1
|
Rmili F, Frikha F, Chamkha M, Sayari A, Fendri A. Structure elucidation of Staphylococcus capitis lipase. Molecular dynamics simulations to investigate the effects of calcium and zinc ions on the structural stability. J Biomol Struct Dyn 2023; 41:10450-10462. [PMID: 36546696 DOI: 10.1080/07391102.2022.2159528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/10/2022] [Indexed: 12/24/2022]
Abstract
Cold-adapted and organic solvent tolerant lipases have significant potential in a wide range of synthetic reactions in industry. But there are no sufficient studies on how these enzymes interacts with their substrates. Herein, the predicted structure and function of the Staphylococcus capitis lipase (SCL) are studied. Given the high amino acid sequence homology with the Staphylococcus simulans lipase (SSL), 3D structure models of closed and open forms of the S. capitis lipase were built using the structure of SSL as template. The models suggested the presence of a main lid and a second lid that may act with the former as a double door to control the access to the active site. The SCL models also allowed us to identify key residues involved in binding substrates, calcium or zinc ions. By following this model and utilizing molecular dynamics (MD) simulations, the stability of the S. capitis lipase at low temperatures could be explained in the presence and in the absence of calcium and zinc. Due to its thermolability, the SCL is extremely valuable for different biotechnological applications in a wide variety of industries from molecular biology to detergency to food and beverage preparation.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Fatma Rmili
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, Engineering National School of Sfax (ENIS), University of Sfax, Sfax, Tunisia
| | - Fakher Frikha
- Laboratory of Molecular and Cellular Screening Processes Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Mohamed Chamkha
- Laboratory of Environmental Bioprocesses, Centre of Biotechnology of Sfax, University of Sfax, Sfax, Tunisia
| | - Adel Sayari
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, Engineering National School of Sfax (ENIS), University of Sfax, Sfax, Tunisia
| | - Ahmed Fendri
- Laboratory of Biochemistry and Enzymatic Engineering of Lipases, Engineering National School of Sfax (ENIS), University of Sfax, Sfax, Tunisia
| |
Collapse
|
2
|
Vahidi SH, Monhemi H, Hassani Sabzevar B, Eftekhari M. Electrostatic interactions of enzymes in non-aqueous conditions: insights from molecular dynamics simulations. J Biomol Struct Dyn 2023:1-14. [PMID: 37965802 DOI: 10.1080/07391102.2023.2280775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/01/2023] [Indexed: 11/16/2023]
Abstract
Electrostatic interactions of enzymes and their effects on enzyme activity and stability are poorly understood in non-aqueous conditions. Here, we investigate the contribution of the electrostatic interactions on the stability and activity of enzymes in the non-aqueous environment using molecular dynamics simulations. Lipase was selected as active and lysozyme as inactive model enzymes in non-aqueous media. Hexane was used as a common non-aqueous solvent model. In agreement with the previous experiments, simulations show that lysozyme has more structural instabilities than lipase in hexane. The number of hydrogen bonds and salt bridges of both enzymes is dramatically increased in hexane. In contrast to the other opinions, we show that the increase of the electrostatic interactions in non-aqueous media is not so favorable for enzymatic function and stability. In this condition, the newly formed hydrogen bonds and salt bridges can partially denature the local structure of the enzymes. For lysozyme, the changes in electrostatic interactions occur in all domains including the active site cleft, which leads to enzyme inactivation and destabilization. Interestingly, most of the changes in electrostatic interactions of lipase occur far from the active site regions. Therefore, the active site entrance regions remain functional in hexane. The results of this study reveal how the changes in electrostatic interactions can affect enzyme stability and activity in non-aqueous conditions. Moreover, we show for the first time how some enzymes, such as lipase, remain active in a non-aqueous environment.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- S Hooman Vahidi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - Hassan Monhemi
- Department of Chemistry, Faculty of Sciences, University of Neyshabur, Neyshabur, Iran
| | | | - Mohammad Eftekhari
- Department of Chemistry, Faculty of Sciences, University of Neyshabur, Neyshabur, Iran
| |
Collapse
|
3
|
Dulęba J, Siódmiak T, Marszałł MP. The influence of substrate systems on the enantioselective and lipolytic activity of immobilized Amano PS from Burkholderia cepacia lipase (APS-BCL). Process Biochem 2022. [DOI: 10.1016/j.procbio.2022.06.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
4
|
Li YM, Yuan J, Ren H, Ji CY, Tao Y, Wu Y, Chou LY, Zhang YB, Cheng L. Fine-Tuning the Micro-Environment to Optimize the Catalytic Activity of Enzymes Immobilized in Multivariate Metal-Organic Frameworks. J Am Chem Soc 2021; 143:15378-15390. [PMID: 34478271 DOI: 10.1021/jacs.1c07107] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The artificial engineering of an enzyme's structural conformation to enhance its activity is highly desired and challenging. Anisotropic reticular chemistry, best illustrated in the case of multivariate metal-organic frameworks (MTV-MOFs), provides a platform to modify a MOF's pore and inner-surface with functionality variations on frameworks to optimize the interior environment and to enhance the specifically targeted property. In this study, we altered the functionality and ratio of linkers in zeolitic imidazolate frameworks (ZIFs), a subclass of MOFs, with the MTV approach to demonstrate a strategy that allows us to optimize the activity of the encapsulated enzyme by continuously tuning the framework-enzyme interaction through the hydrophilicity change in the pores' microenvironment. To systematically study this interaction, we developed the component-adjustment-ternary plot (CAT) method to approach the optimal activity of the encapsulated enzyme BCL and revealed a nonlinear correlation, first incremental and then decremental, between the BCL activity and the hydrophilic linker' ratios in MTV-ZIF-8. These findings indicated there is a spatial arrangement of functional groups along the three-dimensional space across the ZIF-8 crystal with a unique sequence that could change the enzyme structure between closed-lid and open-lid conformations. These conformation changes were confirmed by FTIR spectra and fluorescence studies. The optimized BCL@ZIF-8 is not only thermally and chemically more stable than free BCL in solution, but also doubles the catalytic reactivity in the kinetic resolution reaction with 99% ee of the products.
