1
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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.
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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
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2
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Tjørnelund HD, Vind J, Brask J, Woodley JM, Peters GH. Candida antarctica lipase B performance in organic solvent at varying water activities studied by molecular dynamics simulations. Comput Struct Biotechnol J 2023; 21:5451-5462. [PMID: 38022691 PMCID: PMC10665702 DOI: 10.1016/j.csbj.2023.10.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Applications of lipases in low-water environments are found across a broad range of industries, including the pharmaceutical and oleochemical sectors. This includes condensation reactions in organic solvents where the enzyme activity has been found to depend strongly on both the solvent and the water activity (aw). Despite several experimental and computational studies, knowledge is largely empirical, and a general predictive approach is much needed. To close this gap, we chose native Candida antarctica lipase B (CALB) and two mutants thereof and used molecular dynamics (MD) simulations to gain a molecular understanding of the effect of aw on the specific activity of CALB in hexane. Based on the simulations, we propose four criteria to understand the performance of CALB in organic media, which is supported by enzyme kinetics experiments. First, the lipase must be stable in the organic solvent, which was the case for native CALB and the two mutants studied here. Secondly, water clusters that form and grow close to the active site must not block the path of substrate molecules into the active site. Thirdly, the lipase's lid must not cover the active site. Finally, mutations and changes in aw must not disrupt the geometry of the active site. We show that mutating specific residues close to the active site can hinder water cluster formation and growth, making the lipase resistant to changes in aw. Our computational screening criteria could potentially be used to screen in-silico designed variants, so only promising candidates could be pushed forward to characterisation.
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Affiliation(s)
- Helena D. Tjørnelund
- Department of Chemistry, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | | | | | - John M. Woodley
- Department of Chemical and Biochemical Engineering, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
| | - Günther H.J. Peters
- Department of Chemistry, Technical University of Denmark, 2800 Kgs Lyngby, Denmark
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3
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Fernandez-Lopez L, Roda S, Robles-Martín A, Muñoz-Tafalla R, Almendral D, Ferrer M, Guallar V. Enhancing the Hydrolytic Activity of a Lipase towards Larger Triglycerides through Lid Domain Engineering. Int J Mol Sci 2023; 24:13768. [PMID: 37762071 PMCID: PMC10530837 DOI: 10.3390/ijms241813768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 08/23/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Lipases have valuable potential for industrial use, particularly those mostly active against water-insoluble substrates, such as triglycerides composed of long-carbon chain fatty acids. However, in most cases, engineered variants often need to be constructed to achieve optimal performance for such substrates. Protein engineering techniques have been reported as strategies for improving lipase characteristics by introducing specific mutations in the cap domain of esterases or in the lid domain of lipases or through lid domain swapping. Here, we improved the lipase activity of a lipase (WP_075743487.1, or LipMRD) retrieved from the Marine Metagenomics MarRef Database and assigned to the Actinoalloteichus genus. The improvement was achieved through site-directed mutagenesis and by substituting its lid domain (FRGTEITQIKDWLTDA) with that of Rhizopus delemar lipase (previously R. oryzae; UniProt accession number, I1BGQ3) (FRGTNSFRSAITDIVF). The results demonstrated that the redesigned mutants gain activity against bulkier triglycerides, such as glyceryl tridecanoate and tridodecanoate, olive oil, coconut oil, and palm oil. Residue W89 (LipMRD numbering) appears to be key to the increase in lipase activity, an increase that was also achieved with lid swapping. This study reinforces the importance of the lid domains and their amino acid compositions in determining the substrate specificity of lipases, but the generalization of the lid domain swapping between lipases or the introduction of specific mutations in the lid domain to improve lipase activity may require further investigation.
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Affiliation(s)
- Laura Fernandez-Lopez
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain; (L.F.-L.); (D.A.)
| | - Sergi Roda
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
| | - Ana Robles-Martín
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
- PhD Programme, Faculty of Pharmacy and Food Science, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - Rubén Muñoz-Tafalla
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
- PhD Programme, Faculty of Pharmacy and Food Science, Universitat de Barcelona (UB), 08007 Barcelona, Spain
| | - David Almendral
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain; (L.F.-L.); (D.A.)
| | - Manuel Ferrer
- Instituto de Catalisis y Petroleoquimica (ICP), CSIC, 28049 Madrid, Spain; (L.F.-L.); (D.A.)
| | - Víctor Guallar
- Department of Life Sciences, Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain; (S.R.); (A.R.-M.); (R.M.-T.)
- Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
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4
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Wijaya T, Kitao A. Energetic and Kinetic Origins of CALB Interfacial Activation Revealed by PaCS-MD/MSM. J Phys Chem B 2023; 127:7431-7441. [PMID: 37562019 PMCID: PMC10476181 DOI: 10.1021/acs.jpcb.3c02041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 07/21/2023] [Indexed: 08/12/2023]
Abstract
The conformational dynamics of Candida antarctica lipase B (CALB) was investigated by molecular dynamics (MD) simulation, parallel cascade selection MD (PaCS-MD), and the Markov state model (MSM) and mainly focused on the lid-opening motion closely related to substrate binding. All-atom MD simulation of CALB was conducted in water and on the interface of water and tricaprylin. CALB initially situated in water and separated by layers of water from the interface is spontaneously adsorbed onto the tricaprylin surface during MD simulation. The opening and closing motions of the lid are simulated by PaCS-MD, and subsequent MSM analysis provided the free-energy landscape and time scale of the conformational transitions among the closed, semiopen, and open states. The closed state is the most stable in the water system, but the stable conformation in the interface system shifts to the semiopen state. These effects could explain the energetics and kinetics origin of the previously reported interfacial activation of CALB. These findings could help expand the application of CALB toward a wide variety of substrates.
