51
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The role of Pseudomonas cepacia lipase in the asymmetric synthesis of heterocyclic based compounds. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.molcatb.2015.08.022] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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52
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Stauch B, Fisher SJ, Cianci M. Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation. J Lipid Res 2015; 56:2348-58. [PMID: 26447231 PMCID: PMC4655990 DOI: 10.1194/jlr.m063388] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 11/20/2022] Open
Abstract
Lipases (EC 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates, such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of considerable physiological significance with high interest also for their industrial applications. The hydrolysis reaction follows a two-step mechanism, or “interfacial activation,” with adsorption of the enzyme to a heterogeneous interface and subsequent enhancement of the lipolytic activity. Among lipases, Candida antarctica lipase B (CALB) has never shown any significant interfacial activation, and a closed conformation of CALB has never been reported, leading to the conclusion that its behavior was due to the absence of a lid regulating the access to the active site. The lid open and closed conformations and their protonation states are observed in the crystal structure of CALB at 0.91 Å resolution. Having the open and closed states at atomic resolution allows relating protonation to the conformation, indicating the role of Asp145 and Lys290 in the conformation alteration. The findings explain the lack of interfacial activation of CALB and offer new elements to elucidate this mechanism, with the consequent implications for the catalytic properties and classification of lipases.
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Affiliation(s)
- Benjamin Stauch
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Robinson College, University of Cambridge, Cambridge CB3 9AN, United Kingdom
| | - Stuart J Fisher
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Michele Cianci
- European Molecular Biology Laboratory (EMBL), Deutsches Elektronen-Synchrotron (DESY), Hamburg 22607, Germany
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53
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Filice M, Romero O, Aires A, Guisan JM, Rumbero A, Palomo JM. Preparation of an Immobilized Lipase-Palladium Artificial Metalloenzyme as Catalyst in the Heck Reaction: Role of the Solid Phase. Adv Synth Catal 2015. [DOI: 10.1002/adsc.201500014] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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54
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Jammer S, Rizkov D, Gelman F, Lev O. Quantitative structure-activity relationship correlation between molecular structure and the Rayleigh enantiomeric enrichment factor. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2015; 17:1370-1376. [PMID: 26153539 DOI: 10.1039/c5em00084j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
It was recently demonstrated that under environmentally relevant conditions the Rayleigh equation is valid to describe the enantiomeric enrichment - conversion relationship, yielding a proportional constant called the enantiomeric enrichment factor, εER. In the present study we demonstrate a quantitative structure-activity relationship model (QSAR) that describes well the dependence of εER on molecular structure. The enantiomeric enrichment factor can be predicted by the linear Hansch model, which correlates biological activity with physicochemical properties. Enantioselective hydrolysis of sixteen derivatives of 2-(phenoxy)propionate (PPMs) have been analyzed during enzymatic degradation by lipases from Pseudomonas fluorescens (PFL), Pseudomonas cepacia (PCL), and Candida rugosa (CRL). In all cases the QSAR relationships were significant with R(2) values of 0.90-0.93, and showed high predictive abilities with internal and external validations providing QLOO(2) values of 0.85-0.87 and QExt(2) values of 0.8-0.91. Moreover, it is demonstrated that this model enables differentiation between enzymes with different binding site shapes. The enantioselectivity of PFL and PCL was dictated by electronic properties, whereas the enantioselectivity of CRL was determined by lipophilicity and steric factors. The predictive ability of the QSAR model demonstrated in the present study may serve as a helpful tool in environmental studies, assisting in source tracking of unstudied chiral compounds belonging to a well-studied homologous series.
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Affiliation(s)
- S Jammer
- The Casali Center of Applied Chemistry, The Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel.
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55
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Piper DE, Romanow WG, Gunawardane RN, Fordstrom P, Masterman S, Pan O, Thibault ST, Zhang R, Meininger D, Schwarz M, Wang Z, King C, Zhou M, Walker NPC. The high-resolution crystal structure of human LCAT. J Lipid Res 2015. [PMID: 26195816 DOI: 10.1194/jlr.m059873] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
LCAT is intimately involved in HDL maturation and is a key component of the reverse cholesterol transport (RCT) pathway which removes excess cholesterol molecules from the peripheral tissues to the liver for excretion. Patients with loss-of-function LCAT mutations exhibit low levels of HDL cholesterol and corneal opacity. Here we report the 2.65 Å crystal structure of the human LCAT protein. Crystallization required enzymatic removal of N-linked glycans and complex formation with a Fab fragment from a tool antibody. The crystal structure reveals that LCAT has an α/β hydrolase core with two additional subdomains that play important roles in LCAT function. Subdomain 1 contains the region of LCAT shown to be required for interfacial activation, while subdomain 2 contains the lid and amino acids that shape the substrate binding pocket. Mapping the naturally occurring mutations onto the structure provides insight into how they may affect LCAT enzymatic activity.