Collapse
Affiliation(s)
- Yi-Ming Li
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
| | - Jian Yuan
- Avogadral Solutions, 3130 Grants Lake Boulevard #18641, Sugar Land, Texas 77496, United States
| | - Hao Ren
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
| | - Chun-Yan Ji
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
| | - Yu Tao
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yahui Wu
- Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Lien-Yang Chou
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, P. R. China
| | - Yue-Biao Zhang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, P. R. China
| | - Lin Cheng
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
| |
Collapse
|
5
|
Mohammadi-Mahani H, Badoei-dalfard A, Karami Z. Synthesis and characterization of cross-linked lipase-metal hybrid nanoflowers on graphene oxide with increasing the enzymatic stability and reusability. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2021.108038] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
|
6
|
Structure and Dynamics of an Archeal Monoglyceride Lipase from Palaeococcus ferrophilus as Revealed by Crystallography and In Silico Analysis. Biomolecules 2021; 11:biom11040533. [PMID: 33916727 PMCID: PMC8065475 DOI: 10.3390/biom11040533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 01/06/2023] Open
Abstract
The crystallographic analysis of a lipase from Palaeococcus ferrophilus (PFL) previously annotated as a lysophospholipase revealed high structural conservation with other monoglyceride lipases, in particular in the lid domain and substrate binding pockets. In agreement with this observation, PFL was shown to be active on various monoacylglycerols. Molecular Dynamics (MD) studies performed in the absence and in the presence of ligands further allowed characterization of the dynamics of this system and led to a systematic closure of the lid compared to the crystal structure. However, the presence of ligands in the acyl-binding pocket stabilizes intermediate conformations compared to the crystal and totally closed structures. Several lid-stabilizing or closure elements were highlighted, i.e., hydrogen bonds between Ser117 and Ile204 or Asn142 and its facing amino acid lid residues, as well as Phe123. Thus, based on this complementary crystallographic and MD approach, we suggest that the crystal structure reported herein represents an open conformation, at least partially, of the PFL, which is likely stabilized by the ligand, and it brings to light several key structural features prone to participate in the closure of the lid.
Collapse
|
7
|
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.
Collapse
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.
| |
Collapse
|
8
|
Tailoring a stable and recyclable nanobiocatalyst by immobilization of surfactant treated Burkholderia cepacia lipase on polyaniline nanofibers for biocatalytic application. Int J Biol Macromol 2020; 161:573-586. [DOI: 10.1016/j.ijbiomac.2020.06.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 12/18/2022]
|
9
|
Santana JL, Oliveira JM, Nascimento JS, Mattedi S, Krause LC, Freitas LS, Cavalcanti EB, Pereira MM, Lima ÁS, Soares CMF. Continuous flow reactor based with an immobilized biocatalyst for the continuous enzymatic transesterification of crude coconut oil. Biotechnol Appl Biochem 2020; 67:404-413. [PMID: 31930535 DOI: 10.1002/bab.1885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/30/2019] [Indexed: 11/06/2022]
Abstract
Here, we have assessed the use of one packed bed or two packed bed reactors in series in which Burkholderia cepacia lipase (BCL) was immobilized on protic ionic liquid (PIL)-modified silica and used as a biocatalyst for the transesterification of crude coconut oil. Reaction parameters including volumetric flow, temperature, and molar ratio were evaluated. The conversion of transesterification reaction products (ethyl esters) was determined using gas chromatography and the quantities of intermediate products (diglyceride and monoglyceride [MG]) were assessed using high-performance liquid chromatography. Packed bed reactors in series produced ethyl esters with the greatest efficiency, achieving 65.27% conversion after 96 H at a volumetric flow rate of 0.50 mL Min-1 at 40 °C and a 1:9 molar ratio of oil to ethanol. Further, within the first 24 H of the reaction, increased MG (54.5%) production was observed. Molecular docking analyses were performed to evaluate the catalytic step of coconut oil transesterification in the presence of BCL. Molecular docking analysis showed that triglycerides have a higher affinity energy (-5.7 kcal mol-1 ) than the smallest MG (-6.0 kcal mol-1 ), therefore, BCL catalyzes the conversion of triglycerides rather than MG, which is consistent with experimental results.
Collapse
Affiliation(s)
- Juliana L Santana
- Instituto de Tecnologia e Pesquisa-ITP, Universidade Tiradentes, Aracaju, SE, Brazil
| | - Juliana M Oliveira
- Instituto de Tecnologia e Pesquisa-ITP, Universidade Tiradentes, Aracaju, SE, Brazil
| | - Jamily S Nascimento
- Instituto de Tecnologia e Pesquisa-ITP, Universidade Tiradentes, Aracaju, SE, Brazil
| | - Silvana Mattedi
- Departamento de Engenharia Química, Universidade Federal da Bahia, Salvador, BA, Brazil
| | - Laiza C Krause
- Núcleo de Estudo em Sistemas Coloidais-NUESC, Universidade Tiradentes, Aracaju, SE, Brazil
| | - Lisiane S Freitas
- Departamento de Química, Universidade Federal de Sergipe, São Cristóvão, Sergipe, SE, Brazil
| | - Eliane B Cavalcanti
- Instituto de Tecnologia e Pesquisa-ITP, Universidade Tiradentes, Aracaju, SE, Brazil
| | - Matheus M Pereira
- CICECO, Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, Aveiro, Portugal
| | - Álvaro S Lima
- Instituto de Tecnologia e Pesquisa-ITP, Universidade Tiradentes, Aracaju, SE, Brazil
| | - Cleide M F Soares
- Instituto de Tecnologia e Pesquisa-ITP, Universidade Tiradentes, Aracaju, SE, Brazil
| |
Collapse
|
10
|
Verma N, Dollinger P, Kovacic F, Jaeger KE, Gohlke H. The Membrane-Integrated Steric Chaperone Lif Facilitates Active Site Opening of Pseudomonas aeruginosa Lipase A. J Comput Chem 2019; 41:500-512. [PMID: 31618459 DOI: 10.1002/jcc.26085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 09/22/2019] [Accepted: 09/25/2019] [Indexed: 12/19/2022]
Abstract
Lipases are essential and widely used biocatalysts. Hence, the production of lipases requires a detailed understanding of the molecular mechanism of its folding and secretion. Lipase A from Pseudomonas aeruginosa, PaLipA, constitutes a prominent example that has additional relevance because of its role as a virulence factor in many diseases. PaLipA requires the assistance of a membrane-integrated steric chaperone, the lipase-specific foldase Lif, to achieve its enzymatically active state. However, the molecular mechanism of how Lif activates its cognate lipase has remained elusive. Here, we show by molecular dynamics simulations at the atomistic level and potential of mean force computations that Lif catalyzes the activation process of PaLipA by structurally stabilizing an intermediate PaLipA conformation, particularly a β-sheet in the region of residues 17-30, such that the opening of PaLipA's lid domain is facilitated. This opening allows substrate access to PaLipA's catalytic site. A surprising and so far not fully understood aspect of our study is that the open state of PaLipA is unstable compared to the closed one according to our computational and in vitro biochemical results. We thus speculate that further interactions of PaLipA with the Xcp secretion machinery and/or components of the extracellular matrix contribute to the remaining activity of secreted PaLipA. © 2019 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Neha Verma
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätstr. 1, 40225, Düsseldorf, Germany
| | - Peter Dollinger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Filip Kovacic
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| | - Holger Gohlke
- Institute for Pharmaceutical and Medicinal Chemistry, Heinrich Heine University Düsseldorf, Universitätstr. 1, 40225, Düsseldorf, Germany.,John von Neumann Institute for Computing (NIC), Jülich Supercomputing Centre (JSC) and Institute for Complex Systems-Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, 52426, Jülich, Germany
| |
Collapse
|
11
|
Rodrigues RC, Virgen-Ortíz JJ, dos Santos JC, Berenguer-Murcia Á, Alcantara AR, Barbosa O, Ortiz C, Fernandez-Lafuente R. Immobilization of lipases on hydrophobic supports: immobilization mechanism, advantages, problems, and solutions. Biotechnol Adv 2019; 37:746-770. [DOI: 10.1016/j.biotechadv.2019.04.003] [Citation(s) in RCA: 287] [Impact Index Per Article: 57.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 12/13/2022]
|
12
|
Sadaf A, Grewal J, Jain I, Kumari A, Khare SK. Stability and structure of Penicillium chrysogenum lipase in the presence of organic solvents. Prep Biochem Biotechnol 2018; 48:977-983. [PMID: 30461349 DOI: 10.1080/10826068.2018.1525566] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The present work describes the enzymatic properties of Penicillium chrysogenum lipase and its behavior in the presence of organic solvents. The temperature and pH optima of the purified lipase was found to be 55 °C and pH 8.0 respectively. The lipase displayed remarkable stability in both polar and non-polar solvents upto 50% (v/v) concentrations for 72 h. A structural perspective of the purified lipase in different organic solvents was gained by using circular dichroism and intrinsic fluorescence spectroscopy. The native lipase consisted of a predominant α-helix structure which was maintained in both polar and non-polar solvents with the exception of ethyl butyrate where the activity was decreased and the structure was disrupted. The quenching of fluorescence intensity in the presence of organic solvents indicated the transformation of the lipase microenviroment P. chrysogenum lipase offers an interesting system for understanding the solvent stability mechanisms which could be used for rationale designing of engineered lipase biocatalysts for application in organic synthesis in non-aqueous media.
