1
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Chen G, Khan IM, He W, Li Y, Jin P, Campanella OH, Zhang H, Huo Y, Chen Y, Yang H, Miao M. Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects. Compr Rev Food Sci Food Saf 2022; 21:2688-2714. [PMID: 35470946 DOI: 10.1111/1541-4337.12965] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/17/2022] [Accepted: 03/25/2022] [Indexed: 02/06/2023]
Abstract
The applications of lipases in esterification, amidation, and transesterification have broadened their potential in the production of fine compounds with high cumulative values. Mostly, the catalytic triad of lipases is covered by either one or two mobile peptides called the "lid" that control the substrate channel to the catalytic center. The lid holds unique conformational allostery via interfacial activation to regulate the dynamics and catalytic functions of lipases, thereby highlighting its importance in redesigning these enzymes for industrial applications. The structural characteristic of lipase, the dynamics of lids, and the roles of lid in lipase catalysis were summarized, providing opportunities for rebuilding lid region by biotechniques (e.g., metagenomic technology and protein engineering) and enzyme immobilization. The review focused on the advantages and disadvantages of strategies rebuilding the lid region. The main shortcomings of biotechnologies on lid rebuilding were discussed such as negative effects on lipase (e.g., a decrease of activity). Additionally, the main shortcomings (e.g., enzyme desorption at high temperatre) in immobilization on hydrophobic supports via interfacial action were presented. Solutions to the mentioned problems were proposed by combinations of computational design with biotechnologies, and improvements of lipase immobilization (e.g., immobilization protocols and support design). Finally, the review provides future perspectives about designing hyperfunctional lipases as biocatalysts in the food industry based on lid conformation and dynamics.
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Affiliation(s)
- Gang Chen
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China.,State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
| | - Wensen He
- School of Food Science and Technology, Jiangsu University, Zhenjiang, China
| | - Yongxin Li
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Peng Jin
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Osvaldo H Campanella
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China.,Department of Food Science and Technology, Ohio State University, Columbus, Ohio, USA
| | - Haihua Zhang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yanrong Huo
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Yang Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Huqing Yang
- College of Food and Health, Zhejiang Agriculture and Forest University, Hangzhou, China
| | - Ming Miao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, China
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2
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Qin X, Zhong J, Wang Y. A mutant T1 lipase homology modeling, and its molecular docking and molecular dynamics simulation with fatty acids. J Biotechnol 2021; 337:24-34. [PMID: 34197821 DOI: 10.1016/j.jbiotec.2021.06.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/25/2021] [Indexed: 11/18/2022]
Abstract
A thermostable T1 lipase from Geobacillus zalihae exhibits broad substrate specificity and good potential application in fats and oils. However, structural insight into the enzyme against substrates is poorly understood at the molecular level. Herein, the study aimed to examine interactions between a mutant T1 lipase (Mut-T1 lipase) and selected fatty acids (caprylic, myristic, stearic, oleic, linoleic and linolenic acids) by performing molecular docking and molecular dynamics (MD) simulation. The structure of Mut-T1 lipase obtained by homology modeling was reliable for molecular docking and MD simulation. Molecular docking revealed that Mut-T1 lipase showed low binding affinity for caprylic acid (-4.97 kcal/mol) compared to the other fatty acids (-5.65 to -6.88 kcal/mol). However, the conformation of Mut-T1 lipase-caprylic acid complex was comparably stable during the simulation, in terms of less root-mean square fluctuation. Besides, solvent accessible surface area value of Mut-T1 lipase-fatty acid complexes decreased with increasing chain length of fatty acid. van der Waals interactions were requisite in maintaining complex stability during the binding process. This work provides structural insight into interactions between the lipase and the fatty acids, which will facilitate design and applications of new mutants of T1 lipase in modifying fats and oils.
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Affiliation(s)
- Xiaoli Qin
- College of Food Science, Southwest University, Chongqing, 400715, PR China
| | - Jinfeng Zhong
- College of Food Science, Southwest University, Chongqing, 400715, PR China
| | - Yonghua Wang
- College of Food Science and Technology, South China University of Technology, Guangzhou, 510006, PR China.
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3
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Qiu J, Han R, Wang C. Microbial halophilic lipases: A review. J Basic Microbiol 2021; 61:594-602. [PMID: 34096085 DOI: 10.1002/jobm.202100107] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/23/2021] [Indexed: 11/08/2022]
Abstract
Microbial lipases are commercially significant due to their versatile catalytic function of hydrolysis triacylglycerol. Among these, lipases from extremophiles are optimal for industrial application. Halophilic microorganisms living in a high salinity environment, such as the ocean, salt lakes, salt wells, and so on, produce halophilic lipases. In recent decades, many remarkable achievements have been made related to the properties and application of halophilic lipases. This review offers information collected over the last decades on halophilic lipase sources as well as advances in production, factors influencing activity, stability under various conditions, structural characteristics, progress in industrial applications such as food flavor modification, biodiesel production, and waste treatment, to provide theoretical and methodological references for the research in this direction.