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Affiliation(s)
- Derek E Piper
- Therapeutic Discovery Amgen Inc., South San Francisco, CA 94080
| | | | | | | | | | - Oscar Pan
- Therapeutic Discovery, Amgen Inc., Burnaby, BC V5A1V7, Canada
| | | | - Richard Zhang
- Therapeutic Discovery Amgen Inc., South San Francisco, CA 94080
| | | | - Margrit Schwarz
- Metabolic Disorders, Amgen Inc., South San Francisco, CA 94080
| | - Zhulun Wang
- Therapeutic Discovery Amgen Inc., South San Francisco, CA 94080
| | - Chadwick King
- Therapeutic Discovery, Amgen Inc., Burnaby, BC V5A1V7, Canada
| | - Mingyue Zhou
- Metabolic Disorders, Amgen Inc., South San Francisco, CA 94080
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56
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Structure and function of lysosomal phospholipase A2 and lecithin:cholesterol acyltransferase. Nat Commun 2015; 6:6250. [PMID: 25727495 PMCID: PMC4397983 DOI: 10.1038/ncomms7250] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2014] [Accepted: 01/07/2015] [Indexed: 11/22/2022] Open
Abstract
Lysosomal phospholipase A2 (LPLA2) and lecithin:cholesterol acyltransferase (LCAT) belong to a structurally uncharacterized family of key lipid metabolizing enzymes responsible for lung surfactant catabolism and for reverse cholesterol transport, respectively. Whereas LPLA2 is predicted to underlie the development of drug-induced phospholipidosis, somatic mutations in LCAT cause fish eye disease and familial LCAT deficiency. Here we describe several high resolution crystal structures of human LPLA2 and a low resolution structure of LCAT that confirms its close structural relationship to LPLA2. Insertions in the α/β hydrolase core of LPLA2 form domains that are responsible for membrane interaction and binding the acyl chains and head groups of phospholipid substrates. The LCAT structure suggests the molecular basis underlying human disease for most of the known LCAT missense mutations, and paves the way for rational development of new therapeutics to treat LCAT deficiency, atherosclerosis and acute coronary syndrome.
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57
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Lima LN, Oliveira GC, Rojas MJ, Castro HF, Da Rós PCM, Mendes AA, Giordano RLC, Tardioli PW. Immobilization of Pseudomonas fluorescens lipase on hydrophobic supports and application in biodiesel synthesis by transesterification of vegetable oils in solvent-free systems. J Ind Microbiol Biotechnol 2015; 42:523-35. [PMID: 25626526 DOI: 10.1007/s10295-015-1586-9] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 01/13/2015] [Indexed: 10/24/2022]
Abstract
This work describes the preparation of biocatalysts for ethanolysis of soybean and babassu oils in solvent-free systems. Polystyrene, Amberlite (XAD-7HP), and octyl-silica were tested as supports for the immobilization of Pseudomonas fluorescens lipase (PFL). The use of octyl-silica resulted in a biocatalyst with high values of hydrolytic activity (650.0 ± 15.5 IU/g), immobilization yield (91.3 ± 0.3 %), and recovered activity (82.1 ± 1.5 %). PFL immobilized on octyl-silica was around 12-fold more stable than soluble PFL, at 45 °C and pH 8.0, in the presence of ethanol at 36 % (v/v). The biocatalyst provided high vegetable oil transesterification yields of around 97.5 % after 24 h of reaction using babassu oil and around 80 % after 48 h of reaction using soybean oil. The PFL-octyl-silica biocatalyst retained around 90 % of its initial activity after five cycles of transesterification of soybean oil. Octyl-silica is a promising support that can be used to immobilize PFL for subsequent application in biodiesel synthesis.
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Affiliation(s)
- Lionete N Lima
- Graduate Program in Chemical Engineering, Federal University of São Carlos, Rodovia Washington Luiz, km 235, São Carlos, SP, 13565-905, Brazil
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58
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Skariyachan S, Megha M, Kini MN, Mukund KM, Rizvi A, Vasist K. Selection and screening of microbial consortia for efficient and ecofriendly degradation of plastic garbage collected from urban and rural areas of Bangalore, India. ENVIRONMENTAL MONITORING AND ASSESSMENT 2015; 187:4174. [PMID: 25504187 DOI: 10.1007/s10661-014-4174-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
Industrialization and urbanization have led to massive accumulation of plastic garbage all over India. The persistence of plastic in soil and aquatic environment has become ecological threat to the metropolitan city such as Bangalore, India. Present study investigates an ecofriendly, efficient and cost-effective approach for plastic waste management by the screening of novel microbial consortia which are capable of degrading plastic polymers. Plastic-contaminated soil and water samples were collected from six hot spots of urban and rural areas of Bangalore. The plastic-degrading bacteria were enriched, and degradation ability was determined by zone of clearance method. The percentage of polymer degradation was initially monitored by weight loss method, and the main isolates were characterized by standard microbiology protocols. These isolates were used to form microbial consortia, and the degradation efficiency of the consortia was compared with individual isolate and known strains obtained from the Microbial Type Culture Collection (MTCC) and Gene Bank, India. One of the main enzymes responsible for polymer degradation was identified, and the biodegradation mechanism was hypothesized by bioinformatics studies. From this study, it is evident that the bacteria utilized the plastic polymer as a sole source of carbon and showed 20-50% weight reduction over a period of 120 days. The two main bacteria responsible for the degradation were microbiologically characterized to be Pseudomonas spp. These bacteria could grow optimally at 37 °C in pH 9.0 and showed 35-40% of plastic weight reduction over 120 days. These isolates were showed better degradation ability than known strains from MTCC. The current study further revealed that the microbial consortia formulated by combining Psuedomonas spp. showed 40 plastic weight reduction over a period of 90 days. Further, extracellular lipase, one of the main enzymes responsible for polymer degradation, was identified. The computational docking studies suggested that polyethylene glycol and polystyrene present in the plastics might have good interaction towards the microbial lipase with stable binding and interacting forces which probably could be one of the reasons for the degradative mechanisms.