Collapse
Affiliation(s)
- Ayesha Sadaf
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
| | - Jasneet Grewal
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
| | - Isha Jain
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
| | - Arti Kumari
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
| | - Sunil K Khare
- a Enzyme and Microbial Biochemistry Lab, Department of Chemistry , Indian Institute of Technology Delhi , New Delhi , India
| |
Collapse
|
13
|
Che Hussian CHA, Raja Abd Rahman RNZ, Thean Chor AL, Salleh AB, Mohamad Ali MS. Enhancement of a protocol purifying T1 lipase through molecular approach. PeerJ 2018; 6:e5833. [PMID: 30479887 PMCID: PMC6241395 DOI: 10.7717/peerj.5833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/27/2018] [Indexed: 12/04/2022] Open
Abstract
T1 Lipase is a thermostable secretary protein of Geobacillus zalihae strain previously expressed in a prokaryotic system and purified using three-step purification: affinity 1, affinity 2, and ion exchange chromatography (IEX). This approach is time consuming and offers low purity and recovery yield. In order to enhance the purification strategy of T1 lipase, affinity 2 was removed so that after affinity 1, the cleaved Glutathione S-transferase (GST) and matured T1 lipase could be directly separated through IEX. Therefore, a rational design of GST isoelectric point (pI) was implemented by prediction using ExPASy software in order to enhance the differences of pI values between GST and matured T1 lipase. Site-directed mutagenesis at two locations flanking the downstream region of GST sequences (H215R and G213R) was successfully performed. Double point mutations changed the charge on GST from 6.10 to 6.53. The purified lipase from the new construct GST tag mutant-T1 was successfully purified using two steps of purification with 6,849 U/mg of lipase specific activity, 33% yield, and a 44-fold increase in purification. Hence, the increment of the pI values in the GST tag fusion T1 lipase resulted in a successful direct separation through IEX and lead to successful purification.
Collapse
Affiliation(s)
- Che Haznie Ayu Che Hussian
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Adam Leow Thean Chor
- Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Universiti Putra Malaysia, Serdang, Selangor, Malaysia.,Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| |
Collapse
|
14
|
Mathpati AC, Bhanage BM. Prediction of enantioselectivity of lipase catalyzed kinetic resolution using umbrella sampling. J Biotechnol 2018; 283:70-80. [DOI: 10.1016/j.jbiotec.2018.07.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/21/2018] [Accepted: 07/18/2018] [Indexed: 12/21/2022]
|
15
|
Kato G, Sato A, Tokuyama H. Continuous Esterification using Lipase-Entrapped Amphiphilic Copolymeric Gel Beads. KAGAKU KOGAKU RONBUN 2018. [DOI: 10.1252/kakoronbunshu.44.185] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Gakuto Kato
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology
| | - Ayumi Sato
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology
| | - Hideaki Tokuyama
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology
| |
Collapse
|
16
|
Escorcia AM, van Rijn JPM, Cheng GJ, Schrepfer P, Brück TB, Thiel W. Molecular dynamics study of taxadiene synthase catalysis. J Comput Chem 2018; 39:1215-1225. [PMID: 29450907 DOI: 10.1002/jcc.25184] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 01/25/2018] [Accepted: 01/26/2018] [Indexed: 01/10/2023]
Abstract
Molecular dynamics (MD) simulations have been performed to study the dynamic behavior of noncovalent enzyme carbocation complexes involved in the cyclization of geranylgeranyl diphosphate to taxadiene catalyzed by taxadiene synthase (TXS). Taxadiene and the observed four side products originate from the deprotonation of carbocation intermediates. The MD simulations of the TXS carbocation complexes provide insights into potential deprotonation mechanisms of such carbocations. The MD results do not support a previous hypothesis that carbocation tumbling is a key factor in the deprotonation of the carbocations by pyrophosphate. Instead water bridges are identified which may allow the formation of side products via multiple proton transfer reactions. A novel reaction path for taxadiene formation is proposed on the basis of the simulations. © 2018 Wiley Periodicals, Inc.
Collapse
Affiliation(s)
- Andrés M Escorcia
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | | | - Gui-Juan Cheng
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| | - Patrick Schrepfer
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Thomas B Brück
- Professorship of Industrial Biocatalysis, Department of Chemistry, Technical University Munich, Lichtenberg Str. 4, Garching, 85748, Germany
| | - Walter Thiel
- Max-Planck-Institut fu¨r Kohlenforschung, Kaiser-Wilhelm-Platz 1, Mu¨lheim, 45470, Germany
| |
Collapse
|
17
|
Soni S, Dwivedee BP, Chand Banerjee U. Facile fabrication of a recyclable nanobiocatalyst: immobilization of Burkholderia cepacia lipase on carbon nanofibers for the kinetic resolution of a racemic atenolol intermediate. RSC Adv 2018; 8:27763-27774. [PMID: 35542692 PMCID: PMC9083555 DOI: 10.1039/c8ra05463k] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 07/25/2018] [Indexed: 11/21/2022] Open
Abstract
Immobilization of surfactant treated Burkholderia cepacia lipase on the surface of carbon nanofibers was performed via two different methods: adsorption and covalent attachment.