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Affiliation(s)
- Tegar
N. Wijaya
- School
of Life Science and Technology, Tokyo Institute
of Technology. 2-12-1
Ookayama, Meguro-ku, Tokyo 152-8550, Japan
- Department
of Chemistry, Universitas Pertamina, Jl. Teuku Nyak Arief, Simprug, Jakarta 12220, Indonesia
| | - Akio Kitao
- School
of Life Science and Technology, Tokyo Institute
of Technology. 2-12-1
Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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5
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Fang Y, Liu F, Shi Y, Yang T, Xin Y, Gu Z, Shi G, Zhang L. N-terminal lid swapping contributes to the substrate specificity and activity of thermophilic lipase TrLipE. Front Microbiol 2023; 14:1193955. [PMID: 37434709 PMCID: PMC10332459 DOI: 10.3389/fmicb.2023.1193955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 06/12/2023] [Indexed: 07/13/2023] Open
Abstract
TrLipE is a thermophilic lipase that has potential commercial applications because of its catalytic ability under extreme conditions. Consistent with most lipases, the lid of TrLipE is located over the catalytic pocket, controls the substrate channel to the active center, and regulates the substrate specificity, activity, and stability of the enzyme through conformational changes. TrLipE from Thermomicrobium roseum has potential industrial applications, which is hindered by its weak enzymatic activity. Here, 18 chimeras (TrL1-TrL18) were reconstructed by N-terminal lid swapping between TrLipE and structurally similar enzymes. The results showed that the chimeras had a similar pH range and optimum pH as wild TrLipE but a narrower temperature range of 40-80°C, and TrL17 and the other chimeras showed lower optimum temperatures of 70°C and 60°C, respectively. In addition, the half-lives of the chimeras were lower than those of TrLipE under optimum temperature conditions. Molecular dynamics simulations indicated that chimeras had high RMSD, RMSF, and B-factor values. When p-nitrophenol esters with different chains were used as substrates, compared with TrLipE, most of the chimeras had a low Km and high kcat value. The chimeras TrL2, TrL3, TrL17, and TrL18 could specifically catalyze the substrate 4-nitrophenyl benzoate, with TrL17 showing the highest kcat/Km value of 363.88 ± 15.83 L⋅min-1⋅mmol-1. Mutants were then designed by investigating the binding free energies of TrL17 and 4-nitrophenyl benzoate. The results indicated that single, double, and triple substitution variants (M89W and I206N; E33W/I206M and M89W/I206M; and M89W/I206M/L21I and M89W/I206N/L21I, respectively) presented approximately 2- to 3-fold faster catalysis of 4-nitrophenyl benzoate than the wild TrL17. Our observations will facilitate the development of the properties and industrial applications of TrLipE.
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Affiliation(s)
- Yakun Fang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Fan Liu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Yi Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Ting Yang
- Wuxi Food Safety Inspection and Test Center, Technology Innovation Center of Special Food for State Market Regulation, Wuxi, Jiangsu, China
| | - Yu Xin
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhenghua Gu
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Guiyang Shi
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
| | - Liang Zhang
- National Engineering Research Center for Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, Jiangsu, China
- Jiangsu Provincial Engineering Research Center for Bioactive Product Processing, Jiangnan University, Wuxi, Jiangsu, China
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6
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Role of N-Terminal Extensional Long α-Helix in the Arylesterase from Lacticaseibacillus rhamnosus GG on Catalysis and Stability. Catalysts 2023. [DOI: 10.3390/catal13020441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023] Open
Abstract
In the α/β hydrolases superfamily, the extra module modulated enzymatic activity, substrate specificity, and stability. The functional role of N-terminal extensional long α-helix (Ala2-Glu29, designated as NEL-helix) acting as the extra module in the arylesterase LggEst from Lacticaseibacillus rhamnosus GG had been systemically investigated by deletion mutagenesis, biochemical characterization, and biophysical methods. The deletion of the NEL-helix did not change the overall structure of this arylesterase. The deletion of the NEL-helix led to the shifting of optimal pH into the acidity and the loss of thermophilic activity. The deletion of the NEL-helix produced a 10.6-fold drop in catalytic activity towards the best substrate pNPC10. NEL-Helix was crucial for the thermostability, chemical resistance, and organic solvents tolerance. The deletion of the NEL-helix did not change the overall rigidity of enzyme structure and only reduced the local rigidity of the active site. Sodium deoxycholate might partially replenish the loss of activity caused by the deletion of the NEL-helix. Our research further enriched the functional role of the extra module on catalysis and stability in the α/β hydrolase fold superfamily.
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7
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Feiten MC, Morigi I, Di Luccio M, Oliveira JV. Activity and stability of lipase from Candida Antarctica after treatment in pressurized fluids. Biotechnol Lett 2023; 45:287-298. [PMID: 36592260 DOI: 10.1007/s10529-022-03335-x] [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: 03/14/2022] [Revised: 10/13/2022] [Accepted: 11/28/2022] [Indexed: 01/03/2023]
Abstract
Lipase B from Candida antarctica (CalB) is one of the biocatalysts most used in organic synthesis due to its ability to act in several medium, wide substrate specificity and enantioselectivity, tolerance to non-aqueous environment, and resistance to thermal deactivation. Thus, the objective of this work was to treat CalB in supercritical carbon dioxide (SC-CO2) and liquefied petroleum gas (LPG), and measure its activity before and after high-pressure treatment. Residual specific hydrolytic activities of 132% and 142% were observed when CalB was exposed to SC-CO2 at 35 ℃, 75 bar and 1 h and to LPG at 65 ℃, 30 bar and 1 h, respectively. Residual activity of the enzyme treated at high pressure was still above 100% until the 20th day of storage at low temperatures. There was no difference on the residual activity loss of CalB treated with LPG and stored at different temperatures over time. Greater difference was observed between CalB treated with CO2 and flash-frozen in liquid nitrogen (- 196 ℃) followed by storage in freezer (- 10 ℃) and CalB stored in freezer at - 10 ℃. Such findings encourage deeper studies on CalB as well as other enzymes behavior under different types of pressurized fluids aiming at industrial application.
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Affiliation(s)
- Mirian Cristina Feiten
- Department of Technology, State University of Maringá (UEM), Angelo Moreira da Fonseca Ave, Umuarama, Paraná, 87506-370, Brazil.
| | - Iasmin Morigi
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), Technology Center/C.P. 476, Florianópolis, Santa Catarina, 88040-900, Brazil
| | - Marco Di Luccio
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), Technology Center/C.P. 476, Florianópolis, Santa Catarina, 88040-900, Brazil
| | - José Vladimir Oliveira
- Department of Chemical and Food Engineering, Federal University of Santa Catarina (UFSC), Technology Center/C.P. 476, Florianópolis, Santa Catarina, 88040-900, Brazil
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8
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Nicolás P, Lassalle VL, Ferreira ML. Evaluation of biocatalytic pathways in the synthesis of polyesters: Towards a greener production of surgical sutures. POLYM ADVAN TECHNOL 2022. [DOI: 10.1002/pat.5900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Paula Nicolás
- Catalysis group PLAPIQUI‐UNS‐CONICET Bahía Blanca Argentina
- Departamento de Química Universidad Nacional del Sur Bahía Blanca Argentina
| | - Verónica L. Lassalle
- Departamento de Química Universidad Nacional del Sur Bahía Blanca Argentina
- Applied Hybrid Nanomaterials group INQUISUR‐UNS‐CONICET Bahía Blanca Argentina
| | - María L. Ferreira
- Catalysis group PLAPIQUI‐UNS‐CONICET Bahía Blanca Argentina
- Departamento de Química Universidad Nacional del Sur Bahía Blanca Argentina
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9
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Nazarian Z, Arab SS. Solvent-dependent activity of Candida antarctica lipase B and its correlation with a regioselective mono aza-Michael addition - experimental and molecular dynamics simulation studies. Heliyon 2022; 8:e10336. [PMID: 36090210 PMCID: PMC9449572 DOI: 10.1016/j.heliyon.2022.e10336] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Revised: 05/21/2022] [Accepted: 08/12/2022] [Indexed: 11/18/2022] Open
Abstract
With the aim of gaining understanding of the molecular basis of commercially available Candida antarctica lipase B (CALB) immobilized on polyacrylic resin catalyzed regioselective mono aza-Michael addition of Benzhydrazide to Diethyl maleate we decided to carry out molecular dynamics (MD) simulation studies in parallel with our experimental study. We found a correlation between the activity of CALB and the choice of solvent. Our study showed that solvent affects the performance of the enzyme due to the binding of solvent molecules to the enzyme active site region, and the solvation energy of substrates in the different solvents. We also found that CALB is only active in nonpolar solvent (i.e. Hexane), and therefore we investigated the influence of Hexane on the catalytic activity of CALB for the reaction. The results of this study and related experimental validation from our studies have been discussed here.