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Affiliation(s)
- Sinosh Skariyachan
- R & D Centre, Department of Biotechnology Engineering, Dayananda Sagar Institutions, Bangalore, Karnataka, 560 078, India,
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59
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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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60
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Roussel A, Amara S, Nyyssölä A, Mateos-Diaz E, Blangy S, Kontkanen H, Westerholm-Parvinen A, Carrière F, Cambillau C. A Cutinase from Trichoderma reesei with a lid-covered active site and kinetic properties of true lipases. J Mol Biol 2014; 426:3757-3772. [PMID: 25219509 DOI: 10.1016/j.jmb.2014.09.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2014] [Revised: 09/02/2014] [Accepted: 09/04/2014] [Indexed: 02/05/2023]
Abstract
Cutinases belong to the α/β-hydrolase fold family of enzymes and degrade cutin and various esters, including triglycerides, phospholipids and galactolipids. Cutinases are able to degrade aggregated and soluble substrates because, in contrast with true lipases, they do not have a lid covering their catalytic machinery. We report here the structure of a cutinase from the fungus Trichoderma reesei (Tr) in native and inhibitor-bound conformations, along with its enzymatic characterization. A rare characteristic of Tr cutinase is its optimal activity at acidic pH. Furthermore, Tr cutinase, in contrast with classical cutinases, possesses a lid covering its active site and requires the presence of detergents for activity. In addition to the presence of the lid, the core of the Tr enzyme is very similar to other cutinase cores, with a central five-stranded β-sheet covered by helices on either side. The catalytic residues form a catalytic triad involving Ser164, His229 and Asp216 that is covered by the two N-terminal helices, which form the lid. This lid opens in the presence of surfactants, such as β-octylglucoside, and uncovers the catalytic crevice, allowing a C11Y4 phosphonate inhibitor to bind to the catalytic serine. Taken together, these results reveal Tr cutinase to be a member of a new group of lipolytic enzymes resembling cutinases but with kinetic and structural features of true lipases and a heightened specificity for long-chain triglycerides.
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Affiliation(s)
- Alain Roussel
- Architecture et Fonction des Macromolécules Biologiques, Aix Marseille Université, 13284 Marseille Cedex 09, France; Architecture et Fonction des Macromolécules Biologiques, UMR7257, Centre National de la Recherche Scientifique, 13288 Marseille Cedex 09, France
| | - Sawsan Amara
- Aix Marseille Université, UMR7282, Centre National de la Recherche Scientifique, 13402 Marseille Cedex 20, France
| | - Antti Nyyssölä
- VTT Biotechnology, P. O. Box 1000, FIN-02044 VTT, Finland
| | - Eduardo Mateos-Diaz
- Aix Marseille Université, UMR7282, Centre National de la Recherche Scientifique, 13402 Marseille Cedex 20, France
| | - Stéphanie Blangy
- Architecture et Fonction des Macromolécules Biologiques, Aix Marseille Université, 13284 Marseille Cedex 09, France; Architecture et Fonction des Macromolécules Biologiques, UMR7257, Centre National de la Recherche Scientifique, 13288 Marseille Cedex 09, France
| | | | | | - Frédéric Carrière
- Aix Marseille Université, UMR7282, Centre National de la Recherche Scientifique, 13402 Marseille Cedex 20, France
| | - Christian Cambillau
- Architecture et Fonction des Macromolécules Biologiques, Aix Marseille Université, 13284 Marseille Cedex 09, France; Architecture et Fonction des Macromolécules Biologiques, UMR7257, Centre National de la Recherche Scientifique, 13288 Marseille Cedex 09, France.
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61
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Sun Y, Yin S, Feng Y, Li J, Zhou J, Liu C, Zhu G, Guo Z. Molecular basis of the general base catalysis of an α/β-hydrolase catalytic triad. J Biol Chem 2014; 289:15867-79. [PMID: 24737327 DOI: 10.1074/jbc.m113.535641] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The serine-histidine-aspartate triad is well known for its covalent, nucleophilic catalysis in a diverse array of enzymatic transformations. Here we show that its nucleophilicity is shielded and its catalytic role is limited to being a specific general base by an open-closed conformational change in the catalysis of (1R,6R)-2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (or MenH), a typical α/β-hydrolase fold enzyme in the vitamin K biosynthetic pathway. This enzyme is found to adopt an open conformation without a functional triad in its ligand-free form and a closed conformation with a fully functional catalytic triad in the presence of its reaction product. The open-to-closed conformational transition involves movement of half of the α-helical cap domain, which causes extensive structural changes in the α/β-domain and forces the side chain of the triad histidine to adopt an energetically disfavored gauche conformation to form the functional triad. NMR analysis shows that the inactive open conformation without a triad prevails in ligand-free solution and is converted to the closed conformation with a properly formed triad by the reaction product. Mutation of the residues crucial to this open-closed transition either greatly decreases or completely eliminates the enzyme activity, supporting an important catalytic role for the structural change. These findings suggest that the open-closed conformational change tightly couples formation of the catalytic triad to substrate binding to enhance the substrate specificities and simultaneously shield the nucleophilicity of the triad, thus allowing it to expand its catalytic power beyond the nucleophilic catalysis.
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Affiliation(s)
- Yueru Sun
- From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and
| | - Shuhui Yin
- From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and
| | - Yitao Feng
- From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and
| | - Jie Li
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Jiahai Zhou
- State Key Laboratory of Bio-organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai 200032, China
| | - Changdong Liu
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and Division of Life Sciences, and
| | - Guang Zhu
- State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and Division of Life Sciences, and
| | - Zhihong Guo
- From the Department of Chemistry, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong Special Administrative Region (SAR), China and
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62
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Rozeboom HJ, Godinho LF, Nardini M, Quax WJ, Dijkstra BW. Crystal structures of two Bacillus carboxylesterases with different enantioselectivities. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1844:567-75. [PMID: 24418394 DOI: 10.1016/j.bbapap.2014.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/02/2014] [Accepted: 01/05/2014] [Indexed: 01/08/2023]
Abstract
Naproxen esterase (NP) from Bacillus subtilis Thai I-8 is a carboxylesterase that catalyzes the enantioselective hydrolysis of naproxenmethylester to produce S-naproxen (E>200). It is a homolog of CesA (98% sequence identity) and CesB (64% identity), both produced by B. subtilis strain 168. CesB can be used for the enantioselective hydrolysis of 1,2-O-isopropylideneglycerol (solketal) esters (E>200 for IPG-caprylate). Crystal structures of NP and CesB, determined to a resolution of 1.75Å and 2.04Å, respectively, showed that both proteins have a canonical α/β hydrolase fold with an extra N-terminal helix stabilizing the cap subdomain. The active site in both enzymes is located in a deep hydrophobic groove and includes the catalytic triad residues Ser130, His274, and Glu245. A product analog, presumably 2-(2-hydroxyethoxy)acetic acid, was bound in the NP active site. The enzymes have different enantioselectivities, which previously were shown to result from only a few amino acid substitutions in the cap domain. Modeling of a substrate in the active site of NP allowed explaining the different enantioselectivities. In addition, Ala156 may be a determinant of enantioselectivity as well, since its side chain appears to interfere with the binding of certain R-enantiomers in the active site of NP. However, the exchange route for substrate and product between the active site and the solvent is not obvious from the structures. Flexibility of the cap domain might facilitate such exchange. Interestingly, both carboxylesterases show higher structural similarity to meta-cleavage compound (MCP) hydrolases than to other α/β hydrolase fold esterases.