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Affiliation(s)
- Junjie Qiu
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Rui Han
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
| | - Chuan Wang
- College of Bioengineering, Sichuan University of Science and Engineering, Zigong, China
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4
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Maiangwa J, Hamdan SH, Mohamad Ali MS, Salleh AB, Zaliha Raja Abd Rahman RN, Shariff FM, Leow TC. Enhancing the stability of Geobacillus zalihae T1 lipase in organic solvents and insights into the structural stability of its variants. J Mol Graph Model 2021; 105:107897. [PMID: 33770705 DOI: 10.1016/j.jmgm.2021.107897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 03/04/2021] [Accepted: 03/04/2021] [Indexed: 11/28/2022]
Abstract
Critical to the applications of proteins in non-aqueous enzymatic processes is their structural dynamics in relation to solvent polarity. A pool of mutants derived from Geobacillus zalihae T1 lipase was screened in organic solvents (methanol, ethanol, propanol, butanol and pentanol) resulting in the selection of six mutants at initial screening (A83D/K251E, R21C, G35D/S195 N, K84R/R103C/M121I/T272 M and R106H/G327S). Site-directed mutagenesis further yielded quadruple mutants A83D/M121I/K251E/G327S and A83D/M121I/S195 N/T272 M, both of which had improved activity after incubation in methanol. The km and kcat values of these mutants vary marginally with the wild-type enzyme in the methanol/substrate mixture. Thermally induced unfolding of mutants was accompanied with some loss of secondary structure content. The root mean square deviations (RMSD) and B-factors revealed that changes in the structural organization are intertwined with an interplay of the protein backbone with organic solvents. Spatially exposed charged residues showed correlations between the solvation dynamics of the methanol solvent and the hydrophobicity of the residues. The short distances of the radial distribution function provided the required distances for hydrogen bond formation and hydrophobic interactions. These dynamic changes demonstrate newly formed structural interactions could be targeted and incorporated experimentally on the basis of solvent mobility and mutant residues.
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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, 43400, UPM Serdang, Selangor, Malaysia; Department of Microbiology Kaduna State University, Nigeria; Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, 43400, UPM Serdang, Selangor, Malaysia
| | - Siti Hajar Hamdan
- Department of Biochemistry, Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, 43400, UPM Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Department of Biochemistry, Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, 43400, UPM Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, 43400, UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Department of Microbiology, Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Institute of Bioscience, 43400, UPM Serdang, Universiti Putra Malaysia Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Enzyme Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, 43400, UPM Serdang, Selangor, Malaysia; Enzyme Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Science, Universiti Putra Malaysia Serdang, 43400, UPM Serdang, Selangor, Malaysia; Institute of Bioscience, 43400, UPM Serdang, Universiti Putra Malaysia Serdang, Selangor, Malaysia.
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5
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Rodríguez-Salarichs J, García de Lacoba M, Prieto A, Martínez MJ, Barriuso J. Versatile Lipases from the Candida rugosa-like Family: A Mechanistic Insight Using Computational Approaches. J Chem Inf Model 2021; 61:913-920. [PMID: 33555857 PMCID: PMC8479805 DOI: 10.1021/acs.jcim.0c01151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Lipases
are enzymes able to catalyze the hydrolysis or synthesis
of triglycerides, depending on the reaction conditions, whereas sterol
esterases show the same ability on sterol esters. Structurally, both
kinds of enzymes display an α/β-hydrolase fold, with a
substrate-binding pocket formed by a hydrophobic cavity covered by
a mobile lid. However, it has been reported that some lipases from
the Candida rugosa-like family display
wide substrate specificity on both triglycerides and sterol esters.
Among them, enzymes with different biotechnological applications,
such as the lipase isoenzymes produced by C. rugosa and the sterol esterase from Ophiostoma piceae, have been exhaustively characterized and their crystal structures
are available. Differences in substrate affinity among these proteins
have been attributed to changes in their hydrophobicity. In this work,
we analyzed the full catalytic mechanisms of these proteins using
molecular dynamics tools, gaining insight into their mechanistic properties.
In addition, we developed an in silico protocol to
predict the substrate specificity using C. rugosa and O. piceae lipases as model enzymes
and triglycerides and cholesterol esters with different fatty acid
chain lengths as model substrates. The protocol was validated by comparing
the in silico results with those described in the
literature. These results would be useful to perform virtual screening
of substrates for enzymes of the C. rugosa-like family with unknown catalytic properties.
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Affiliation(s)
- Javier Rodríguez-Salarichs
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Mario García de Lacoba
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Alicia Prieto
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - María Jesús Martínez
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas Margarita Salas, Department of Environmental Biology, Consejo Superior de Investigaciones Científicas CSIC, Ramiro de Maeztu 9, 28040 Madrid, Spain
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6
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Sankar S, Ponnuraj K. Less explored plant lipases: Modeling and molecular dynamics simulations of plant lipases in different solvents and temperatures to understand structure-function relationship. Int J Biol Macromol 2020; 164:3546-3558. [DOI: 10.1016/j.ijbiomac.2020.08.227] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 08/05/2020] [Accepted: 08/29/2020] [Indexed: 01/14/2023]
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7
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Novel thermostable lipase produced by a thermo-halophilic bacterium that catalyses hydrolytic and transesterification reactions. Heliyon 2020; 6:e04520. [PMID: 32743102 PMCID: PMC7385455 DOI: 10.1016/j.heliyon.2020.e04520] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/18/2020] [Accepted: 07/17/2020] [Indexed: 12/14/2022] Open
Abstract
Lipase belongs to the class of hydrolytic enzymes that are widely used in the biotechnology industries. The goal of this research was to purify and characterize lipase produced from a thermo-halophilic bacterium, namely Pria Laot Sabang 80 (PLS 80). Purification was performed using ammonium sulphate fractionation, followed by gel filtration chromatography using Sepharose Cl-6B. After purification, the enzyme had a specific activity of 326.6 U/mg with a purity of 6.02 higher than the crude extract; with a molecular weight of around 50 kDa. The optimum activity was observed at 70 °C and pH 9. The activity increased in the presence of 10 mM Mn2+, K+ and Ca2+ ions, while Hg2+ only slightly increased the enzyme activity. In contrast, the activity decreased in 10 mM Mg2+, Zn2+, Co2+, EDTA, and PMSF. The enzyme showed good hydrolytic activity on long fatty acids substrates (p-nitrophenyl palmitate) with a value of 35.5 U/mL. It was also able to catalyze a transesterification reaction. GC-MS result showed that the biodiesel consisted of methyl octanoate (5.3%), methyl caprate (12.4%), methyl laurate (34.1%), methyl myristate (10.7%), methyl palmitate (3.9%), and methyl stearate (1.2%) when using coconut oil as the substrate. The results suggested that the lipase from PLS 80 had unique attributes that could be useful in various industrial applications.