Collapse
Affiliation(s)
- Surbhi Soni
- Department of Biotechnology
- National Institute of Pharmaceutical Education and Research
- India
| | - Bharat Prasad Dwivedee
- Department of Pharmaceutical Technology (Biotechnology)
- National Institute of Pharmaceutical Education and Research
- India
| | - Uttam Chand Banerjee
- Department of Pharmaceutical Technology (Biotechnology)
- National Institute of Pharmaceutical Education and Research
- India
| |
Collapse
|
18
|
Maiangwa J, Mohamad Ali MS, Salleh AB, Rahman RNZRA, Normi YM, Mohd Shariff F, Leow TC. Lid opening and conformational stability of T1 Lipase is mediated by increasing chain length polar solvents. PeerJ 2017; 5:e3341. [PMID: 28533982 PMCID: PMC5438581 DOI: 10.7717/peerj.3341] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 04/21/2017] [Indexed: 11/20/2022] Open
Abstract
The dynamics and conformational landscape of proteins in organic solvents are events of potential interest in nonaqueous process catalysis. Conformational changes, folding transitions, and stability often correspond to structural rearrangements that alter contacts between solvent molecules and amino acid residues. However, in nonaqueous enzymology, organic solvents limit stability and further application of proteins. In the present study, molecular dynamics (MD) of a thermostable Geobacillus zalihae T1 lipase was performed in different chain length polar organic solvents (methanol, ethanol, propanol, butanol, and pentanol) and water mixture systems to a concentration of 50%. On the basis of the MD results, the structural deviations of the backbone atoms elucidated the dynamic effects of water/organic solvent mixtures on the equilibrium state of the protein simulations in decreasing solvent polarity. The results show that the solvent mixture gives rise to deviations in enzyme structure from the native one simulated in water. The drop in the flexibility in H2O, MtOH, EtOH and PrOH simulation mixtures shows that greater motions of residues were influenced in BtOH and PtOH simulation mixtures. Comparing the root mean square fluctuations value with the accessible solvent area (SASA) for every residue showed an almost correspondingly high SASA value of residues to high flexibility and low SASA value to low flexibility. The study further revealed that the organic solvents influenced the formation of more hydrogen bonds in MtOH, EtOH and PrOH and thus, it is assumed that increased intraprotein hydrogen bonding is ultimately correlated to the stability of the protein. However, the solvent accessibility analysis showed that in all solvent systems, hydrophobic residues were exposed and polar residues tended to be buried away from the solvent. Distance variation of the tetrahedral intermediate packing of the active pocket was not conserved in organic solvent systems, which could lead to weaknesses in the catalytic H-bond network and most likely a drop in catalytic activity. The conformational variation of the lid domain caused by the solvent molecules influenced its gradual opening. Formation of additional hydrogen bonds and hydrophobic interactions indicates that the contribution of the cooperative network of interactions could retain the stability of the protein in some solvent systems. Time-correlated atomic motions were used to characterize the correlations between the motions of the atoms from atomic coordinates. The resulting cross-correlation map revealed that the organic solvent mixtures performed functional, concerted, correlated motions in regions of residues of the lid domain to other residues. These observations suggest that varying lengths of polar organic solvents play a significant role in introducing dynamic conformational diversity in proteins in a decreasing order of polarity.
Collapse
Affiliation(s)
- Jonathan Maiangwa
- Department of Cell and Molecular Biology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Serlangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Department of Biochemistry/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Department of Biochemistry/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Department of Microbiology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Yahaya M Normi
- Department of Cell and Molecular Biology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Serlangor, Malaysia
| | - Fairolniza Mohd Shariff
- Department of Microbiology/Enzyme Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Department of Cell and Molecular Biology/Enzyme and Microbial Technology Research center/Faculty of Biotechnology and Biomolecular Science/Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| |
Collapse
|
19
|
de Oliveira IP, Jara GE, Martínez L. Molecular mechanism of activation of Burkholderia cepacia lipase at aqueous–organic interfaces. Phys Chem Chem Phys 2017; 19:31499-31507. [DOI: 10.1039/c7cp04466f] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Structure and thermodynamics of lipase activation at aqueous–organic interfaces.
Collapse
Affiliation(s)
- Ivan Pires de Oliveira
- Institute of Chemistry and Center for Computational Engineering & Science
- University of Campinas
- Campinas
- Brazil
| | - Gabriel Ernesto Jara
- Institute of Chemistry and Center for Computational Engineering & Science
- University of Campinas
- Campinas
- Brazil
| | - Leandro Martínez
- Institute of Chemistry and Center for Computational Engineering & Science
- University of Campinas
- Campinas
- Brazil
| |
Collapse
|
20
|
Escorcia AM, Sen K, Daza MC, Doerr M, Thiel W. Quantum Mechanics/Molecular Mechanics Insights into the Enantioselectivity of the O-Acetylation of (R,S)-Propranolol Catalyzed by Candida antarctica Lipase B. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02310] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Andrés M. Escorcia
- Grupo
de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Kakali Sen
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
| | - Martha C. Daza
- Grupo
de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Markus Doerr
- Grupo
de Bioquímica Teórica, Universidad Industrial de Santander, Cra 27 Calle 9, Bucaramanga, Colombia
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim, Germany
| |
Collapse
|
21
|
Skjold-Jørgensen J, Vind J, Svendsen A, Bjerrum MJ. Understanding the activation mechanism ofThermomyces lanuginosuslipase using rational design and tryptophan-induced fluorescence quenching. EUR J LIPID SCI TECH 2016. [DOI: 10.1002/ejlt.201600059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
| | | | | | - Morten J. Bjerrum
- Department of Chemistry; University of Copenhagen; Copenhagen Denmark
| |
Collapse
|
22
|
Mathpati AC, Bhanage BM. Combined docking and molecular dynamics study of lipase catalyzed kinetic resolution of 1-phenylethanol in organic solvents. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.12.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
|
23
|
Lid dynamics of porcine pancreatic lipase in non-aqueous solvents. Biochim Biophys Acta Gen Subj 2016; 1860:2326-34. [DOI: 10.1016/j.bbagen.2016.05.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 04/17/2016] [Accepted: 05/03/2016] [Indexed: 01/06/2023]
|
24
|
Haque N, Prabhu NP. Lid closure dynamics of porcine pancreatic lipase in aqueous solution. Biochim Biophys Acta Gen Subj 2016; 1860:2313-25. [DOI: 10.1016/j.bbagen.2016.05.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2015] [Revised: 04/17/2016] [Accepted: 05/03/2016] [Indexed: 10/21/2022]
|
25
|
Skjold-Jørgensen J, Vind J, Moroz OV, Blagova E, Bhatia VK, Svendsen A, Wilson KS, Bjerrum MJ. Controlled lid-opening in Thermomyces lanuginosus lipase- An engineered switch for studying lipase function. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:20-27. [PMID: 27693248 DOI: 10.1016/j.bbapap.2016.09.016] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Revised: 09/09/2016] [Accepted: 09/26/2016] [Indexed: 11/16/2022]
Abstract
Here, we present a lipase mutant containing a biochemical switch allowing a controlled opening and closing of the lid independent of the environment. The closed form of the TlL mutant shows low binding to hydrophobic surfaces compared to the binding observed after activating the controlled switch inducing lid-opening. We directly show that lipid binding of this mutant is connected to an open lid conformation demonstrating the impact of the exposed amino acid residues and their participation in binding at the water-lipid interface. The switch was created by introducing two cysteine residues into the protein backbone at sites 86 and 255. The crystal structure of the mutant shows the successful formation of a disulfide bond between C86 and C255 which causes strained closure of the lid-domain. Control of enzymatic activity and binding was demonstrated on substrate emulsions and natural lipid layers. The locked form displayed low enzymatic activity (~10%) compared to wild-type. Upon release of the lock, enzymatic activity was fully restored. Only 10% binding to natural lipid substrates was observed for the locked lipase compared to wild-type, but binding was restored upon adding reducing agent. QCM-D measurements revealed a seven-fold increase in binding rate for the unlocked lipase. The TlL_locked mutant shows structural changes across the protein important for understanding the mechanism of lid-opening and closing. Our experimental results reveal sites of interest for future mutagenesis studies aimed at altering the activation mechanism of TlL and create perspectives for generating tunable lipases that activate under controlled conditions.