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Affiliation(s)
- Zohreh Nazarian
- Faculty of Biological Sciences, Tarbiat Modares University, Jalal Highway, Tehran 14115-154, Iran
- Department of Chemistry and Petroleum Sciences, Shahid Beheshti University, Evin, Tehran 1983963113, Iran
- Corresponding author.
| | - Seyed Shahriar Arab
- Faculty of Biological Sciences, Tarbiat Modares University, Jalal Highway, Tehran 14115-154, Iran
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10
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Todea A, Fortuna S, Ebert C, Asaro F, Tomada S, Cespugli M, Hollan F, Gardossi L. Rational Guidelines for the Two-Step Scalability of Enzymatic Polycondensation: Experimental and Computational Optimization of the Enzymatic Synthesis of Poly(glycerolazelate). CHEMSUSCHEM 2022; 15:e202102657. [PMID: 35199480 PMCID: PMC9320960 DOI: 10.1002/cssc.202102657] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 02/11/2022] [Indexed: 06/14/2023]
Abstract
The lipase-catalyzed polycondensation of azelaic acid and glycerol is investigated according to a Design-of-Experiment approach that helps to elucidate the effect of experimental variables on monomer conversion, Mn and regioselectivity of acylation of glycerol. Chemometric analysis shows that after 24 h the reaction proceeds regardless of the presence of the enzyme. Accordingly, the biocatalyst was removed after a first step of synthesis and the chain elongation continued at 80 °C. That allowed the removal of the biocatalyst and the preservation of its activity: pre-requites for efficient applicability at industrial scale. The experimental study, combined with docking-based computational analysis, provides rational guidelines for the optimization of the regioselective acylation of glycerol. The process is scaled up to 73.5 g of monomer. The novelty of the present study is the rigorous control of the reaction conditions and of the integrity of the immobilized biocatalyst, which serve to avoiding any interference of free enzyme or fines released in the reaction mixture. The quantitative analysis of the effect of experimental conditions and the overcoming of some major technical bottlenecks for the scalability of enzymatic polycondensation opens new scenarios for industrial exploitation.
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Affiliation(s)
- Anamaria Todea
- Department of Chemical and Pharmaceutical SciencesInstitution University of TriesteAddress 1 Via L. Giorgieri 134127TriesteItaly
| | - Sara Fortuna
- Department of Chemical and Pharmaceutical SciencesInstitution University of TriesteAddress 1 Via L. Giorgieri 134127TriesteItaly
- Current address: CONCEPT Lab, Istituto Italiano di Tecnologia (IIT)I-16152GenovaItaly
| | - Cynthia Ebert
- Department of Chemical and Pharmaceutical SciencesInstitution University of TriesteAddress 1 Via L. Giorgieri 134127TriesteItaly
| | - Fioretta Asaro
- Department of Chemical and Pharmaceutical SciencesInstitution University of TriesteAddress 1 Via L. Giorgieri 134127TriesteItaly
| | - Stefano Tomada
- Department of Chemical and Pharmaceutical SciencesInstitution University of TriesteAddress 1 Via L. Giorgieri 134127TriesteItaly
| | - Marco Cespugli
- Department of Chemical and Pharmaceutical SciencesInstitution University of TriesteAddress 1 Via L. Giorgieri 134127TriesteItaly
| | - Fabio Hollan
- Department of Chemical and Pharmaceutical SciencesInstitution University of TriesteAddress 1 Via L. Giorgieri 134127TriesteItaly
| | - Lucia Gardossi
- Department of Chemical and Pharmaceutical SciencesInstitution University of TriesteAddress 1 Via L. Giorgieri 134127TriesteItaly
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11
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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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12
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13
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Carvalho HF, Ferrario V, Pleiss J. Molecular Mechanism of Methanol Inhibition in CALB-Catalyzed Alcoholysis: Analyzing Molecular Dynamics Simulations by a Markov State Model. J Chem Theory Comput 2021; 17:6570-6582. [PMID: 34494846 DOI: 10.1021/acs.jctc.1c00559] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lipases are widely used enzymes that catalyze hydrolysis and alcoholysis of fatty acid esters. At high concentrations of small alcohols such as methanol or ethanol, many lipases are inhibited by the substrate. The molecular basis of the inhibition of Candida antarctica lipase B (CALB) by methanol was investigated by unbiased molecular dynamics (MD) simulations, and the substrate binding kinetics was analyzed by Markov state models (MSMs). The modeled fluxes of productive methanol binding at concentrations between 50 mM and 5.5 M were in good agreement with the experimental activity profile of CALB, with a peak at 300 mM. The kinetic and structural analysis uncovered the molecular basis of CALB inhibition. Beyond 300 mM, the kinetic bottleneck results from crowding of methanol in the substrate access channel, which is caused by the gradual formation of methanol patches close to Leu140 (helix α5), Leu278, and Ile285 (helix α10) at a distance of 4-5 Å from the active site. Our findings demonstrate the usefulness of unbiased MD simulations to study enzyme-substrate interactions at realistic substrate concentrations and the feasibility of scale-bridging by an MSM analysis to derive kinetic information.
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Affiliation(s)
- Henrique F Carvalho
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Valerio Ferrario
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Biochemistry and Technical Biochemistry, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
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14
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Sharath A, Haque N, Prabhu NP. Spontaneous lid closure and substrate-induced lid opening dynamics of human pancreatic lipase-related protein 2: A computational study. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128365] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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15
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Figueiredo PR, Almeida BC, Dourado DFAR, Sousa AF, Silvestre AJD, Carvalho ATP. Enzymatic Synthesis of Poly(caprolactone): A QM/MM Study. ChemCatChem 2020. [DOI: 10.1002/cctc.202000780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Pedro R. Figueiredo
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
| | - Beatriz C. Almeida
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
| | - Daniel F. A. R. Dourado
- Almac Sciences Department of Biocatalysis and Isotope Chemistry Almac House 20 Seagoe Industrial Estate Craigavon BT63 5QD Northern Ireland UK
| | | | | | - Alexandra T. P. Carvalho
- CNC – Center for Neuroscience and Cell Biology Institute for Interdisciplinary Research (IIIUC) University of Coimbra 3004-504 Coimbra Portugal
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16
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Breger JC, Susumu K, Lasarte-Aragonés G, Díaz SA, Brask J, Medintz IL. Quantum Dot Lipase Biosensor Utilizing a Custom-Synthesized Peptidyl-Ester Substrate. ACS Sens 2020; 5:1295-1304. [PMID: 32096987 DOI: 10.1021/acssensors.9b02291] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lipases are an important class of lipid hydrolyzing enzymes that play significant roles in many aspects of cell biology and digestion; they also have large roles in commercial food and biofuel preparation and are being targeted for pharmaceutical development. Given these, and many other biotechnological roles, sensitive and specific biosensors capable of monitoring lipase activity in a quantitative manner are critical. Here, we describe a Förster resonance energy transfer (FRET)-based biosensor that originates from a custom-synthesized ester substrate displaying a peptide at one end and a dye acceptor at the other. These substrates were ratiometrically self-assembled to luminescent semiconductor quantum dot (QD) donors by metal affinity coordination using the appended peptide's terminal hexahistidine motif to give rise to the full biosensing construct. This resulted in a high rate of FRET between the QD donor and the proximal substrate's dye acceptor. The lipase hydrolyzed the intervening target ester bond in the peptide substrate which, in turn, displaced the dye acceptor containing component and altered the rate of FRET in a concentration-dependent manner. Specifics of the substrate's stepwise synthesis are described along with the sensors assembly, characterization, and application in a quantitative proof-of-concept demonstration assay that is based on an integrated Michaelis-Menten kinetic approach. The utility of this unique nanoparticle-based architecture within a sensor configuration is then discussed.