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8
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Druteika G, Sadauskas M, Malunavicius V, Lastauskiene E, Statkeviciute R, Savickaite A, Gudiukaite R. New engineered Geobacillus lipase GD-95RM for industry focusing on the cleaner production of fatty esters and household washing product formulations. World J Microbiol Biotechnol 2020; 36:41. [DOI: 10.1007/s11274-020-02816-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/20/2020] [Indexed: 12/19/2022]
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9
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Bauer TL, Buchholz PCF, Pleiss J. The modular structure of α/β-hydrolases. FEBS J 2019; 287:1035-1053. [PMID: 31545554 DOI: 10.1111/febs.15071] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/15/2019] [Accepted: 09/19/2019] [Indexed: 12/22/2022]
Abstract
The α/β-hydrolase fold family is highly diverse in sequence, structure and biochemical function. To investigate the sequence-structure-function relationships, the Lipase Engineering Database (https://led.biocatnet.de) was updated. Overall, 280 638 protein sequences and 1557 protein structures were analysed. All α/β-hydrolases consist of the catalytically active core domain, but they might also contain additional structural modules, resulting in 12 different architectures: core domain only, additional lids at three different positions, three different caps, additional N- or C-terminal domains and combinations of N- and C-terminal domains with caps and lids respectively. In addition, the α/β-hydrolases were distinguished by their oxyanion hole signature (GX-, GGGX- and Y-types). The N-terminal domains show two different folds, the Rossmann fold or the β-propeller fold. The C-terminal domains show a β-sandwich fold. The N-terminal β-propeller domain and the C-terminal β-sandwich domain are structurally similar to carbohydrate-binding proteins such as lectins. The classification was applied to the newly discovered polyethylene terephthalate (PET)-degrading PETases and MHETases, which are core domain α/β-hydrolases of the GX- and the GGGX-type respectively. To investigate evolutionary relationships, sequence networks were analysed. The degree distribution followed a power law with a scaling exponent γ = 1.4, indicating a highly inhomogeneous network which consists of a few hubs and a large number of less connected sequences. The hub sequences have many functional neighbours and therefore are expected to be robust toward possible deleterious effects of mutations. The cluster size distribution followed a power law with an extrapolated scaling exponent τ = 2.6, which strongly supports the connectedness of the sequence space of α/β-hydrolases. DATABASE: Supporting data about domains from other proteins with structural similarity to the N- or C-terminal domains of α/β-hydrolases are available in Data Repository of the University of Stuttgart (DaRUS) under doi: https://doi.org/10.18419/darus-458.
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Affiliation(s)
- Tabea L Bauer
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
| | - Patrick C F Buchholz
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Germany
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10
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Mohamed RA, Salleh AB, Leow TC, Yahaya NM, Abdul Rahman MB. Site-directed mutagenesis: role of lid region for T1 lipase specificity. Protein Eng Des Sel 2018; 31:221-229. [DOI: 10.1093/protein/gzy023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Accepted: 08/27/2018] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rauda A Mohamed
- Laboratory of Enzyme Technology, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abu Bakar Salleh
- Laboratory of Enzyme Technology, Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Thean Chor Leow
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Normi M Yahaya
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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11
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Efficient heterologous expression, functional characterization and molecular modeling of annular seabream digestive phospholipase A2. Chem Phys Lipids 2018. [DOI: 10.1016/j.chemphyslip.2017.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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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.
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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
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13
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Tang Q, Lan D, Yang B, Khan FI, Wang Y. Site-directed mutagenesis studies of hydrophobic residues in the lid region of T1 lipase. EUR J LIPID SCI TECH 2016. [DOI: 10.1002/ejlt.201600107] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Qingyun Tang
- School of Food Science and Engineering; State Key Laboratory of Pulp and Paper Engineering; South China University of Technology; Guangzhou P. R. China
| | - Dongming Lan
- School of Food Science and Engineering; State Key Laboratory of Pulp and Paper Engineering; South China University of Technology; Guangzhou P. R. China
| | - Bo Yang
- School of Bioscience and Bioengineering; South China University of Technology; Guangzhou P. R. China
| | - Faez Iqbal Khan
- School of Chemistry and Chemical Engineering; Henan University of Technology; Zhengzhou P.R. China
| | - Yonghua Wang
- School of Food Science and Engineering; State Key Laboratory of Pulp and Paper Engineering; South China University of Technology; Guangzhou P. R. China
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14
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Asymmetric hydrolysis of dimethyl-3-phenylglutarate in sequential batch reactor operation catalyzed by immobilized Geobacillus thermocatenulatus lipase. Catal Today 2015. [DOI: 10.1016/j.cattod.2014.12.039] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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15
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Zhao D, Peng C, Zhou J. Lipase adsorption on different nanomaterials: a multi-scale simulation study. Phys Chem Chem Phys 2015; 17:840-50. [DOI: 10.1039/c4cp04696j] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Adsorption orientations of lipase on different nanomaterials with different surface chemistry.