Collapse
Affiliation(s)
- Jakob Skjold-Jørgensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark; Novozymes A/S, Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Jesper Vind
- Novozymes A/S, Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Olga V Moroz
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK
| | - Elena Blagova
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK
| | | | | | - Keith S Wilson
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, UK.
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark.
| |
Collapse
|
26
|
Cheung DL. Conformations of Myoglobin-Derived Peptides at the Air-Water Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:4405-4414. [PMID: 27077474 DOI: 10.1021/acs.langmuir.5b04619] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The conformational change exhibited by proteins at liquid interfaces, such as the air-water and oil-water interfaces, has long been of interest both for understanding protein structure outside of native environments and for applications in areas including food technology and pharmaceuticals. Using molecular simulation, this article studies the conformations of two peptides derived from myoglobin, for which the emulsification behavior has been studied. Both peptides were found to readily adsorb onto the air-water interface, with one of these (experimentally, the more effective stabilizer) adopting a flat, extended conformation and the other peptide remaining close to its solution conformation.
Collapse
Affiliation(s)
- David L Cheung
- School of Chemistry, National University of Ireland Galway , Galway, Ireland
| |
Collapse
|
27
|
Papaleo E, Saladino G, Lambrughi M, Lindorff-Larsen K, Gervasio FL, Nussinov R. The Role of Protein Loops and Linkers in Conformational Dynamics and Allostery. Chem Rev 2016; 116:6391-423. [DOI: 10.1021/acs.chemrev.5b00623] [Citation(s) in RCA: 239] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elena Papaleo
- Computational
Biology Laboratory, Unit of Statistics, Bioinformatics and Registry, Danish Cancer Society Research Center, Strandboulevarden 49, 2100 Copenhagen, Denmark
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Giorgio Saladino
- Department
of Chemistry, University College London, London WC1E 6BT, United Kingdom
| | - Matteo Lambrughi
- Department
of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza
della Scienza 2, 20126 Milan, Italy
| | - Kresten Lindorff-Larsen
- Structural
Biology and NMR Laboratory, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark
| | | | - Ruth Nussinov
- Cancer
and Inflammation Program, Leidos Biomedical Research, Inc., Frederick
National Laboratory for Cancer Research, National Cancer Institute Frederick, Frederick, Maryland 21702, United States
- Sackler Institute
of Molecular Medicine, Department of Human Genetics and Molecular
Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| |
Collapse
|
28
|
Sato R, Tokuyama H. In Situ Enzyme Entrapments in Macroporous Polymeric Organogels Using A Water-in-Oil Emulsion-Gelation Method for Reactions in Organic Media. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2016. [DOI: 10.1252/jcej.15we055] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ryuichi Sato
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology
| | - Hideaki Tokuyama
- Department of Chemical Engineering, Tokyo University of Agriculture and Technology
| |
Collapse
|
29
|
Ke C, Fan Y, Chen Y, Xu L, Yan Y. A new lipase–inorganic hybrid nanoflower with enhanced enzyme activity. RSC Adv 2016. [DOI: 10.1039/c6ra01564f] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new hybrid nanoflower biocatalyst was synthesized using the organic component of Burkholderia cepacia lipase and inorganic component of calcium phosphate.
Collapse
Affiliation(s)
- C. Ke
- 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
| | - Y. Fan
- 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
| | - Y. Chen
- 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
| | - L. Xu
- 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
| | - Y. 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
| |
Collapse
|
30
|
Skjold-Jørgensen J, Vind J, Svendsen A, Bjerrum MJ. Lipases That Activate at High Solvent Polarities. Biochemistry 2015; 55:146-56. [PMID: 26645098 DOI: 10.1021/acs.biochem.5b01114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Thermomyces lanuginosus lipase (TlL) and related lipases become activated in low-polarity environments that exist at the water-lipid interface where a structural change of the "lid" region occurs. In this work, we have investigated the activation of TlL (Lipase_W89) and certain lid mutants, containing either a single positive charge mutation, E87K (Lipase_K87_W89), within the lid region or a lid residue composition of both lipase and esterase character (Hybrid_W89) as a function of solvent polarity. Activation differences between the variants and TlL were studied by a combination of biophysical and theoretical methods. To investigate the structural changes taking place in the lid region upon lipase activation, we used a fluorescence-based method measuring the efficiency of Trp89 in the lid to quench the fluorescence of a bimane molecule attached in front (C255) and behind (C61) the lid. These structural changes were compared to the enzymatic activity of each variant at the water-substrate interface and to theoretical calculations of the energies associated with lid opening as a function of the dielectric constant (ε) of the environment. Our results show that the lid in Lipase_K87_W89 undergoes a pronounced structural transition toward an open conformation around ε = 50, whereas only small changes are detected for Lipase_W89 ascribed to the stabilizing effect of the positive charge mutation on the open lid conformation. Interestingly, Hybrid_W89, with the same charge as Lipase_W89, shows a stabilization of the open lid even more pronounced at high solvent polarities than that of Lipase_K87_W89, allowing activation at ε < 80. This is further indicated by measurement of the lipase activity for each variant showing that Hybrid_W89 is more quickly activated at the water-lipid interface of a true, natural substrate. Combined, we show that a correlation exists between structural changes and enzymatic activities detected on one hand and theoretical calculations on lid opening energies on the other. These results highlight the key role that the lid plays in determining the polarity-dependent activation of lipases.