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Affiliation(s)
- Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
| | - Kimihiro Susumu
- Optical Sciences Division, U.S. Naval Research Laboratory, Code 5600, Washington, District of Columbia 20375, United States
- KeyW Corporation, Hanover, Maryland 21076, United States
| | - Guillermo Lasarte-Aragonés
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
- Department of Bioengineering, George Mason University, Fairfax, Virginia 22030, United States
| | - Sebastián A. Díaz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
| | - Jesper Brask
- Novozymes A/S, Biologiens Vej 2, 2800 Kgs. Lyngby, Denmark
| | - Igor L. Medintz
- Center for Bio/Molecular Science and Engineering, U.S. Naval Research Laboratory, Code 6900, Washington, District of Columbia 20375, United States
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17
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Quarter of a Century after: A Glimpse at the Conformation and Mechanism of Candida antarctica Lipase B. CRYSTALS 2020. [DOI: 10.3390/cryst10050404] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Lipase B from Candida antarctica (CAL-B) belongs to the family of α/β-hydrolases, and is one from the most extensively used biocatalysts in the kinetic resolution of amines and alcohols in a racemic state, in the desymmetrization of diacetates or diols, and in the stereoselective synthesis of chiral intermediate compounds for obtaining the various pharmaceuticals and agents which protect plants. There are also many cases of promiscuous reactions catalyzed by CAL-B. The number of very important results appeared recently in the literature in the years 2015–2019, regarding the crystal structure and conformation of CAL-B molecule. Before 2015, there was a long period of a complete lack of information concerning this enzyme’s structure. The earlier reports about CAL-B structure were dated between 1994–1995, and did not provide enough conclusions about the mechanism of the enzyme. The recently solved structures give a hint of the enzyme mechanism in three dimensions.
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18
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Lu C, Peng X, Lu D, Liu Z. Global and Kinetic Profiles of Substrate Diffusion in Candida antarctica Lipase B: Molecular Dynamics with the Markov-State Model. ACS OMEGA 2020; 5:9806-9812. [PMID: 32391467 PMCID: PMC7203684 DOI: 10.1021/acsomega.9b04432] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/27/2020] [Indexed: 06/11/2023]
Abstract
Profiling substrate diffusion pathways with kinetic information, which accounts for the dynamic nature of enzyme-substrate interaction, can enable molecular reengineering of enzymes and process optimization of enzymatic catalysis. Candida antarctica lipase B (CALB) is extensively used for producing various chemicals because of its rich catalytic mechanisms, broad substrate spectrum, thermal stability, and tolerance to organic solvents. In this study, an all-atom molecular dynamics (MD) combined with Markov-state models (MSMs) implemented in pyEMMA was proposed to simulate diffusion pathways of 4-nitrophenyl ester (4NPE), a commonly used substrate, from the surface into the active site of CALB. Six important metastable conformations of CALB were identified in the diffusion process, including a closed state. An induced-fit mechanism incorporating multiple pathways with molecular information was proposed, which might find unprecedented applications for the rational design of lipase for green catalysis.
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Affiliation(s)
- Chenlin Lu
- Department of Chemical
Engineering, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Chemical Engineering, Ministry of Education, Beijing 100084, China
| | - Xue Peng
- Department of Chemical
Engineering, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Chemical Engineering, Ministry of Education, Beijing 100084, China
| | - Diannan Lu
- Department of Chemical
Engineering, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Chemical Engineering, Ministry of Education, Beijing 100084, China
| | - Zheng Liu
- Department of Chemical
Engineering, Tsinghua University, Beijing 100084, China
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19
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Silvestrini L, Cianci M. Principles of lipid-enzyme interactions in the limbus region of the catalytic site of Candida antarctica Lipase B. Int J Biol Macromol 2020; 158:358-363. [PMID: 32380114 DOI: 10.1016/j.ijbiomac.2020.04.061] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Revised: 03/30/2020] [Accepted: 04/07/2020] [Indexed: 11/25/2022]
Abstract
Lipases (E.C. 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates such as triacylglycerols and phospholipids. Candida antarctica Lipase B (CALB) acts in aqueous as well as in low-water media, thus being of considerable biochemical significance with high interest also for its industrial applications. The hydrolysis reaction follows a two-step mechanism, or 'interfacial activation', with adsorption of the enzyme to a heterogeneous interface and subsequent enhancement of the lipolytic activity. Once positioned within the catalytic triad, substrates are then hydrolysed, and products released. However, the intermediate steps of substrate transfer from the lipidic-aqueous phase to the enzyme surface and then down to the catalytic site are still unclear. By inhibiting CALB with ethyl phosphonate and incubating with glyceryl tributyrate (2,3-di(butanoyloxy)propyl butanoate), the crystal structure of the lipid-enzyme complex, at 1.55 Å resolution, shows the tributyrin in the limbus region of active site. The substrate is found 10 Å above the catalytic Ser, with the glycerol backbone pre-aligned for further processing by key interactions via an extended water network with α-helix10 and α-helix5. The findings offer new elements to elucidate the mechanism of substrate recognition, transfer and catalysis of Candida antarctica Lipase B (CALB) and lipases in general.