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Affiliation(s)
- Daohui Zhao
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Chunwang Peng
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
| | - Jian Zhou
- School of Chemistry and Chemical Engineering
- Guangdong Provincial Key Lab for Green Chemical Product Technology
- South China University of Technology
- Guangzhou
- P. R. China
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16
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Wu X, Xu P, Wang J, Xu Y, Fu T, Zhang D, Zhao M, Liu J, Shen H, Xiu Z, Li G. Folding mechanisms of Trefoil Knot proteins studied by molecular dynamics simulations and Go-model. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 827:93-110. [PMID: 25387962 DOI: 10.1007/978-94-017-9245-5_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Most proteins need to avoid the complex topologies when folding into the native structures, but some proteins with nontrivial topologies have been found in nature. Here we used protein unfolding simulations under high temperature and all-atom Gō-model to investigate the folding mechanisms for two trefoil knot proteins. Results show that, the contacts in β-sheet are important to the formation of knot protein, and if these contacts disappeared, the knot protein would be easy to untie. In the Gō-model simulations, the folding processes of the two knot proteins are similar. The compact structures of the two knot proteins with the native contacts in β-sheet are formed in transition state, and the intermediate state has loose C-terminal. This model also reveals the detailed folding mechanisms for the two proteins.
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Affiliation(s)
- Xue Wu
- Laboratory of Molecular Modeling and Design, State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, Liaoning, China
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17
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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.
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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
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18
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Cao H, Deng L, Lei M, Wang F, Tan T. The role of temperature and solvent microenvironment on the activity of Yarrowia lipolytica Lipase 2: Insights from molecular dynamics simulation. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.08.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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19
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Jiang Y, Li L, Zhang H, Feng W, Tan T. Lid Closure Mechanism of Yarrowia lipolytica Lipase in Methanol Investigated by Molecular Dynamics Simulation. J Chem Inf Model 2014; 54:2033-41. [DOI: 10.1021/ci500163y] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yang Jiang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lingli Li
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haiyang Zhang
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Wei Feng
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Tianwei Tan
- Beijing
Key Lab of Bioprocess,
College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
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20
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Qin XL, Lan DM, Zhong JF, Liu L, Wang YH, Yang B. Fatty acid specificity of T1 lipase and its potential in acylglycerol synthesis. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2014; 94:1614-1621. [PMID: 24338705 DOI: 10.1002/jsfa.6468] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 10/03/2013] [Accepted: 11/04/2013] [Indexed: 06/03/2023]
Abstract
BACKGROUND T1 lipase has received considerable attention due to its thermostability. Fatty acid specificity of T1 lipase (crude and purified) was investigated, and its potential in the synthesis of acylglycerols was also evaluated. RESULTS Fatty acid specificity of T1 lipase (crude and purified) was investigated in the esterification of fatty acids (C6:0 to C18:3), suggesting that crude and purified T1 lipase had the lowest preference for C18:0 [specificity constant (1/α) = 0.08] followed by C18:1 (1/α = 0.12) and showed the highest preference for C8:0 (1/α = 1). A structural model was constructed to briefly explore interactions between the lipase and its substrate. Furthermore, crude T1 lipase-catalysed synthesis of diacylglycerols (DAGs) and monoacylglycerols (MAGs) by esterification of glycerol with C18:1 was studied for evaluating its potential in acylglycerols synthesis. The optimal conditions were glycerol/oleic acid molar ratio 5:1, the lipase concentration 9.7 U g(-1) of substrates, water content 50 g kg(-1) of substrates and temperature 50 °C, which yielded 42.25% DAGs, 26.34% MAGs and 9.18% triacylglycerols at 2 h. CONCLUSION DAGs and MAGs were synthesised in good yields although C18:1 (a much poorer substrate) was used. Our work demonstrates that T1 lipase, which was discovered to show 1,3-regio-selectivity, is a promising biocatalyst for lipids modification.
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Affiliation(s)
- Xiao-Li Qin
- College of Food Sciences, Southwest University, Chongqing, 400715, People's Republic of China; College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, 510640, People's Republic of China
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21
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Abedi Karjiban R, Lim WZ, Basri M, Abdul Rahman MB. Molecular Dynamics of Thermoenzymes at High Temperature and Pressure: A Review. Protein J 2014; 33:369-76. [DOI: 10.1007/s10930-014-9568-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Qin XL, Huang HH, Lan DM, Wang YH, Yang B. Typoselectivity of Crude Geobacillus sp. T1 Lipase Fused with a Cellulose-Binding Domain and Its Use in the Synthesis of Structured Lipids. J AM OIL CHEM SOC 2013. [DOI: 10.1007/s11746-013-2347-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Ping J, Hao P, Li YX, Wang JF. Molecular dynamics studies on the conformational transitions of adenylate kinase: a computational evidence for the conformational selection mechanism. BIOMED RESEARCH INTERNATIONAL 2013; 2013:628536. [PMID: 23936827 PMCID: PMC3712241 DOI: 10.1155/2013/628536] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 06/13/2013] [Indexed: 12/22/2022]
Abstract
Escherichia coli adenylate kinase (ADK) is a monomeric phosphotransferase enzyme that catalyzes reversible transfer of phosphoryl group from ATP to AMP with a large-scale domain motion. The detailed mechanism for this conformational transition remains unknown. In the current study, we performed long time-scale molecular dynamics simulations on both open and closed states of ADK. Based on the structural analyses of the simulation trajectories, we detected over 20 times conformational transitions between the open and closed states of ADK and identified two novel conformations as intermediate states in the catalytic processes. With these findings, we proposed a possible mechanism for the large-scale domain motion of Escherichia coli ADK and its catalytic process: (1) the substrate free ADK adopted an open conformation; (2) ATP bound with LID domain closure; (3) AMP bound with NMP domain closure; (4) phosphoryl transfer occurred with ATP, and AMP converted into two ADPs, and no conformational transition was detected in the enzyme; (5) LID domain opened with one ADP released; (6) another ADP released with NMP domain open. As both open and closed states sampled a wide range of conformation transitions, our simulation strongly supported the conformational selection mechanism for Escherichia coli ADK.
