our molecular modelling study the two 3-(aryloxy)-1,2-propanediols enantiomers bind in the BCL active site in different orientations. To derive a quantitative structure-activity relationship (QSAR), the difference in the interaction energy between two enantiomers with each amino acid residue was computed. These residue-based energy differences were then subjected to chemometric analysis and 3D QSAR models were derived. The models were able to unambiguously predict the fast-reacting enantiomer and the approximate magnitude of the enantioselectivity. The study enabled identification of interactions between the substrate and the lipase amino acid residues that play key roles in secondary alcohol enantiodifferentiation. From the results, it was possible to propose modifications of both, substrate and protein, which would directionally modify enantioselectivity of BCL towards secondary aryl-alcohols.
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Affiliation(s)
- Sanja Tomić
- Ruder Bosković Institute, PO Box 180, HR-10002 Zagreb, Croatia.
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