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Affiliation(s)
- Lucia Silvestrini
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy
| | - Michele Cianci
- Department of Agricultural, Food and Environmental Sciences, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
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20
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A Series of Novel Esters of Capsaicin Analogues Catalyzed by Candida antarctica Lipases. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0290-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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21
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Wu Z, Liu H, Xu L, Chen HF, Feng Y. Algorithm-based coevolution network identification reveals key functional residues of the α/β hydrolase subfamilies. FASEB J 2020; 34:1983-1995. [PMID: 31907985 DOI: 10.1096/fj.201900948rr] [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: 04/12/2019] [Revised: 10/02/2019] [Accepted: 10/21/2019] [Indexed: 11/11/2022]
Abstract
Covariant residues identified by computational algorithms have provided new insights into enzyme evolutionary routes. However, the reliability and accuracy of routine statistical coupling analysis (SCA) are unable to satisfy the needs of protein engineering because SCA depends only on sequence information. Here, we set up a new SCA algorithm, SCA.SIM, by integrating structure information and MD simulation data. The more reliable covariant residues with high-quality scores are obtained from sequence alignment weighted by residual movement for eight related subfamilies, belonging to α/β hydrolase family, with Candida antarctica lipase B (CALB). The 38 predicted covariant residues are tested for function by high-throughput quantitative evaluation in combination with activity and thermostability assays of a mutant library and deep sequencing. Based on the landscapes of both activity and thermostability, most mutants play key roles in catalysis, and some mutants gain 2.4- to 6-fold increase in half-life at 50°C and 9- to 12-fold improvement in catalytic efficiency. The activity of double mutants for A225F/T103A is higher than those of A225F and T103A which means that SCA.SIM method might be useful for identifying the allosteric coupling. The SCA.SIM algorithm can be used for protein coevolution and enzyme engineering research.
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Affiliation(s)
- Zhiyun Wu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Lishi Xu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.,Shanghai Center for Bioinformation Technology, Shanghai, China
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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22
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Santos YLDL, Chew-Fajardo YL, Brault G, Doucet N. Dissecting the evolvability landscape of the CalB active site toward aromatic substrates. Sci Rep 2019; 9:15588. [PMID: 31666622 PMCID: PMC6821916 DOI: 10.1038/s41598-019-51940-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 10/07/2019] [Indexed: 01/17/2023] Open
Abstract
A key event in the directed evolution of enzymes is the systematic use of mutagenesis and selection, a process that can give rise to mutant libraries containing millions of protein variants. To this day, the functional analysis and identification of active variants among such high numbers of mutational possibilities is not a trivial task. Here, we describe a combinatorial semi-rational approach to partly overcome this challenge and help design smaller and smarter mutant libraries. By adapting a liquid medium transesterification assay in organic solvent conditions with a combination of virtual docking, iterative saturation mutagenesis, and residue interaction network (RIN) analysis, we engineered lipase B from P. antarctica (CalB) to improve enzyme recognition and activity against the bulky aromatic substrates and flavoring agents methyl cinnamate and methyl salicylate. Substrate-imprinted docking was used to target active-site positions involved in enzyme-substrate and enzyme-product complexes, in addition to identifying 'hot spots' most likely to yield active variants. This iterative semi-rational design strategy allowed selection of CalB variants exhibiting increased activity in just two rounds of site-saturation mutagenesis. Beneficial replacements were observed by screening only 0.308% of the theoretical library size, illustrating how semi-rational approaches with targeted diversity can quickly facilitate the discovery of improved activity variants relevant to a number of biotechnological applications.
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Affiliation(s)
- Yossef López de Los Santos
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Ying Lian Chew-Fajardo
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Guillaume Brault
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada
| | - Nicolas Doucet
- Centre Armand-Frappier Santé Biotechnologie, Institut National de la Recherche Scientifique (INRS), Université du Québec, 531 Boulevard des Prairies, Laval, QC, H7V 1B7, Canada.
- PROTEO, the Québec Network for Research on Protein Function, Engineering, and Applications, 1045 Avenue de la Médecine, Université Laval, Quebec City, QC, G1V 0A6, Canada.
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23
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Figueiredo P, Almeida BC, Carvalho ATP. Enzymatic Polymerization of PCL-PEG Co-polymers for Biomedical Applications. Front Mol Biosci 2019; 6:109. [PMID: 31681797 PMCID: PMC6811512 DOI: 10.3389/fmolb.2019.00109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 10/04/2019] [Indexed: 11/25/2022] Open
Abstract
Biodegradable polymers, obtained via chemical synthesis, are currently employed in a wide range of biomedical applications. However, enzymatic polymerization is an attractive alternative because it is more sustainable and safer. Many lipases can be employed in ring-opening polymerization (ROP) of biodegradable polymers. Nevertheless, the harsh conditions required in industrial context are not always compatible with their enzymatic activity. In this work, we have studied a thermophilic carboxylesterase and the commonly used Lipase B from Candida antarctica (CaLB) for tailored synthesis of amphiphilic polyesters for biomedical applications. We have conducted Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) MD simulations of the synthesis of Polycaprolactone-Polyethylene Glycol (PCL-PEG) model co-polymers. Our insights about the reaction mechanisms are important for the design of customized enzymes capable to synthesize different polyesters for biomedical applications.
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Affiliation(s)
| | | | - Alexandra T. P. Carvalho
- Center for Neuroscience and Cell Biology, Institute for Interdisciplinary Research (IIIUC), University of Coimbra, Coimbra, Portugal
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24
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Artificial cysteine-lipases with high activity and altered catalytic mechanism created by laboratory evolution. Nat Commun 2019; 10:3198. [PMID: 31324776 PMCID: PMC6642262 DOI: 10.1038/s41467-019-11155-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 06/24/2019] [Indexed: 11/13/2022] Open
Abstract
Engineering artificial enzymes with high activity and catalytic mechanism different from naturally occurring enzymes is a challenge in protein design. For example, many attempts have been made to obtain active hydrolases by introducing a Ser → Cys exchange at the respective catalytic triads, but this generally induced a breakdown of activity. We now report that this long-standing dogma no longer pertains, provided additional mutations are introduced by directed evolution. By employing Candida antarctica lipase B (CALB) as the model enzyme with the Ser-His-Asp catalytic triad, a highly active cysteine-lipase having a Cys-His-Asp catalytic triad and additional mutations W104V/A281Y/A282Y/V149G can be evolved, showing a 40-fold higher catalytic efficiency than wild-type CALB in the hydrolysis of 4-nitrophenyl benzoate, and tolerating bulky substrates. Crystal structures, kinetics, MD simulations and QM/MM calculations reveal dynamic features and explain all results, including the preference of a two-step mechanism involving the zwitterionic pair Cys105−/His224+ rather than a concerted process. Candida antarctica lipase B (CALB) is a serine lipase. Here, the authors use directed evolution to exchange serine with cysteine in the catalytic triad of the enzyme, thereby obtaining a highly active CALB variant that — unlike the wild type — accommodates bulky substrates.