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Affiliation(s)
- Jie Ping
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai Chinese Academy of Sciences, Shanghai 200025, China
| | - Pei Hao
- Pathogen Diagnostic Center, Institut Pasteur of Shanghai Chinese Academy of Sciences, Shanghai 200025, China
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, China
| | - Yi-Xue Li
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, China
- Bioinformatics Center, Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Jing-Fang Wang
- Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235, China
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
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24
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Cong S, Ma XT, Li YX, Wang JF. Structural Basis for the Mutation-Induced Dysfunction of Human CYP2J2: A Computational Study. J Chem Inf Model 2013; 53:1350-7. [DOI: 10.1021/ci400003p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Shan Cong
- Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Center for Systems Biomedicine,
Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xiao-Tu Ma
- Key Laboratory of Systems Biomedicine
(Ministry of Education), Shanghai Center for Systems Biomedicine,
Shanghai Jiao Tong University, Shanghai 200240, China
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25
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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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26
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Liu Y, Liu BY, Hao P, Li X, Li YX, Wang JF. π-π Stacking mediated drug-drug interactions in human CYP2E1. Proteins 2013; 81:945-54. [PMID: 23349037 DOI: 10.1002/prot.24260] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2012] [Accepted: 01/11/2013] [Indexed: 11/07/2022]
Abstract
Because of having many low molecular mass substrates, CYP2E1 is of particular interests to the pharmaceutical industry. Many evidences showed that this enzyme can adopt multiple substrates to significantly reduce the oxidation rate of the substrates. The detailed mechanism for this observation is still unclear. In the current study, we employed GPU-accelerated molecular dynamics simulations to study the multiple-binding mode of human CYP2E1, with an aim of offering a mechanistic explanation for the unexplained multiple-substrate binding. Our results showed that Thr303 and Phe478 were key factors for the substrate recognition and multiple-substrate binding. The former can form a significant hydrogen bond to recognize and position the substrate in the productive binding orientation in the active site. The latter acted as a mediator for the substrate communications via π-π stacking interactions. In the multiple-binding mode, the aforementioned π-π stacking interactions formed by the aromatic rings of both substrates and Phe478 drove the first substrate far away from the catalytic center, orienting in an additional binding position and going against the substrate metabolism. All these findings could give atomic insights into the detailed mechanism for the multiple-substrate binding in human CYP2E1, providing useful information for the drug metabolism mechanism and personalized use of clinical drugs.
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Affiliation(s)
- Yue Liu
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
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27
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Computational design of glutamate dehydrogenase in Bacillus subtilis natto. J Mol Model 2013; 19:1919-27. [PMID: 23338837 DOI: 10.1007/s00894-013-1755-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 01/02/2013] [Indexed: 10/27/2022]
Abstract
Bacillus subtilis natto is widely used in industry to produce natto, a traditional and popular Japanese soybean food. However, during its secondary fermentation, high amounts of ammonia are released to give a negative influence on the flavor of natto. Glutamate dehydrogenase (GDH) is a key enzyme for the ammonia produced and released, because it catalyzes the oxidative deamination of glutamate to alpha-ketoglutarate using NAD(+) or NADP(+) as co-factor during carbon and nitrogen metabolism processes. To solve this problem, we employed multiple computational methods model and re-design GDH from Bacillus subtilis natto. Firstly, a structure model of GDH with cofactor NADP(+) was constructed by threading and ab initio modeling. Then the substrate glutamate were flexibly docked into the structure model to form the substrate-binding mode. According to the structural analysis of the substrate-binding mode, Lys80, Lys116, Arg196, Thr200, and Ser351 in the active site were found could form a significant hydrogen bonding network with the substrate, which was thought to play a crucial role in the substrate recognition and position. Thus, these residues were then mutated into other amino acids, and the substrate binding affinities for each mutant were calculated. Finally, three single mutants (K80A, K116Q, and S351A) were found to have significant decrease in the substrate binding affinities, which was further supported by our biochemical experiments.
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28
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Scaffold-based pan-agonist design for the PPARα, PPARβ and PPARγ receptors. PLoS One 2012; 7:e48453. [PMID: 23119024 PMCID: PMC3485212 DOI: 10.1371/journal.pone.0048453] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 09/26/2012] [Indexed: 12/25/2022] Open
Abstract
As important members of nuclear receptor superfamily, Peroxisome proliferator-activated receptors (PPAR) play essential roles in regulating cellular differentiation, development, metabolism, and tumorigenesis of higher organisms. The PPAR receptors have 3 identified subtypes: PPARα, PPARβ and PPARγ, all of which have been treated as attractive targets for developing drugs to treat type 2 diabetes. Due to the undesirable side-effects, many PPAR agonists including PPARα/γ and PPARβ/γ dual agonists are stopped by US FDA in the clinical trials. An alternative strategy is to design novel pan-agonist that can simultaneously activate PPARα, PPARβ and PPARγ. Under such an idea, in the current study we adopted the core hopping algorithm and glide docking procedure to generate 7 novel compounds based on a typical PPAR pan-agonist LY465608. It was observed by the docking procedures and molecular dynamics simulations that the compounds generated by the core hopping and glide docking not only possessed the similar functions as the original LY465608 compound to activate PPARα, PPARβ and PPARγ receptors, but also had more favorable conformation for binding to the PPAR receptors. The additional absorption, distribution, metabolism and excretion (ADME) predictions showed that the 7 compounds (especially Cpd#1) hold high potential to be novel lead compounds for the PPAR pan-agonist. Our findings can provide a new strategy or useful insights for designing the effective pan-agonists against the type 2 diabetes.