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Affiliation(s)
- Henriëtte J Rozeboom
- Laboratory of Biophysical Chemistry, Centre of Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Luis F Godinho
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Marco Nardini
- Laboratory of Biophysical Chemistry, Centre of Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Wim J Quax
- Department of Pharmaceutical Biology, Groningen Research Institute of Pharmacy, University of Groningen, Antonius Deusinglaan 1, 9713AV Groningen, The Netherlands
| | - Bauke W Dijkstra
- Laboratory of Biophysical Chemistry, Centre of Life Sciences, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands.
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63
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Zhu X, Fryd M, Valentine AM, Wayland BB. Corona charge selective micelle degradation catalyzed by P. cepacia lipase isoforms. Chem Commun (Camb) 2014; 50:964-7. [DOI: 10.1039/c3cc47740a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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64
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Hwang HT, Qi F, Yuan C, Zhao X, Ramkrishna D, Liu D, Varma A. Lipase-catalyzed process for biodiesel production: Protein engineering and lipase production. Biotechnol Bioeng 2013; 111:639-53. [PMID: 24284881 DOI: 10.1002/bit.25162] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/16/2013] [Accepted: 11/20/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Hyun Tae Hwang
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Feng Qi
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Chongli Yuan
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Xuebing Zhao
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Doraiswami Ramkrishna
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Dehua Liu
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Arvind Varma
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
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65
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Li X, Xu L, Wang G, Zhang H, Yan Y. Conformation studies on Burkholderia cenocepacia lipase via resolution of racemic 1-phenylethanol in non-aqueous medium and its process optimization. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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66
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John S, Thangapandian S, Lazar P, Son M, Park C, Lee KW. New insights in the activation of human cholesterol esterase to design potent anti-cholesterol drugs. Mol Divers 2013; 18:119-31. [PMID: 24173651 DOI: 10.1007/s11030-013-9464-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Accepted: 07/19/2013] [Indexed: 12/01/2022]
Abstract
Primary hypercholesterolemia is the root cause for major health issues like coronary heart disease and atherosclerosis. Regulating plasma cholesterol level, which is the product of biosynthesis as well as dietary intake, has become one of the major therapeutic strategies to effectively control these diseases. Human cholesterol esterase (hCEase) is an interesting target involved in the regulation of plasma cholesterol level and thus inhibition of this enzyme is highly effective in the treatment of hypercholesterolemia. This study was designed to understand the activation mechanism that enables the enzyme to accommodate long chain fatty acids and to identify the structural elements for the successful catalysis. Primarily the activation efficiencies of three different bile salts were studied and compared using molecular dynamics simulations. Based on the conformations of major surface loops, hydrogen bond interactions, and distance analyses, taurocholate was concluded as the preferred activator of the enzyme. Furthermore, the importance of two bile salt binding sites (proximal and remote) and the crucial role of 7α-OH group of the bile salts in the activation of hCEase was examined and evidenced. The results of our study explain the structural insights of the activation mechanism and show the key features of the bile salts responsible for the enzyme activation which are very useful in hypolipidemic drug designing strategies.
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Affiliation(s)
- Shalini John
- Division of Applied Life Science (BK21 Program), Systems and Synthetic Agrobiotech Center (SSAC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Research Institute of Natural Science (RINS), Gyeongsang National University (GNU), 501 Jinju-daero, Gazwa-dong, Jinju, 660-701, Republic of Korea
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Li X, Huang S, Xu L, Yan Y. Improving activity and enantioselectivity of lipase via immobilization on macroporous resin for resolution of racemic 1- phenylethanol in non-aqueous medium. BMC Biotechnol 2013; 13:92. [PMID: 24168516 PMCID: PMC4228463 DOI: 10.1186/1472-6750-13-92] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Accepted: 10/23/2013] [Indexed: 11/18/2022] Open
Abstract
Background Burkholderia cepacia lipase (BCL) has been proved to be capable of resolution reactions. However, its free form usually exhibits low stability, bad resistance and no reusability, which restrict its further industrial applications. Therefore, it is of great importance to improve the catalytic performance of free lipase in non-aqueous medium. Results In this work, macroporous resin NKA (MPR-NKA) was utilized as support for lipase immobilization. Racemic transesterification of 1-phenylethanol with vinyl acetate was chosen as model reaction. Compared with its free form, the enzyme activity and enantioselectivity (ees) of the immobilized lipase have been significantly enhanced. The immobilized BCL exhibited a satisfactory thermostability over a wide range of temperature (from 10 to 65°C) and an excellent catalytic efficiency. After being used for more than 30 successive batches, the immobilized lipase still kept most of its activity. In comparison with other immobilized lipases, the immobilized BCL also exhibits better catalytic efficiency, which indicates a significant potential in industrial applications. Conclusion The results of this study have proved that MPR-NKA was an excellent support for immobilization of lipase via the methods of N2 adsorption–desorption, scanning electron microscopy (SEM), energy dispersive spectroscopy (EDS) and Fourier transform-infrared spectroscopy (FT-IR). The improvement of enzyme activity and ees for the immobilized lipase was closely correlated with the alteration of its secondary structure. This information may contribute to a better understanding of the mechanism of immobilization and enzymatic biotransformation in non-aqueous medium.