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25
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Huang W, Lan D, Popowicz GM, Zak KM, Zhao Z, Yuan H, Yang B, Wang Y. Structure and characterization of
Aspergillus fumigatus
lipase B with a unique, oversized regulatory subdomain. FEBS J 2019; 286:2366-2380. [DOI: 10.1111/febs.14814] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Revised: 03/01/2019] [Accepted: 03/21/2019] [Indexed: 12/26/2022]
Affiliation(s)
- Weiqian Huang
- School of Bioscience and Bioengineering South China University of Technology Guangzhou China
| | - Dongming Lan
- School of Food Science and Engineering South China University of Technology Guangzhou China
| | | | - Krzysztof M. Zak
- Institute of Structural Biology Helmholtz Zentrum München Neuherberg Germany
| | - Zexin Zhao
- School of Bioscience and Bioengineering South China University of Technology Guangzhou China
| | - Hong Yuan
- School of Food Science and Engineering South China University of Technology Guangzhou China
| | - Bo Yang
- School of Bioscience and Bioengineering South China University of Technology Guangzhou China
| | - Yonghua Wang
- School of Food Science and Engineering South China University of Technology Guangzhou China
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center) Guangzhou China
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26
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Höck H, Engel S, Weingarten S, Keul H, Schwaneberg U, Möller M, Bocola M. Comparison of Candida antarctica Lipase B Variants for Conversion of ε-Caprolactone in Aqueous Medium-Part 2. Polymers (Basel) 2018; 10:E524. [PMID: 30966558 PMCID: PMC6415414 DOI: 10.3390/polym10050524] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 04/26/2018] [Accepted: 05/10/2018] [Indexed: 12/22/2022] Open
Abstract
Enzyme-catalyzed ring-opening polymerization of lactones is a method of increasing interest for the synthesis of polyesters. In the present work, we investigated which changes in the structure of Candida antarctica lipase B (CaLB) shift the catalytic equilibrium between esterification and hydrolysis towards polymerization. Therefore, we present two concepts: (i) removing the glycosylation of CaLB to increase the surface hydrophobicity; and (ii) introducing a hydrophobic lid adapted from Pseudomonas cepacia lipase (PsCL) to enhance the interaction of a growing polymer chain to the elongated lid helix. The deglycosylated CaLB (CaLB-degl) was successfully generated by site-saturation mutagenesis of asparagine 74. Furthermore, computational modeling showed that the introduction of a lid helix at position Ala148 was structurally feasible and the geometry of the active site remained intact. Via overlap extension PCR the lid was successfully inserted, and the variant was produced in large scale in Pichia pastoris with glycosylation (CaLB-lid) and without (CaLB-degl-lid). While the lid variants show a minor positive effect on the polymerization activity, CaLB-degl showed a clearly reduced hydrolytic and enhanced polymerization activity. Immobilization in a hydrophobic polyglycidol-based microgel intensified this effect such that a higher polymerization activity was achieved, compared to the "gold standard" Novozym® 435.
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Affiliation(s)
- Heidi Höck
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Stefan Engel
- DWI-Leibniz Institute for Interactive Materials and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Simone Weingarten
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Helmut Keul
- DWI-Leibniz Institute for Interactive Materials and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Ulrich Schwaneberg
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Martin Möller
- DWI-Leibniz Institute for Interactive Materials and Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
| | - Marco Bocola
- DWI-Leibniz Institute for Interactive Materials and Institute of Biotechnology, RWTH Aachen University, Forckenbeckstraße 50, D-52056 Aachen, Germany.
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27
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Tomer SO, Soni HP. Enzymatic monoesterification of symmetric diols: restriction of molecular conformations influences selectivity. Org Biomol Chem 2017; 15:8990-8997. [PMID: 29044278 DOI: 10.1039/c7ob01951c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have experimentally demonstrated that by 'locking' the molecular conformation through the introduction of a double or triple bond in the center of a symmetric diol, enzymatic monoesterification can be achieved selectively. The enzyme Candida antarctica lipase B, generally used for the transesterification of diols, can be effectively used for the monoesterification of symmetrical diols in an unbuffered system also. By varying the chain length of a carboxylic acid moiety, we have established that optimum selectivity and efficiency can be achieved in the range of 4.8 to 5.0 pKa values. Selectivity can be improved up to 98.75% for a monoester in an overall 73% yield (mixture of a monoester and a diester) when but-2-yne-1,4-diol reacted with hexanoic acid. Water, a by-product, provides an interfacial environment for the enzyme to work in the organic reaction medium. The uniqueness of the reported monoesterification protocol is that it involves only the mechanical stirring of the reaction mixture at room temperature in the presence of the enzyme for 24 h. High percentage yield with selectivity for a monoester, easier product isolation and overall, environmental sustainability are added advantages. The synthesized monoesters are characterized by using HNMR and high resolution mass spectrometry (HRMS).
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Affiliation(s)
- Sanjiv O Tomer
- Department of Chemistry, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara-390 002, Gujarat, India.
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28
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Jan AH, Dubreucq É, Subileau M. Revealing the Roles of Subdomains in the Catalytic Behavior of Lipases/Acyltransferases Homologous to CpLIP2 through Rational Design of Chimeric Enzymes. Chembiochem 2017; 18:941-950. [DOI: 10.1002/cbic.201600672] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Anne-Hélène Jan
- Montpellier Supagro; UMR 1208 IATE; 2 place Viala 34060 Montpellier cedex 2 France
| | - Éric Dubreucq
- Montpellier Supagro; UMR 1208 IATE; 2 place Viala 34060 Montpellier cedex 2 France
| | - Maeva Subileau
- Montpellier Supagro; UMR 1208 IATE; 2 place Viala 34060 Montpellier cedex 2 France
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29
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Syal P, Gupta R. Heterologous expression of lipases YLIP4, YLIP5, YLIP7, YLIP13, and YLIP15 fromYarrowia lipolyticaMSR80 inEscherichia coli: Substrate specificity, kinetic comparison, and enantioselectivity. Biotechnol Appl Biochem 2017; 64:851-861. [DOI: 10.1002/bab.1542] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Accepted: 10/16/2016] [Indexed: 01/14/2023]
Affiliation(s)
- Poonam Syal
- Department of Microbiology; University of Delhi South Campus; New Delhi India
| | - Rani Gupta
- Department of Microbiology; University of Delhi South Campus; New Delhi India
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30
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Benson SP, Pleiss J. Self-Assembly Nanostructures of Triglyceride-Water Interfaces Determine Functional Conformations of Candida antarctica Lipase B. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3151-3159. [PMID: 28274117 DOI: 10.1021/acs.langmuir.6b04570] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Candida antarctica lipase B (CalB) acts as a lipase when adsorbed to an acylglyceride interface and as an esterase when exposed to an aqueous environment. The effect of the molecular self-assembly nanostructure of triglyceride-water interfaces on structural conformations of adsorbed CalB and the implications to its catalytic function were studied by molecular dynamics simulations. Systems of CalB adsorbed to interfaces and solvated in water were compared. The two environments induced relative motions of helices α5 and α10 that resulted in open and closed conformations. The open conformation was stabilized by interactions between the polar and nonpolar amino acids of α5 and α10 and the nanostructure of triglyceride aggregates, which self-assembled into crystalline-like patterns of alternating polar and nonpolar lamellae. Thus, the structure of CalB has been adapted by evolution to the geometric constraints imposed by the interface nanostructure for optimized catalytic activity. Helices α5 and α10 have two functions. As mobile elements, they ensure access of bulky substrates to the active site in the open conformation. As a part of the active site pocket, they ensure binding of substrate molecules in a productive orientation near the active site. In water, access to the binding site is limited, and the smaller substrate binding site is beneficial for the binding of small, water-soluble substrates. The CalB crystal structure commonly used for protein engineering studies represents an intermediate state between open and closed, and may thus not be adequate to assess the function of CalB, neither as lipase nor as esterase.