Collapse
Affiliation(s)
- Jakob Skjold-Jørgensen
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark.,Novozymes A/S , Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Jesper Vind
- Novozymes A/S , Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Allan Svendsen
- Novozymes A/S , Brudelysvej 35, DK-2880 Bagværd, Denmark
| | - Morten J Bjerrum
- Department of Chemistry, University of Copenhagen , Universitetsparken 5, DK-2100 Copenhagen, Denmark
| |
Collapse
|
31
|
Tyukhtenko S, Karageorgos I, Rajarshi G, Zvonok N, Pavlopoulos S, Janero DR, Makriyannis A. Specific Inter-residue Interactions as Determinants of Human Monoacylglycerol Lipase Catalytic Competency: A ROLE FOR GLOBAL CONFORMATIONAL CHANGES. J Biol Chem 2015; 291:2556-65. [PMID: 26555264 DOI: 10.1074/jbc.m115.670257] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Indexed: 11/06/2022] Open
Abstract
The serine hydrolase monoacylglycerol lipase (MGL) functions as the main metabolizing enzyme of 2-arachidonoyl glycerol, an endocannabinoid signaling lipid whose elevation through genetic or pharmacological MGL ablation exerts therapeutic effects in various preclinical disease models. To inform structure-based MGL inhibitor design, we report the direct NMR detection of a reversible equilibrium between active and inactive states of human MGL (hMGL) that is slow on the NMR time scale and can be modulated in a controlled manner by pH, temperature, and select point mutations. Kinetic measurements revealed that hMGL substrate turnover is rate-limited across this equilibrium. We identify a network of aromatic interactions and hydrogen bonds that regulates hMGL active-inactive state interconversion. The data highlight specific inter-residue interactions within hMGL modulating the enzymes function and implicate transitions between active (open) and inactive (closed) states of the hMGL lid domain in controlling substrate access to the enzymes active site.
Collapse
Affiliation(s)
- Sergiy Tyukhtenko
- From the Center for Drug Discovery and Departments of Pharmaceutical Sciences and Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000 and
| | - Ioannis Karageorgos
- From the Center for Drug Discovery and Departments of Pharmaceutical Sciences and Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000 and
| | - Girija Rajarshi
- From the Center for Drug Discovery and Departments of Pharmaceutical Sciences and Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000 and
| | - Nikolai Zvonok
- From the Center for Drug Discovery and Departments of Pharmaceutical Sciences and Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000 and
| | - Spiro Pavlopoulos
- From the Center for Drug Discovery and Departments of Pharmaceutical Sciences and Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000 and
| | - David R Janero
- From the Center for Drug Discovery and Departments of Pharmaceutical Sciences and Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000 and
| | - Alexandros Makriyannis
- From the Center for Drug Discovery and Departments of Pharmaceutical Sciences and Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115-5000 and King Abdulaziz University, Jeddah, 22254, Saudi Arabia
| |
Collapse
|
32
|
Skjold-Jørgensen J, Bhatia VK, Vind J, Svendsen A, Bjerrum MJ, Farrens D. The Enzymatic Activity of Lipases Correlates with Polarity-Induced Conformational Changes: A Trp-Induced Quenching Fluorescence Study. Biochemistry 2015; 54:4186-96. [PMID: 26087334 DOI: 10.1021/acs.biochem.5b00328] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Triacylglycerol hydrolases (EC 3.1.1.3) are thought to become activated when they encounter the water-lipid interface causing a "lid" region to move and expose the catalytic site. Here, we tested this idea by looking for lid movements in Thermomyces lanuginosus lipase (TL lipase), and in variants with a mutated lid region of esterase (Esterase) and esterase/lipase (Hybrid) character. To measure lid movements, we employed the tryptophan-induced quenching (TrIQ) fluorescence method to measure how effectively a Trp residue on the lid of these mutants (at position 87 or 89) could quench a fluorescent probe (bimane) placed at nearby site 255 on the protein. To test if lid movement is induced when the enzyme detects a lower-polarity environment (such as at the water-lipid interface), we performed these studies in solvents with different dielectric constants (ε). The results show that lid movement is highly dependent on the particular lid residue composition and solvent polarity. The data suggest that in aqueous solution (ε = 80), the Esterase lid is in an "open" conformation, whereas for the TL lipase and Hybrid, the lid remains "closed". At lower solvent polarities (ε < 46), the lid region for all of the mutants is more "open". Interestingly, these behaviors mirror the structural changes thought to take place upon activation of the enzyme at the water-lipid interface. Together, these results support the idea that lipases are more active in low-polarity solvents because the lid adopts an "open" conformation and indicate that relatively small conformational changes in the lid region play a key role in the activation mechanism of these enzymes.
Collapse
Affiliation(s)
- Jakob Skjold-Jørgensen
- †Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen, Denmark.,‡Novozymes A/S, Brudelysvej 35, DK 2880 Bagværd, Denmark
| | | | - Jesper Vind
- ‡Novozymes A/S, Brudelysvej 35, DK 2880 Bagværd, Denmark
| | - Allan Svendsen
- ‡Novozymes A/S, Brudelysvej 35, DK 2880 Bagværd, Denmark
| | - Morten J Bjerrum
- †Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK 2100 Copenhagen, Denmark
| | | |
Collapse
|
33
|
Fendri A, Frikha F, Louati H, Bou Ali M, Gargouri H, Gargouri Y, Miled N. Cloning and molecular modeling of a thermostable carboxylesterase from the chicken uropygial glands. J Mol Graph Model 2014; 56:1-9. [PMID: 25541525 DOI: 10.1016/j.jmgm.2014.11.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 11/24/2014] [Accepted: 11/30/2014] [Indexed: 01/09/2023]
Abstract
Starting from total uropygial glands mRNAs, chicken uropygial carboxylesterase (cuCES) cDNA was synthesized by RT-PCR and cloned into the PGEM-T vector. Amino acid sequence of the cuCES is compared to that of human liver carboxylesterase 1 (hCES1). Given the high amino acid sequence homology between the two enzymes, a 3-D structure model of the chicken carboxylesterase was built using the structure of hCES1 as template. By following this model and utilizing molecular dynamics (MD) simulations, the resistance of the chicken carboxylesterase at high temperatures could be explained. The docking of substrate analogs into the cuCES active site was used to explain the fact that the chicken carboxylesterase cannot hydrolyze efficiently large substrate molecules.