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Affiliation(s)
| | | | | | - Yunjun Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China.
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68
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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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69
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Ren B, Wu M, Wang Q, Peng X, Wen H, McKinstry WJ, Chen Q. Crystal Structure of Tannase from Lactobacillus plantarum. J Mol Biol 2013; 425:2737-51. [DOI: 10.1016/j.jmb.2013.04.032] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 04/26/2013] [Accepted: 04/27/2013] [Indexed: 10/26/2022]
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70
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Zhu X, Fryd M, Wayland BB. Kinetic-mechanistic studies of lipase-polymer micelle binding and catalytic degradation: Enzyme interfacial activation. Polym Degrad Stab 2013. [DOI: 10.1016/j.polymdegradstab.2013.03.016] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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71
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Ellis EE, Adkins CT, Galovska NM, Lavis LD, Johnson RJ. Decoupled roles for the atypical, bifurcated binding pocket of the ybfF hydrolase. Chembiochem 2013; 14:1134-44. [PMID: 23670977 DOI: 10.1002/cbic.201300085] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Indexed: 11/08/2022]
Abstract
Serine hydrolases have diverse intracellular substrates, biological functions, and structural plasticity, and are thus important for biocatalyst design. Amongst serine hydrolases, the recently described ybfF enzyme family are promising novel biocatalysts with an unusual bifurcated substrate-binding cleft and the ability to recognize commercially relevant substrates. We characterized in detail the substrate selectivity of a novel ybfF enzyme from Vibrio cholerae (Vc-ybfF) by using a 21-member library of fluorogenic ester substrates. We assigned the roles of the two substrate-binding clefts in controlling the substrate selectivity and folded stability of Vc-ybfF by comprehensive substitution analysis. The overall substrate preference of Vc-ybfF was for short polar chains, but it retained significant activity with a range of cyclic and extended esters. This broad substrate specificity combined with the substitutional analysis demonstrates that the larger binding cleft controls the substrate specificity of Vc-ybfF. Key selectivity residues (Tyr116, Arg120, Tyr209) are also located at the larger binding pocket and control the substrate specificity profile. In the structure of ybfF the narrower binding cleft contains water molecules prepositioned for hydrolysis, but based on substitution this cleft showed only minimal contribution to catalysis. Instead, the residues surrounding the narrow binding cleft and at the entrance to the binding pocket contributed significantly to the folded stability of Vc-ybfF. The relative contributions of each cleft of the binding pocket to the catalytic activity and folded stability of Vc-ybfF provide a valuable map for designing future biocatalysts based on the ybfF scaffold.
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Affiliation(s)
- Elizabeth E Ellis
- Department of Chemistry, Butler University, 4600 Sunset Ave, Indianapolis, IN 46208-3443, USA
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72
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Zhu X, Sharma VD, Fryd M, Ilies MA, Wayland BB. Enzyme and acid catalyzed degradation of PEG45-b-PBO0,6,9-b-PCL60 micelles: Increased hydrolytic stability by engineering the hydrophilic–hydrophobic interface. POLYMER 2013. [DOI: 10.1016/j.polymer.2013.03.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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73
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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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74
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Housaindokht MR, Monhemi H. The open lid conformation of the lipase is explored in the compressed gas: New insights from molecular dynamic simulation. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2012.11.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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75
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Determination of amino acids and dipeptides is correlated significantly with optimum temperatures of microbial lipases. ANN MICROBIOL 2013. [DOI: 10.1007/s13213-012-0475-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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76
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Structure–function analysis of a new bacterial lipase: Effect of local structure reorganization on lipase activity. Int J Biol Macromol 2013; 54:180-5. [DOI: 10.1016/j.ijbiomac.2012.12.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Revised: 12/10/2012] [Accepted: 12/11/2012] [Indexed: 11/20/2022]
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77
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Filippova EV, Weston LA, Kuhn ML, Geissler B, Gehring AM, Armoush N, Adkins CT, Minasov G, Dubrovska I, Shuvalova L, Winsor JR, Lavis LD, Satchell KJF, Becker DP, Anderson WF, Johnson RJ. Large scale structural rearrangement of a serine hydrolase from Francisella tularensis facilitates catalysis. J Biol Chem 2013; 288:10522-35. [PMID: 23430251 DOI: 10.1074/jbc.m112.446625] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Tularemia is a deadly, febrile disease caused by infection by the gram-negative bacterium, Francisella tularensis. Members of the ubiquitous serine hydrolase protein family are among current targets to treat diverse bacterial infections. Herein we present a structural and functional study of a novel bacterial carboxylesterase (FTT258) from F. tularensis, a homologue of human acyl protein thioesterase (hAPT1). The structure of FTT258 has been determined in multiple forms, and unexpectedly large conformational changes of a peripheral flexible loop occur in the presence of a mechanistic cyclobutanone ligand. The concomitant changes in this hydrophobic loop and the newly exposed hydrophobic substrate binding pocket suggest that the observed structural changes are essential to the biological function and catalytic activity of FTT258. Using diverse substrate libraries, site-directed mutagenesis, and liposome binding assays, we determined the importance of these structural changes to the catalytic activity and membrane binding activity of FTT258. Residues within the newly exposed hydrophobic binding pocket and within the peripheral flexible loop proved essential to the hydrolytic activity of FTT258, indicating that structural rearrangement is required for catalytic activity. Both FTT258 and hAPT1 also showed significant association with liposomes designed to mimic bacterial or human membranes, respectively, even though similar structural rearrangements for hAPT1 have not been reported. The necessity for acyl protein thioesterases to have maximal catalytic activity near the membrane surface suggests that these conformational changes in the protein may dually regulate catalytic activity and membrane association in bacterial and human homologues.