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Affiliation(s)
- Sven P Benson
- Institute of Technical Biochemistry, University of Stuttgart , Allmandring 31, D - 70569 Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart , Allmandring 31, D - 70569 Stuttgart, Germany
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31
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Khan FI, Lan D, Durrani R, Huan W, Zhao Z, Wang Y. The Lid Domain in Lipases: Structural and Functional Determinant of Enzymatic Properties. Front Bioeng Biotechnol 2017; 5:16. [PMID: 28337436 PMCID: PMC5343024 DOI: 10.3389/fbioe.2017.00016] [Citation(s) in RCA: 216] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/22/2017] [Indexed: 01/08/2023] Open
Abstract
Lipases are important industrial enzymes. Most of the lipases operate at lipid–water interfaces enabled by a mobile lid domain located over the active site. Lid protects the active site and hence responsible for catalytic activity. In pure aqueous media, the lid is predominantly closed, whereas in the presence of a hydrophobic layer, it is partially opened. Hence, the lid controls the enzyme activity. In the present review, we have classified lipases into different groups based on the structure of lid domains. It has been observed that thermostable lipases contain larger lid domains with two or more helices, whereas mesophilic lipases tend to have smaller lids in the form of a loop or a helix. Recent developments in lipase engineering addressing the lid regions are critically reviewed here. After on, the dramatic changes in substrate selectivity, activity, and thermostability have been reported. Furthermore, improved computational models can now rationalize these observations by relating it to the mobility of the lid domain. In this contribution, we summarized and critically evaluated the most recent developments in experimental and computational research on lipase lids.
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Affiliation(s)
- Faez Iqbal Khan
- School of Food Science and Engineering, South China University of Technology, Guangzhou, China; School of Chemistry and Chemical Engineering, Henan University of Technology, Zhengzhou, China
| | - Dongming Lan
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
| | - Rabia Durrani
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Weiqian Huan
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Zexin Zhao
- School of Bioscience and Bioengineering, South China University of Technology , Guangzhou , China
| | - Yonghua Wang
- School of Food Science and Engineering, South China University of Technology , Guangzhou , China
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Luan B, Zhou R. A novel self-activation mechanism of Candida antarctica lipase B. Phys Chem Chem Phys 2017; 19:15709-15714. [DOI: 10.1039/c7cp02198d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The lipase CALB might have two competing lid-opening mechanisms: self-activation and surface-activation.
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Affiliation(s)
- Binquan Luan
- Computational Biological Center
- IBM Thomas J. Watson Research
- NY 10598
- USA
| | - Ruhong Zhou
- Computational Biological Center
- IBM Thomas J. Watson Research
- NY 10598
- USA
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33
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Zhang M, Ma XN, Li CT, Zhao D, Xing YL, Qiu JH. A correlation between the degradability of poly(butylene succinate)-based copolyesters and catalytic behavior with Candida antarctica lipase B. RSC Adv 2017. [DOI: 10.1039/c7ra05553f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In the present study, the degradation performance of PBS-based copolyesters by CALB was investigated from a molecular point of view.
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Affiliation(s)
- Min Zhang
- Key Laboratory of Auxiliary Chemistry & Technology for Chemical Industry
- Ministry of Education
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Xiao-ning Ma
- Key Laboratory of Auxiliary Chemistry & Technology for Chemical Industry
- Ministry of Education
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Cheng-tao Li
- School of Environmental Science & Engineering
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Dong Zhao
- Key Laboratory of Auxiliary Chemistry & Technology for Chemical Industry
- Ministry of Education
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Yong-lei Xing
- Electronic Materials Research Laboratory
- International Center for Dielectric Research
- Xi'an Jiaotong University
- Xi'an 710049
- China
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34
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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
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35
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Monhemi H, Housaindokht MR. Chemical modification of biocatalyst for function in supercritical CO2: In silico redesign of stable lipase. J Supercrit Fluids 2016. [DOI: 10.1016/j.supflu.2016.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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36
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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]
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37
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Dutta Banik S, Nordblad M, Woodley JM, Peters GH. A Correlation between the Activity of Candida antarctica Lipase B and Differences in Binding Free Energies of Organic Solvent and Substrate. ACS Catal 2016. [DOI: 10.1021/acscatal.6b02073] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sindrila Dutta Banik
- Department
of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, Building
207, 2800 Kongens
Lyngby, Denmark
| | - Mathias Nordblad
- Department
of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kongens Lyngby, Denmark
| | - John M. Woodley
- Department
of Chemical and Biochemical Engineering, Technical University of Denmark, Building 229, 2800 Kongens Lyngby, Denmark
| | - Günther H. Peters
- Department
of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, Building
207, 2800 Kongens
Lyngby, Denmark
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38
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de Souza TC, de S. Fonseca T, da Costa JA, Rocha MVP, de Mattos MC, Fernandez-Lafuente R, Gonçalves LR, S. dos Santos JC. Cashew apple bagasse as a support for the immobilization of lipase B from Candida antarctica: Application to the chemoenzymatic production of (R)-Indanol. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.05.007] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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39
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Jiang Y, Loos K. Enzymatic Synthesis of Biobased Polyesters and Polyamides. Polymers (Basel) 2016; 8:E243. [PMID: 30974520 PMCID: PMC6432488 DOI: 10.3390/polym8070243] [Citation(s) in RCA: 111] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 06/01/2016] [Accepted: 06/06/2016] [Indexed: 11/17/2022] Open
Abstract
Nowadays, "green" is a hot topic almost everywhere, from retailers to universities to industries; and achieving a green status has become a universal aim. However, polymers are commonly considered not to be "green", being associated with massive energy consumption and severe pollution problems (for example, the "Plastic Soup") as a public stereotype. To achieve green polymers, three elements should be entailed: (1) green raw materials, catalysts and solvents; (2) eco-friendly synthesis processes; and (3) sustainable polymers with a low carbon footprint, for example, (bio)degradable polymers or polymers which can be recycled or disposed with a gentle environmental impact. By utilizing biobased monomers in enzymatic polymerizations, many advantageous green aspects can be fulfilled. For example, biobased monomers and enzyme catalysts are renewable materials that are derived from biomass feedstocks; enzymatic polymerizations are clean and energy saving processes; and no toxic residuals contaminate the final products. Therefore, synthesis of renewable polymers via enzymatic polymerizations of biobased monomers provides an opportunity for achieving green polymers and a future sustainable polymer industry, which will eventually play an essential role for realizing and maintaining a biobased and sustainable society.
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Affiliation(s)
- Yi Jiang
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands.
| | - Katja Loos
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
- Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands.