Collapse
Affiliation(s)
- Ahmed Fendri
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax (ENIS), route de Soukra, BPW 3038 Sfax, Tunisia.
| | - Fakher Frikha
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax (ENIS), route de Soukra, BPW 3038 Sfax, Tunisia
| | - Hanen Louati
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax (ENIS), route de Soukra, BPW 3038 Sfax, Tunisia
| | - Madiha Bou Ali
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax (ENIS), route de Soukra, BPW 3038 Sfax, Tunisia
| | - Hela Gargouri
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax (ENIS), route de Soukra, BPW 3038 Sfax, Tunisia
| | - Youssef Gargouri
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax (ENIS), route de Soukra, BPW 3038 Sfax, Tunisia
| | - Nabil Miled
- Laboratoire de Biochimie et de Génie Enzymatique des Lipases, Ecole Nationale d'Ingénieurs de Sfax (ENIS), route de Soukra, BPW 3038 Sfax, Tunisia
| |
Collapse
|
34
|
Benson SP, Pleiss J. Solvent Flux Method (SFM): A Case Study of Water Access to Candida antarctica Lipase B. J Chem Theory Comput 2014; 10:5206-14. [DOI: 10.1021/ct500791e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
35
|
Computational study of the enantioselectivity of the O-acetylation of (R,S)-propranolol catalyzed by Candida antarctica lipase B. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.06.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
36
|
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]
|
37
|
Lousa D, Baptista AM, Soares CM. A molecular perspective on nonaqueous biocatalysis: contributions from simulation studies. Phys Chem Chem Phys 2013; 15:13723-36. [DOI: 10.1039/c3cp51761f] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
38
|
|
39
|
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.
Collapse
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
| |
Collapse
|
40
|
Johnson QR, Nellas RB, Shen T. Solvent-Dependent Gating Motions of an Extremophilic Lipase from Pseudomonas aeruginosa. Biochemistry 2012; 51:6238-45. [DOI: 10.1021/bi300557y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Quentin R. Johnson
- UT-ORNL Graduate School of Genome Science and Technology, Knoxville,
Tennessee 37996, United States
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37830, United States
| | - Ricky B. Nellas
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37830, United States
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Tongye Shen
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37830, United States
- Department of Biochemistry and Cellular & Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| |
Collapse
|
41
|
Ganjalikhany MR, Ranjbar B, Taghavi AH, Tohidi Moghadam T. Functional motions of Candida antarctica lipase B: a survey through open-close conformations. PLoS One 2012; 7:e40327. [PMID: 22808134 PMCID: PMC3393743 DOI: 10.1371/journal.pone.0040327] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2011] [Accepted: 06/07/2012] [Indexed: 12/02/2022] Open
Abstract
Candida antarctica lipase B (CALB) belongs to psychrophilic lipases which hydrolyze carboxyl ester bonds at low temperatures. There have been some features reported about cold-activity of the enzyme through experimental methods, whereas there is no detailed information on its mechanism of action at molecular level. Herein, a comparative molecular dynamics simulation and essential dynamics analysis have been carried out at three temperatures (5, 35 and 50°C) to trace the dominant factors in the psychrophilic properties of CALB under cold condition. The results clearly describe the effect of temperature on CALB with meaningful differences in the flexibility of the lid region (α5 helix), covering residues 141–147. Open- closed conformations have been obtained from different sets of long-term simulations (60 ns) at 5°C gave two reproducible distinct forms of CALB. The starting open conformation became closed immediately at 35 and 50°C during 60 ns of simulation, while a sequential open-closed form was observed at 5°C. These structural alterations were resulted from α5 helical movements, where the closed conformation of active site cleft was formed by displacement of both helix and its side chains. Analysis of normal mode showed concerted motions that are involved in the movement of both α5 and α10 helices. It is suggested that the functional motions needed for lypolytic activity of CALB is constructed from short-range movement of α5, accompanied by long-range movement of the domains connected to the lid region.
Collapse
Affiliation(s)
| | - Bijan Ranjbar
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
- * E-mail:
| | - Amir Hossein Taghavi
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Tahereh Tohidi Moghadam
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| |
Collapse
|
42
|
Lousa D, Baptista AM, Soares CM. Analyzing the molecular basis of enzyme stability in ethanol/water mixtures using molecular dynamics simulations. J Chem Inf Model 2012; 52:465-73. [PMID: 22243049 DOI: 10.1021/ci200455z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One of the drawbacks of nonaqueous enzymology is the fact that enzymes tend to be less stable in organic solvents than in water. There are, however, some enzymes that display very high stabilities in nonaqueous media. In order to take full advantage of the use of nonaqueous solvents in enzyme catalysis, it is essential to elucidate the molecular basis of enzyme stability in these media. Toward this end, we performed μs-long molecular dynamics simulations using two homologous proteases, pseudolysin, and thermolysin, which are known to have considerably different stabilities in solutions containing ethanol. The analysis of the simulations indicates that pseudolysin is more stable than thermolysin in ethanol/water mixtures and that the disulfide bridge between C30 and C58 is important for the stability of the former enzyme, which is consistent with previous experimental observations. Our results indicate that thermolysin has a higher tendency to interact with ethanol molecules (especially through van der Waals contacts) than pseudolysin, which can lead to the disruption of intraprotein hydrophobic interactions and ultimately result in protein unfolding. In the absence of the C30-C58 disulfide bridge, pseudolysin undergoes larger conformational changes, becoming more open and more permeable to ethanol molecules which accumulate in its interior and form hydrophobic interactions with the enzyme, destroying its structure. Our observations are not only in good agreement with several previous experimental findings on the stability of the enzymes studied in ethanol/water mixtures but also give an insight on the molecular determinants of this stability. Our findings may, therefore, be useful in the rational development of enzymes with increased stability in these media.
Collapse
Affiliation(s)
- Diana Lousa
- Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Av. da República, 2780-157 Oeiras, Portugal
| | | | | |
Collapse
|
43
|
Abstract
Interactions of lipases with hydrophobic substrate-water interfaces are of great interest to design improved lipase variants and engineer reaction conditions. This chapter describes the necessary steps to carry out molecular dynamics simulations of Candida antarctica lipase B at tributyrin-water interface using the GROMACS simulation software. Special attention is drawn to the preparation of the protein and the substrate-water interface and to the analysis of the obtained trajectory.