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Affiliation(s)
- Ekaterina V Filippova
- Center for Structural Genomics of Infectious Diseases and the Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois 60611, USA
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78
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Hosseini M, Karkhane AA, Yakhchali B, Shamsara M, Aminzadeh S, Morshedi D, Haghbeen K, Torktaz I, Karimi E, Safari Z. In Silico and Experimental Characterization of Chimeric Bacillus thermocatenulatus Lipase with the Complete Conserved Pentapeptide of Candida rugosa Lipase. Appl Biochem Biotechnol 2012; 169:773-85. [DOI: 10.1007/s12010-012-0014-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2012] [Accepted: 12/03/2012] [Indexed: 10/27/2022]
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79
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Crystal structure of Proteus mirabilis lipase, a novel lipase from the Proteus/psychrophilic subfamily of lipase family I.1. PLoS One 2012; 7:e52890. [PMID: 23300806 PMCID: PMC3530535 DOI: 10.1371/journal.pone.0052890] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2012] [Accepted: 11/23/2012] [Indexed: 12/29/2022] Open
Abstract
Bacterial lipases from family I.1 and I.2 catalyze the hydrolysis of triacylglycerol between 25-45°C and are used extensively as biocatalysts. The lipase from Proteus mirabilis belongs to the Proteus/psychrophilic subfamily of lipase family I.1 and is a promising catalyst for biodiesel production because it can tolerate high amounts of water in the reaction. Here we present the crystal structure of the Proteus mirabilis lipase, a member of the Proteus/psychrophilic subfamily of I.1lipases. The structure of the Proteus mirabilis lipase was solved in the absence and presence of a bound phosphonate inhibitor. Unexpectedly, both the apo and inhibitor bound forms of P. mirabilis lipase were found to be in a closed conformation. The structure reveals a unique oxyanion hole and a wide active site that is solvent accessible even in the closed conformation. A distinct mechanism for Ca²⁺ coordination may explain how these lipases can fold without specific chaperones.
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80
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Rahman MZA, Salleh AB, Rahman RNZRA, Rahman MBA, Basri M, Leow TC. Unlocking the mystery behind the activation phenomenon of T1 lipase: a molecular dynamics simulations approach. Protein Sci 2012; 21:1210-21. [PMID: 22692819 PMCID: PMC3537241 DOI: 10.1002/pro.2108] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2012] [Revised: 06/04/2012] [Accepted: 06/04/2012] [Indexed: 12/30/2022]
Abstract
The activation of lipases has been postulated to proceed by interfacial activation, temperature switch activation, or aqueous activation. Recently, based on molecular dynamics (MD) simulation experiments, the T1 lipase activation mechanism was proposed to involve aqueous activation in addition to a double-flap mechanism. Because the open conformation structure is still unavailable, it is difficult to validate the proposed theory unambiguously to understand the behavior of the enzyme. In this study, we try to validate the previous reports and uncover the mystery behind the activation process using structural analysis and MD simulations. To investigate the effects of temperature and environmental conditions on the activation process, MD simulations in different solvent environments (water and water-octane interface) and temperatures (20, 50, 70, 80, and 100°C) were performed. Based on the structural analysis of the lipases in the same family of T1 lipase (I.5 lipase family), we proposed that the lid domain comprises α6 and α7 helices connected by a loop, thus forming a helix-loop-helix motif involved in interfacial activation. Throughout the MD simulations experiments, lid displacements were only observed in the water-octane interface, not in the aqueous environment with respect to the temperature effect, suggesting that the activation process is governed by interfacial activation coupled with temperature switch activation. Examining the activation process in detail revealed that the large structural rearrangement of the lid domain was caused by the interaction between the hydrophobic residues of the lid with octane, a nonpolar solvent, and this conformation was found to be thermodynamically favorable.
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Affiliation(s)
| | - Abu Bakar Salleh
- Institute of Bioscience, Universiti Putra Malaysia43400 Serdang, Selangor
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia43400 Serdang, Selangor
| | - Raja Noor Zaliha Raja Abdul Rahman
- Institute of Bioscience, Universiti Putra Malaysia43400 Serdang, Selangor
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia43400 Serdang, Selangor
| | | | - Mahiran Basri
- Institute of Bioscience, Universiti Putra Malaysia43400 Serdang, Selangor
- Faculty of Science, Universiti Putra Malaysia43400 Serdang, Selangor
| | - Thean Chor Leow
- Institute of Bioscience, Universiti Putra Malaysia43400 Serdang, Selangor
- Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia43400 Serdang, Selangor
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81
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Enhanced productivity of electrospun polyvinyl alcohol nanofibrous mats using aqueous N,N-dimethylformamide solution and their application to lipase-immobilizing membrane-shaped catalysts. J Biosci Bioeng 2012; 114:204-8. [DOI: 10.1016/j.jbiosc.2012.03.017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 03/28/2012] [Accepted: 03/28/2012] [Indexed: 11/17/2022]
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82
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Zheng J, Xu L, Liu Y, Zhang X, Yan Y. Lipase-coated K2SO4 micro-crystals: preparation, characterization, and application in biodiesel production using various oil feedstocks. BIORESOURCE TECHNOLOGY 2012; 110:224-231. [PMID: 22330591 DOI: 10.1016/j.biortech.2012.01.088] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 01/14/2012] [Accepted: 01/17/2012] [Indexed: 05/31/2023]
Abstract
This study investigated the preparation and characteristics of protein-coated microcrystals (PCMCs) from Pseudomonas cepacia lipase (PS) and K(2)SO(4), and their application in biodiesel synthesis, via single factorial experiments and response surface methodology (RSM), the optimized PCMC-PS exhibited high activity and stability; the optimal temperature was 60°C (which gave 99.83% conversion), although fairly high activity was exhibited after incubation at different temperatures (25-70°C). The organic solvents stability of the PCMC-PS was improved, and it significantly reduced ethanol toxicity. Circular dichroism (CD) analysis revealed the correlation between the conformation and the enzyme activity. The morphology of the PCMC-PS was also confirmed via scanning electron microscopy (SEM). When catalyzed by PCMC-PS, above 83% biodiesel yield was obtained for most of the seven oils tested. The PCMC-PS (washed with hexane) activity remained relatively stable after eight batch reactions, with only a 15.73% reduction in the conversion (from 99.02% to 83.29%).