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29
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Rahman IA, Rahman RNZRA, Salleh AB, Basri M. Formulation and Evaluation of an Automatic Dishwashing Detergent Containing T1 Lipase. J SURFACTANTS DETERG 2012. [DOI: 10.1007/s11743-012-1398-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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30
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Combination of oxyanion Gln114 mutation and medium engineering to influence the enantioselectivity of thermophilic lipase from Geobacillus zalihae. Int J Mol Sci 2012; 13:11666-11680. [PMID: 23109876 PMCID: PMC3472768 DOI: 10.3390/ijms130911666] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 08/10/2012] [Accepted: 08/20/2012] [Indexed: 11/17/2022] Open
Abstract
The substitution of the oxyanion Q114 with Met and Leu was carried out to investigate the role of Q114 in imparting enantioselectivity on T1 lipase. The mutation improved enantioselectivity in Q114M over the wild-type, while enantioselectivity in Q114L was reduced. The enantioselectivity of the thermophilic lipases, T1, Q114L and Q114M correlated better with log p as compared to the dielectric constant and dipole moment of the solvents. Enzyme activity was good in solvents with log p < 3.5, with the exception of hexane which deviated substantially. Isooctane was found to be the best solvent for the esterification of (R,S)-ibuprofen with oleyl alcohol for lipases Q114M and Q114L, to afford E values of 53.7 and 12.2, respectively. Selectivity of T1 was highest in tetradecane with E value 49.2. Solvents with low log p reduced overall lipase activity and dimethyl sulfoxide (DMSO) completely inhibited the lipases. Ester conversions, however, were still low. Molecular sieves employed as desiccant were found to adversely affect catalysis in the lipase variants, particularly in Q114M. The higher desiccant loading also increased viscosity in the reaction and further reduced the efficiency of the lipase-catalyzed esterifications.
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31
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Wang YJ, Wang JF, Ping J, Yu Y, Wang Y, Lian P, Li X, Li YX, Hao P. Computational studies on the substrate interactions of influenza A virus PB2 subunit. PLoS One 2012; 7:e44079. [PMID: 22957044 PMCID: PMC3434214 DOI: 10.1371/journal.pone.0044079] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2011] [Accepted: 07/30/2012] [Indexed: 12/28/2022] Open
Abstract
Influenza virus, which spreads around the world in seasonal epidemics and leads to large numbers of deaths every year, has several ribonucleoproteins in the central core of the viral particle. These viral ribonucleoproteins can specifically bind the conserved 3' and 5' caps of the viral RNAs with responsibility for replication and transcription of the viral RNA in the nucleus of infected cells. A fundamental question of most importance is that how the cap-binding proteins in the influenza virus discriminates between capped RNAs and non-capped ones. To get an answer, we performed molecular dynamics simulations and free energy calculations on the influenza A virus PB2 subunit, an important component of the RNP complexes, with a cap analog m7GTP. Our calculations showed that some key residues in the active site, such as Arg355, His357, Glu361 as well as Gln406, could offer significant hydrogen bonding and hydrophobic interactions with the guanine ring of the cap analog m7GTP to form an aromatic sandwich mechanism for the cap recognition and positioning in the active site. Subsequently, we applied this idea to a virtual screening procedure and identified 5 potential candidates that might be inhibitors against the PB2 subunit. Interestingly, 2 candidates Cpd1 and Cpd2 have been already reported to have inhibitory activities to the influenza virus cap-binding proteins. Further calculation also showed that they had comparatively higher binding affinities to the PB2 subunit than that of m7GTP. We believed that our findings could give an atomic insight into the deeper understanding of the cap recognition and binding mechanism, providing useful information for searching or designing novel drugs against influenza viruses.
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Affiliation(s)
- Ya-Jun Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Jing-Fang Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
- Shanghai Center for Bioinformation and Technology, Shanghai, China
| | - Jie Ping
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Yao Yu
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ying Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Peng Lian
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Jiao Tong University, Shanghai, China
| | - Xuan Li
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Yi-Xue Li
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- Bioinformatics Center, Key Laboratory of Systems Biology, Chinese Academy of Sciences, Shanghai, China
| | - Pei Hao
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- Institute of Pasteur, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
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32
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Wang Y, Wu XL, Wei DQ, Li YX, Wang JF. Autoinhibitory mechanism for the mutation-induced impaired FGF9 signaling. J Chem Inf Model 2012; 52:2422-9. [PMID: 22920789 DOI: 10.1021/ci3003045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Fibroblast growth factor 9 (FGF9), an important member of the fibroblast growth factor (FGF) family, can bind with high affinity to FGFR3 in a heparin-dependent approach. In humans, the deletions and mutations resulting in dysfunction of the FGF9 signaling can cause human skeletal dysplasia and cancers. A mutation (S99N) in this protein has been identified to be associated with significantly impaired FGF signaling considered as a potential cause of synostoses syndrome. However, the detailed mechanism for this observation still remains unknown. In this study, we used molecular dynamics simulations and free energy calculations to study the interactions of FGF9(WT/S99N), FGFR3c, and heparin, with an aim of providing atomic sights into the detailed mechanism for the impaired FGF signaling caused by the S99N mutation. We found that the S99N mutation has a well-ordered C-terminal structure, which can reduce its homodimerization ability so as to break the monomer-dimer equilibrium in the FGF signaling, which is considered as a key factor to regulate extracellular matrix affinity and tissue diffusion in the FGF signaling pathway. The FGF9(WT) monomer can preferentially form a homodimer owing to its comparatively favorable binding free energy. In contrast, the FGF9(S99N) monomer is preferred to bind with the FGFR3c receptor to form an inactive complex, leading to impair FGF signaling. To support our computational findings, we also performed biochemical experiments, which confirm the computational results mentioned above. The impaired FGF signaling is believed to be a potential cause of human synostoses syndrome, implicating an important role for FGF9 in normal joint development.
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Affiliation(s)
- Ying Wang
- Key Laboratory of Systems Biomedicine-Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
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33
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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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34
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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.