Collapse
Affiliation(s)
- Christian C Gruber
- ACIB Austrian Centre of Industrial Biotechnology, c/o Centre of Molecular Biosciences, University of Graz, Graz, Austria
| | | |
Collapse
|
44
|
Kawakami K, Ueno M, Takei T, Oda Y, Takahashi R. Application of a Burkholderia cepacia lipase-immobilized silica monolith micro-bioreactor to continuous-flow kinetic resolution for transesterification of (R, S)-1-phenylethanol. Process Biochem 2012. [DOI: 10.1016/j.procbio.2011.09.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
45
|
Christelle B, Eduardo BDO, Latifa C, Elaine-Rose M, Bernard M, Evelyne RH, Mohamed G, Jean-Marc E, Catherine H. Combined docking and molecular dynamics simulations to enlighten the capacity of Pseudomonas cepacia and Candida antarctica lipases to catalyze quercetin acetylation. J Biotechnol 2011; 156:203-10. [PMID: 21933689 DOI: 10.1016/j.jbiotec.2011.09.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Revised: 08/23/2011] [Accepted: 09/07/2011] [Indexed: 01/03/2023]
Abstract
A combined docking and molecular dynamics protocol was applied to investigate quercetin binding modes within the catalytic cavity of Candida antarctica lipase B (CALB) and Pseudomonas cepacia lipase (PCL), aiming to explain the difference of specificity of these enzymes in acetylation reaction. For both lipases, docking of quercetin yielded two families of conformers with either the quercetin A or B-ring pointing towards the catalytic residues. Molecular dynamics (MD) calculations were subsequently performed on several complexes of each family. MD trajectories were analyzed focusing on the orientation of the acyl donor bound to the catalytic serine towards the oxyanion hole residues and the proximity of quercetin hydroxyl groups to the catalytic residues. Results showed that with CALB, the acetate was not correctly positioned within the oxyanion hole whatever the orientation of quercetin, suggesting that no product could be obtained. With PCL, the acetate remained within the oxyanion hole during all MD trajectories. Depending on quercetin orientation, either the 7-OH group or the 3, 5, 3', 4'-OH groups came alternatively near the catalytic residues, suggesting that all of them could be acylated. The capacity of models to explain the regioselectivity of the reaction was discussed. Key residues and interactions involved in quercetin binding modes were identified and related to the reaction feasibility.
Collapse
Affiliation(s)
- Bidouil Christelle
- Laboratoire Ingénierie des Biomolécules, ENSAIA-INPL, Nancy Université, 2 av. de la Forêt d'Haye, 54500, Vandoeuvre-lès-Nancy, France
| | | | | | | | | | | | | | | | | |
Collapse
|
46
|
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]
|
47
|
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]
|
48
|
Lousa D, Baptista AM, Soares CM. Structural determinants of ligand imprinting: a molecular dynamics simulation study of subtilisin in aqueous and apolar solvents. Protein Sci 2011; 20:379-86. [PMID: 21280129 DOI: 10.1002/pro.569] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The phenomenon known as "ligand imprinting" or "ligand-induced enzyme memory" was first reported in 1988, when Russell and Klibanov observed that lyophilizing subtilisin in the presence of competitive inhibitors (that were subsequently removed) could significantly enhance its activity in an apolar solvent. (Russell and Klibanov, J Biol Chem 1988;263:11624-11626). They further observed that this enhancement did not occur when similar assays were carried out in water. Herein, we shed light on the molecular determinants of ligand imprinting using a molecular dynamics (MD) approach. To simulate the effect of placing an enzyme in the presence of a ligand before its lyophilization, an inhibitor was docked in the active site of subtilisin and 20 ns MD simulations in water were performed. The ligand was then removed and the resulting structure was used for subsequent MD runs using hexane and water as solvents. As a control, the same simulation setup was applied using the structure of subtilisin in the absence of the inhibitor. We observed that the ligand maintains the active site in an open conformation and that this configuration is retained after the removal of the inhibitor, when the simulations are carried out in hexane. In agreement with experimental findings, the structural configuration induced by the ligand is lost when the simulations take place in water. Our analysis of fluctuations indicates that this behavior is a result of the decreased flexibility displayed by enzymes in an apolar solvent, relatively to the aqueous situation.
Collapse
Affiliation(s)
- Diana Lousa
- Laboratório de Modelação de Proteínas, ITQB-UNL, Av. da República, EAN, 2780-157 Oeiras, Portugal
| | | | | |
Collapse
|
49
|
Rehm S, Trodler P, Pleiss J. Solvent-induced lid opening in lipases: a molecular dynamics study. Protein Sci 2011; 19:2122-30. [PMID: 20812327 DOI: 10.1002/pro.493] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
In most lipases, a mobile lid covers the substrate binding site. In this closed structure, the lipase is assumed to be inactive. Upon activation of the lipase by contact with a hydrophobic solvent or at a hydrophobic interface, the lid opens. In its open structure, the substrate binding site is accessible and the lipase is active. The molecular mechanism of this interfacial activation was studied for three lipases (from Candida rugosa, Rhizomucor miehei, and Thermomyces lanuginosa) by multiple molecular dynamics simulations for 25 ns without applying restraints or external forces. As initial structures of the simulations, the closed and open structures of the lipases were used. Both the closed and the open structure were simulated in water and in an organic solvent, toluene. In simulations of the closed lipases in water, no conformational transition was observed. However, in three independent simulations of the closed lipases in toluene the lid gradually opened. Thus, pathways of the conformational transitions were investigated and possible kinetic bottlenecks were suggested. The open structures in toluene were stable, but in water the lid of all three lipases moved towards the closed structure and partially unfolded. Thus, in all three lipases opening and closing was driven by the solvent and independent of a bound substrate molecule.
Collapse
Affiliation(s)
- Sascha Rehm
- Institute of Technical Biochemistry, University of Stuttgart, D-70569 Stuttgart, Germany
| | | | | |
Collapse
|
50
|
Exploring the conformational states and rearrangements of Yarrowia lipolytica Lipase. Biophys J 2011; 99:2225-34. [PMID: 20923657 DOI: 10.1016/j.bpj.2010.07.040] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 07/02/2010] [Accepted: 07/15/2010] [Indexed: 10/19/2022] Open
Abstract
We report the 1.7 Å resolution crystal structure of the Lip2 lipase from Yarrowia lipolytica in its closed conformation. The Lip2 structure is highly homologous to known structures of the fungal lipase family (Thermomyces lanuginosa, Rhizopus niveus, and Rhizomucor miehei lipases). However, it also presents some unique features that are described and discussed here in detail. Structural differences, in particular in the conformation adopted by the so-called lid subdomain, suggest that the opening mechanism of Lip2 may differ from that of other fungal lipases. Because the catalytic activity of lipases is strongly dependent on structural rearrangement of this mobile subdomain, we focused on elucidating the molecular mechanism of lid motion. Using the x-ray structure of Lip2, we carried out extensive molecular-dynamics simulations in explicit solvent environments (water and water/octane interface) to characterize the major structural rearrangements that the lid undergoes under the influence of solvent or upon substrate binding. Overall, our results suggest a two-step opening mechanism that gives rise first to a semi-open conformation upon adsorption of the protein at the water/organic solvent interface, followed by a further opening of the lid upon substrate binding.
Collapse
|