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Affiliation(s)
- Jingjing Zheng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, PR China
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83
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Enhancement of the activity and enantioselectivity of lipase by sol-gel encapsulation immobilization onto β-cyclodextrin-based polymer. Appl Biochem Biotechnol 2012; 166:1927-40. [PMID: 22383051 DOI: 10.1007/s12010-012-9621-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2011] [Accepted: 02/20/2012] [Indexed: 10/28/2022]
Abstract
Candida rugosa lipase was encapsulated within a chemically inert sol-gel support prepared by polycondensation with tetraethoxysilane and octyltriethoxysilane in the presence of β-cyclodextrin-based polymer. The catalytic activity of the encapsulated lipases was evaluated both in the hydrolysis of p-nitrophenylpalmitate and the enantioselective hydrolysis of racemic Naproxen methyl ester. It has been observed that the percent activity yield of the encapsulated lipase was 65 U/g, which is 7.5 times higher than that of the covalently immobilized lipase. The β-cyclodextrin-based encapsulated lipases had higher conversion and enantioselectivity compared with covalently immobilized lipase. The study confirms an excellent enantioselectivity (E >300) for the encapsulated lipase with an enantiomeric excess value of 98% for S-naproxen.
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84
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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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85
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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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86
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Biomimetic affinity purification of Candida antarctica lipase B. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3896-900. [DOI: 10.1016/j.jchromb.2011.10.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Revised: 10/19/2011] [Accepted: 10/31/2011] [Indexed: 11/21/2022]
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87
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Jin Q, Jia G, Zhang Y, Yang Q, Li C. Hydrophobic surface induced activation of Pseudomonas cepacia lipase immobilized into mesoporous silica. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:12016-12024. [PMID: 21851086 DOI: 10.1021/la202794t] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Lipase from Pseudomonas cepacia (PCL) was successfully immobilized into siliceous mesocellular foams (MCFs) with various hydrophobic/hydrophilic surfaces. The catalytic performances of immobilized PCL were investigated using the transesterification reaction and hydrolytic reaction as model reactions. The specific activity of immobilized PCL greatly increased with enhanced surface hydrophobicity of MCFs, mainly because of lipase activation via hydrophobic interaction between alkyl groups in MCFs and the surface loop (so-called "lid") of PCL. Conformational changes of immobilized PCL were further investigated using time-resolved fluorescence spectroscopy with Trp as an intrinsic probe. When the immobilized PCL was suspended in phosphate buffer, short-lived τ(1) shortened and the fractional contribution of τ(1) significantly increased with the increasing level of surface hydrophobicity of MCFs. These results revealed that Trp(s) of the immobilized PCL were surrounded by a hydrophilic microenvironment because of the fact that the opened "lid" permitted the diffusion of water to the active site cleft. However, for the immobilized PCL suspended in n-hexane, long-lived τ(3) increased with the increase of surface hydrophobicity of MCFs. The reduced interaction between Trp(s) and the surrounding protein matrix was due to intercalation of n-hexane into the active site cleft when the lipase was in open conformation. The above results demonstrated that PCL immobilized into MCF with hydrophobic surfaces were in an activated open conformation.
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Affiliation(s)
- Qianru Jin
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, People's Republic of China
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88
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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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89
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Direct recovery of lipase derived from Burkholderia cepacia in recycling aqueous two-phase flotation. Sep Purif Technol 2011. [DOI: 10.1016/j.seppur.2011.06.013] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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90
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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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91
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Mitchell S, Pérez-Ramírez J. Mesoporous zeolites as enzyme carriers: Synthesis, characterization, and application in biocatalysis. Catal Today 2011. [DOI: 10.1016/j.cattod.2010.10.058] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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92
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Papaleo E, Invernizzi G. Conformational plasticity of the calcium-binding pocket in the Burkholderia glumae lipase: Remodeling induced by mutation of calcium coordinating residues. Biopolymers 2010; 95:117-26. [DOI: 10.1002/bip.21541] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 07/28/2010] [Accepted: 08/12/2010] [Indexed: 01/05/2023]
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93
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Martínez-Montero S, Fernández S, Sanghvi YS, Gotor V, Ferrero M. Enzymatic Parallel Kinetic Resolution of Mixtures of d/l 2′-Deoxy and Ribonucleosides: An Approach for the Isolation of β-l-Nucleosides. J Org Chem 2010; 75:6605-13. [DOI: 10.1021/jo101368z] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Saúl Martínez-Montero
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
| | - Susana Fernández
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
| | - Yogesh S. Sanghvi
- Rasayan Inc., 2802 Crystal Ridge Road, Encinitas, California 92024-6615
| | - Vicente Gotor
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
| | - Miguel Ferrero
- Departamento de Química Orgánica e Inorgánica and Instituto Universitario de Biotecnología de Asturias, Universidad de Oviedo, 33006-Oviedo (Asturias), Spain
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94
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Kinetic resolution of a drug precursor by Burkholderia cepacia lipase immobilized by different methodologies on superparamagnetic nanoparticles. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.molcatb.2010.03.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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95
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Lou Z, Li M, Sun Y, Liu Y, Liu Z, Wu W, Rao Z. Crystal structure of a secreted lipase from Gibberella zeae reveals a novel "double-lock" mechanism. Protein Cell 2010; 1:760-70. [PMID: 21203917 PMCID: PMC4875196 DOI: 10.1007/s13238-010-0094-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2010] [Accepted: 07/25/2010] [Indexed: 01/07/2023] Open
Abstract
Fusarium graminearum (sexual stage: Gibberella zeae) is the causative agent of Fusarium Head Blight (FHB), which is one of the most destructive plant disease of cereals, accounting for high grain yield losses, especially for wheat and maize. Like other fungal pathogens, several extracellular enzymes secreted by G. zeae are known to be involved in host infection. Among these secreted lipases, G. zeae lipase (GZEL), which is encoded by the FGL1 gene, was demonstrated to be crucial to G. zeae pathogenicity. However, the precise mechanism of GZEL remains unclear due to a lack of detailed structural information. In this study, we report the crystal structure of GZEL at the atomic level. The structure of GZEL displays distinct structural differences compared to reported homologues and indicates a unique "double lock" enzymatic mechanism. To gain insight into substrate/inhibitor recognition, we proposed a model of GZEL in complex with substrate and the lipase inhibitor ebelactone B (based on the reported structures of GZEL homologues), which defines possible substrate binding sites within the catalytic cleft and suggests an "anti sn-l" binding mode. These results pave the way to elucidating the mechanism of GZEL and thus provide clues for the design of anti-FHB inhibitors.