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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
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Udatha DBRKG, Mapelli V, Panagiotou G, Olsson L. Common and distant structural characteristics of feruloyl esterase families from Aspergillus oryzae. PLoS One 2012; 7:e39473. [PMID: 22745763 PMCID: PMC3382194 DOI: 10.1371/journal.pone.0039473] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 05/21/2012] [Indexed: 11/18/2022] Open
Abstract
Background Feruloyl esterases (FAEs) are important biomass degrading accessory enzymes due to their capability of cleaving the ester links between hemicellulose and pectin to aromatic compounds of lignin, thus enhancing the accessibility of plant tissues to cellulolytic and hemicellulolytic enzymes. FAEs have gained increased attention in the area of biocatalytic transformations for the synthesis of value added compounds with medicinal and nutritional applications. Following the increasing attention on these enzymes, a novel descriptor based classification system has been proposed for FAEs resulting into 12 distinct families and pharmacophore models for three FAE sub-families have been developed. Methodology/Principal Findings The feruloylome of Aspergillus oryzae contains 13 predicted FAEs belonging to six sub-families based on our recently developed descriptor-based classification system. The three-dimensional structures of the 13 FAEs were modeled for structural analysis of the feruloylome. The three genes coding for three enzymes, viz., A.O.2, A.O.8 and A.O.10 from the feruloylome of A. oryzae, representing sub-families with unknown functional features, were heterologously expressed in Pichia pastoris, characterized for substrate specificity and structural characterization through CD spectroscopy. Common feature-based pharamacophore models were developed according to substrate specificity characteristics of the three enzymes. The active site residues were identified for the three expressed FAEs by determining the titration curves of amino acid residues as a function of the pH by applying molecular simulations. Conclusions/Significance Our findings on the structure-function relationships and substrate specificity of the FAEs of A. oryzae will be instrumental for further understanding of the FAE families in the novel classification system. The developed pharmacophore models could be applied for virtual screening of compound databases for short listing the putative substrates prior to docking studies or for post-processing docking results to remove false positives. Our study exemplifies how computational predictions can complement to the information obtained through experimental methods.
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Affiliation(s)
- D. B. R. K. Gupta Udatha
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Valeria Mapelli
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Gianni Panagiotou
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
- Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Lisbeth Olsson
- Department of Chemical and Biological Engineering, Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
- * E-mail:
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Characterization of an extracellular lipase and its chaperone from Ralstonia eutropha H16. Appl Microbiol Biotechnol 2012; 97:2443-54. [DOI: 10.1007/s00253-012-4115-z] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2012] [Revised: 04/16/2012] [Accepted: 04/16/2012] [Indexed: 11/25/2022]
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Wang JF, Chou KC. Insights into the mutation-induced HHH syndrome from modeling human mitochondrial ornithine transporter-1. PLoS One 2012; 7:e31048. [PMID: 22292090 PMCID: PMC3266937 DOI: 10.1371/journal.pone.0031048] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 12/30/2011] [Indexed: 11/25/2022] Open
Abstract
Human mitochondrial ornithine transporter-1 is reported in coupling with the hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome, which is a rare autosomal recessive disorder. For in-depth understanding of the molecular mechanism of the disease, it is crucially important to acquire the 3D structure of human mitochondrial ornithine transporter-1. Since no such structure is available in the current protein structure database, we have developed it via computational approaches based on the recent NMR structure of human mitochondrial uncoupling protein (Berardi MJ, Chou JJ, et al. Nature 2011, 476:109–113). Subsequently, we docked the ligand L-ornithine into the computational structure to search for the favorable binding mode. It was observed that the binding interaction for the most favorable binding mode is featured by six remarkable hydrogen bonds between the receptor and ligand, and that the most favorable binding mode shared the same ligand-binding site with most of the homologous mitochondrial carriers from different organisms, implying that the ligand-binding sites are quite conservative in the mitochondrial carriers family although their sequences similarity is very low with 20% or so. Moreover, according to our structural analysis, the relationship between the disease-causing mutations of human mitochondrial ornithine transporter-1 and the HHH syndrome can be classified into the following three categories: (i) the mutation occurs in the pseudo-repeat regions so as to change the region of the protein closer to the mitochondrial matrix; (ii) the mutation is directly affecting the substrate binding pocket so as to reduce the substrate binding affinity; (iii) the mutation is located in the structural region closer to the intermembrane space that can significantly break the salt bridge networks of the protein. These findings may provide useful insights for in-depth understanding of the molecular mechanism of the HHH syndrome and developing effective drugs against the disease.
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Affiliation(s)
- Jing-Fang Wang
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China.
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Wang JF, Hao P, Li YX, Dai JL, Li X. Exploration of conformational transition in the aryl-binding site of human FXa using molecular dynamics simulations. J Mol Model 2011; 18:2717-25. [PMID: 22116613 DOI: 10.1007/s00894-011-1295-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 10/24/2011] [Indexed: 11/25/2022]
Abstract
Human coagulation Factor X (FX), a member of the vitamin K-dependent serine protease family, is a crucial component of the human coagulation cascade. Activated FX (FXa) participates in forming the prothrombinase complex on activated platelets to convert prothrombin to thrombin in coagulation reactions. In the current study, 30-ns MD simulations were performed on both the open and closed states of human FXa. Root mean squares (RMS) fluctuations showed that structural fluctuations concentrated on the loop regions of FXa, and the presence of a ligand in the closed system resulted in larger fluctuations of the gating residues. The open system had a gating distance from 9.23 to 11.33 Å, i.e., significantly larger than that of the closed system (4.69-6.35 Å), which allows diversified substrates of variable size to enter. Although the solvent accessible surface areas (SASA) of FXa remained the same in both systems, the open system generally had a larger total SASA or hydrophobic SASA (or both) for residues surrounding the S4 pocket. Additionally, more hydrogen bonds were formed in the closed state than in the open state of FXa, which is believed to play a significant role in maintaining the closed confirmation of the aryl-binding site. Based on the results of MD simulations, we propose that an induced-fit mechanism governs the functioning of human coagulation FX, which helps provide a better understanding of the interactions between FXa and its substrate, and the mechanism of the conformational changes involved in human coagulation.