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Affiliation(s)
- Zhiyong Lou
- grid.12527.330000000106623178Laboratory of Structural Biology, Tsinghua University, Beijing, 100084 China
| | - Ming Li
- Novozymes China, 14 Xinxi Lu, Shangdi Zone, Haidian District, Beijing, 100085 China
| | - Yuna Sun
- grid.9227.e0000000119573309National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Ye Liu
- Novozymes China, 14 Xinxi Lu, Shangdi Zone, Haidian District, Beijing, 100085 China
| | - Zheng Liu
- Novozymes China, 14 Xinxi Lu, Shangdi Zone, Haidian District, Beijing, 100085 China
| | - Wenping Wu
- Novozymes China, 14 Xinxi Lu, Shangdi Zone, Haidian District, Beijing, 100085 China
| | - Zihe Rao
- grid.12527.330000000106623178Laboratory of Structural Biology, Tsinghua University, Beijing, 100084 China ,grid.9227.e0000000119573309National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
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96
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Li M, Chen C, Davies DR, Chiu TK. Induced-fit mechanism for prolyl endopeptidase. J Biol Chem 2010; 285:21487-95. [PMID: 20444688 PMCID: PMC2898448 DOI: 10.1074/jbc.m109.092692] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 04/07/2010] [Indexed: 11/06/2022] Open
Abstract
Prolyl peptidases cleave proteins at proline residues and are of importance for cancer, neurological function, and type II diabetes. Prolyl endopeptidase (PEP) cleaves neuropeptides and is a drug target for neuropsychiatric diseases such as post-traumatic stress disorder, depression, and schizophrenia. Previous structural analyses showing little differences between native and substrate-bound structures have suggested a lock-and-key catalytic mechanism. We now directly demonstrate from seven structures of Aeromonus punctata PEP that the mechanism is instead induced fit: the native enzyme exists in a conformationally flexible opened state with a large interdomain opening between the beta-propeller and alpha/beta-hydrolase domains; addition of substrate to preformed native crystals induces a large scale conformational change into a closed state with induced-fit adjustments of the active site, and inhibition of this conformational change prevents substrate binding. Absolute sequence conservation among 28 orthologs of residues at the active site and critical residues at the interdomain interface indicates that this mechanism is conserved in all PEPs. This finding has immediate implications for the use of conformationally targeted drug design to improve specificity of inhibition against this family of proline-specific serine proteases.
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Affiliation(s)
- Min Li
- the Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Changqing Chen
- the Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai 200233, China
| | - David R. Davies
- the Laboratory of Molecular Biology, NIDDK, National Institutes of Health, Bethesda, Maryland 20892, and
| | - Thang K. Chiu
- From the Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, New Orleans, Louisiana 70112
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97
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Angkawidjaja C, Matsumura H, Koga Y, Takano K, Kanaya S. X-ray Crystallographic and MD Simulation Studies on the Mechanism of Interfacial Activation of a Family I.3 Lipase with Two Lids. J Mol Biol 2010; 400:82-95. [DOI: 10.1016/j.jmb.2010.04.051] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Revised: 03/08/2010] [Accepted: 04/26/2010] [Indexed: 11/16/2022]
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98
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Reis P, Watzke H, Leser M, Holmberg K, Miller R. Interfacial mechanism of lipolysis as self-regulated process. Biophys Chem 2010; 147:93-103. [DOI: 10.1016/j.bpc.2010.01.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Revised: 01/17/2010] [Accepted: 01/17/2010] [Indexed: 10/19/2022]
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99
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Bellucci L, Laino T, Tafi A, Botta M. Metadynamics Simulations of Enantioselective Acylation Give Insights into the Catalytic Mechanism of Burkholderia cepacia Lipase. J Chem Theory Comput 2010. [DOI: 10.1021/ct900636w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Luca Bellucci
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Aldo Moro 2, I-53100 Siena, Italy, Physikalisch Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich Switzerland, and IBM Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon Switzerland
| | - Teodoro Laino
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Aldo Moro 2, I-53100 Siena, Italy, Physikalisch Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich Switzerland, and IBM Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon Switzerland
| | - Andrea Tafi
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Aldo Moro 2, I-53100 Siena, Italy, Physikalisch Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich Switzerland, and IBM Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon Switzerland
| | - Maurizio Botta
- Dipartimento Farmaco Chimico Tecnologico, Università degli Studi di Siena, Via Aldo Moro 2, I-53100 Siena, Italy, Physikalisch Chemisches Institut, Universität Zürich, Winterthurerstrasse 190, CH-8057 Zürich Switzerland, and IBM Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon Switzerland
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100
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Rodríguez-Mata M, García-Urdiales E, Gotor-Fernández V, Gotor V. Stereoselective Chemoenzymatic Preparation of β-Amino Esters: Molecular Modelling Considerations in Lipase-Mediated Processes and Application to the Synthesis of (S)-Dapoxetine. Adv Synth Catal 2010. [DOI: 10.1002/adsc.200900676] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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