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Affiliation(s)
- Jing-Fang Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiaotong University, Shanghai, China.
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Li J, Wei DQ, Wang JF, Li YX. A negative cooperativity mechanism of human CYP2E1 inferred from molecular dynamics simulations and free energy calculations. J Chem Inf Model 2011; 51:3217-25. [PMID: 22077825 DOI: 10.1021/ci2004016] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Human cytochrome P450 2E1 (CYP2E1) participates in the metabolism of over 2% of all the oral drugs. A hallmark peculiar feature of this enzyme is that it exhibits a pronounced negative cooperativity in substrate binding. However the mechanism by which the negative cooperativity occurs is unclear. Here, we performed molecular dynamics simulations and free energy calculations on human CYP2E1 to examine the structural differences between the substrate-free and the enzymes with one and two aniline molecules bound. Our results indicate that although the effector substrate does not bind in the active site cavity, it still can directly interact with the active site residues of human CYP2E1. The interaction of the effector substrate with the active site leads to a reorientation of active site residues, which thereby weakens the interactions of the active substrate with this site. We also identify a conserved residue T303 that plays a crucial role in the negative cooperative binding on the short-range effects. This residue is a key factor in the positioning of substrates and in proton delivery to the active site. Additionally, a long-range effect of the effector substrate is identified in which F478 is proposed to play a key role. As located in the interface between the active and effector sites, this residue structurally links the active and effector sites and is found to play a significant role in affecting substrate access and ligand positioning within the active site. In the negative cooperative binding, this residue can decrease the interactions of the active substrate with the active site by π-π stacking which then lowers the hydroxylation activity for the active substrate. These findings are in agreement with previous experimental observations and thus provide detailed atomistic insight into the poorly understood mechanism of the negative cooperativity in human CYP2E1.
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Affiliation(s)
- Jue Li
- College of Life Science and Biotechnology and State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai 200240, China
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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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Lian P, Wei DQ, Wang JF, Chou KC. An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes. PLoS One 2011; 6:e18587. [PMID: 21525996 PMCID: PMC3078132 DOI: 10.1371/journal.pone.0018587] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Accepted: 03/10/2011] [Indexed: 11/18/2022] Open
Abstract
Phospholamban functions as a regulator of Ca(2+) concentration of cardiac muscle cells by triggering the bioactivity of sarcoplasmic reticulum Ca(2+)-ATPase. In order to understand its dynamic mechanism in the environment of bilayer surroundings, we performed long time-scale molecular dynamic simulations based on the high-resolution NMR structure of phospholamban pentamer. It was observed from the molecular dynamics trajectory analyses that the conformational transitions between the "bellflower" and "pinwheel" modes were detected for phospholamban. Particularly, the two modes became quite similar to each other after phospholamban was phosphorylated at Ser16. Based on these findings, an allosteric mechanism was proposed to elucidate the dynamic process of phospholamban interacting with Ca(2+)-ATPase.
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Affiliation(s)
- Peng Lian
- College of Life Science and Biotechnology and Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
| | - Dong-Qing Wei
- College of Life Science and Biotechnology and Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, China
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (DQW); (JFW)
| | - Jing-Fang Wang
- Key Laboratory of Systems Biomedicine, Ministry of Education, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- * E-mail: (DQW); (JFW)
| | - Kuo-Chen Chou
- Gordon Life Science Institute, San Diego, California, United States of America
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Wang JF, Chou KC. Insights from modeling the 3D structure of New Delhi metallo-β-lactamse and its binding interactions with antibiotic drugs. PLoS One 2011; 6:e18414. [PMID: 21494599 PMCID: PMC3073942 DOI: 10.1371/journal.pone.0018414] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2010] [Accepted: 03/04/2011] [Indexed: 11/18/2022] Open
Abstract
New Delhi metallo-beta-lactamase (NDM-1) is an enzyme that makes bacteria resistant to a broad range of beta-lactam antibiotic drugs. This is because it can inactivate most beta-lactam antibiotic drugs by hydrolyzing them. For in-depth understanding of the hydrolysis mechanism, the three-dimensional structure of NDM-1 was developed. With such a structural frame, two enzyme-ligand complexes were derived by respectively docking Imipenem and Meropenem (two typical beta-lactam antibiotic drugs) to the NDM-1 receptor. It was revealed from the NDM-1/Imipenem complex that the antibiotic drug was hydrolyzed while sitting in a binding pocket of NDM-1 formed by nine residues. And for the case of NDM-1/Meropenem complex, the antibiotic drug was hydrolyzed in a binding pocket formed by twelve residues. All these constituent residues of the two binding pockets were explicitly defined and graphically labeled. It is anticipated that the findings reported here may provide useful insights for developing new antibiotic drugs to overcome the resistance problem.
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Affiliation(s)
- Jing-Fang Wang
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, China
- Shanghai Center for Bioinformation and Technology, Shanghai, China
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (J-FW); (K-CC)
| | - Kuo-Chen Chou
- Gordon Life Science Institute, San Diego, California, United States of America
- * E-mail: (J-FW); (K-CC)
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Isolation and identification of lipase producing thermophilic Geobacillus sp. SBS-4S: Cloning and characterization of the lipase. J Biosci Bioeng 2011; 111:272-8. [DOI: 10.1016/j.jbiosc.2010.11.015] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2010] [Revised: 11/15/2010] [Accepted: 11/19/2010] [Indexed: 11/23/2022]
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44
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Zhang J. Comparison studies of the structural stability of rabbit prion protein with human and mouse prion proteins. J Theor Biol 2011; 269:88-95. [DOI: 10.1016/j.jtbi.2010.10.020] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2010] [Revised: 09/07/2010] [Accepted: 10/15/2010] [Indexed: 11/16/2022]
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