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40
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Kim HS, Eom D, Koo YM, Yingling YG. The effect of imidazolium cations on the structure and activity of the Candida antarctica Lipase B enzyme in ionic liquids. Phys Chem Chem Phys 2016; 18:22062-9. [DOI: 10.1039/c6cp02355j] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
To understand how cations affect the enzyme structure and activity of Candida antarctica Lipase B, we performed MD simulations of CALB in four types of ionic liquids with varying sizes of cations and correlated the results with the experimental data.
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Affiliation(s)
- Ho Shin Kim
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
| | - Doyoung Eom
- Department of Biological Engineering
- Inha University
- Incheon
- Republic of Korea
| | - Yoon-Mo Koo
- Department of Biological Engineering
- Inha University
- Incheon
- Republic of Korea
| | - Yaroslava G. Yingling
- Department of Materials Science and Engineering
- North Carolina State University
- Raleigh
- USA
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41
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Wikmark Y, Engelmark Cassimjee K, Lihammar R, Bäckvall JE. Removing the Active-Site Flap in Lipase A fromCandida antarcticaProduces a Functional Enzyme without Interfacial Activation. Chembiochem 2015; 17:141-5. [DOI: 10.1002/cbic.201500471] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Ylva Wikmark
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Karim Engelmark Cassimjee
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Richard Lihammar
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
| | - Jan-E. Bäckvall
- Department of Organic Chemistry; Arrhenius Laboratory; Stockholm University; 106 91 Stockholm Sweden
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42
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Stauch B, Fisher SJ, Cianci M. Open and closed states of Candida antarctica lipase B: protonation and the mechanism of interfacial activation. J Lipid Res 2015; 56:2348-58. [PMID: 26447231 PMCID: PMC4655990 DOI: 10.1194/jlr.m063388] [Citation(s) in RCA: 99] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Indexed: 11/20/2022] Open
Abstract
Lipases (EC 3.1.1.3) are ubiquitous hydrolases for the carboxyl ester bond of water-insoluble substrates, such as triacylglycerols, phospholipids, and other insoluble substrates, acting in aqueous as well as in low-water media, thus being of considerable physiological significance with high interest also for their industrial applications. The hydrolysis reaction follows a two-step mechanism, or “interfacial activation,” with adsorption of the enzyme to a heterogeneous interface and subsequent enhancement of the lipolytic activity. Among lipases, Candida antarctica lipase B (CALB) has never shown any significant interfacial activation, and a closed conformation of CALB has never been reported, leading to the conclusion that its behavior was due to the absence of a lid regulating the access to the active site. The lid open and closed conformations and their protonation states are observed in the crystal structure of CALB at 0.91 Å resolution. Having the open and closed states at atomic resolution allows relating protonation to the conformation, indicating the role of Asp145 and Lys290 in the conformation alteration. The findings explain the lack of interfacial activation of CALB and offer new elements to elucidate this mechanism, with the consequent implications for the catalytic properties and classification of lipases.
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Affiliation(s)
- Benjamin Stauch
- European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, United Kingdom Robinson College, University of Cambridge, Cambridge CB3 9AN, United Kingdom
| | - Stuart J Fisher
- Diamond Light Source, Didcot, Oxfordshire OX11 0DE, United Kingdom
| | - Michele Cianci
- European Molecular Biology Laboratory (EMBL), Deutsches Elektronen-Synchrotron (DESY), Hamburg 22607, Germany
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43
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Zisis T, Freddolino PL, Turunen P, van Teeseling MCF, Rowan AE, Blank KG. Interfacial Activation of Candida antarctica Lipase B: Combined Evidence from Experiment and Simulation. Biochemistry 2015; 54:5969-79. [PMID: 26346632 DOI: 10.1021/acs.biochem.5b00586] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Lipase immobilization is frequently used for altering the catalytic properties of these industrially used enzymes. Many lipases bind strongly to hydrophobic surfaces where they undergo interfacial activation. Candida antarctica lipase B (CalB), one of the most commonly used biocatalysts, is frequently discussed as an atypical lipase lacking interfacial activation. Here we show that CalB displays an enhanced catalytic rate for large, bulky substrates when adsorbed to a hydrophobic interface composed of densely packed alkyl chains. We attribute this increased activity of more than 7-fold to a conformational change that yields a more open active site. This hypothesis is supported by molecular dynamics simulations that show a high mobility for a small "lid" (helix α5) close to the active site. Molecular docking calculations confirm that a highly open conformation of this helix is required for binding large, bulky substrates and that this conformation is favored in a hydrophobic environment. Taken together, our combined approach provides clear evidence for the interfacial activation of CalB on highly hydrophobic surfaces. In contrast to other lipases, however, the conformational change only affects large, bulky substrates, leading to the conclusion that CalB acts like an esterase for small substrates and as a lipase for substrates with large alcohol substituents.
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Affiliation(s)
- Themistoklis Zisis
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Peter L Freddolino
- Department of Biological Chemistry, University of Michigan Medical School , Ann Arbor, Michigan 48109, United States
| | - Petri Turunen
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Muriel C F van Teeseling
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Alan E Rowan
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
| | - Kerstin G Blank
- Institute for Molecules and Materials, Radboud University , Department of Molecular Materials, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands
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44
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Vaquero ME, de Eugenio LI, Martínez MJ, Barriuso J. A novel calb-type lipase discovered by fungal genomes mining. PLoS One 2015; 10:e0124882. [PMID: 25898146 PMCID: PMC4405274 DOI: 10.1371/journal.pone.0124882] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 03/18/2015] [Indexed: 01/20/2023] Open
Abstract
The fungus Pseudozyma antarctica produces a lipase (CalB) with broad substrate specificity, stability, high regio- and enantio-selectivity. It is active in non-aqueous organic solvents and at elevated temperatures. Hence, CalB is a robust biocatalyst for chemical conversions on an industrial scale. Here we report the in silico mining of public metagenomes and fungal genomes to discover novel lipases with high homology to CalB. The candidates were selected taking into account homology and conserved motifs criteria, as well as, phylogeny and 3D model analyses. The most promising candidate (PlicB) presented interesting structural properties. PlicB was expressed in a heterologous host, purified and partially characterized. Further experiments will allow finding novel catalytic properties with biotechnological interest.
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Affiliation(s)
- Maria E. Vaquero
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Laura I. de Eugenio
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Maria J. Martínez
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
| | - Jorge Barriuso
- Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Ramiro de Maeztu 9, 28040 Madrid, Spain
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45
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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]
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46
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Cruz JC, Pfromm PH, Szoszkiewicz R, Rezac ME. Hydrolases on silica surfaces: Coverage-activity–molecular property relationships revealed. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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47
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Engineering of Yarrowia lipolytica lipase Lip8p by circular permutation to alter substrate and temperature characteristics. ACTA ACUST UNITED AC 2014; 41:757-62. [DOI: 10.1007/s10295-014-1428-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2013] [Accepted: 02/25/2014] [Indexed: 10/25/2022]
Abstract
Abstract
Applications of lipases are mainly based on their catalytic efficiency and substrate specificity. In this study, circular permutation (CP), an unconventional protein engineering technique, was employed to acquire active mutants of Yarrowia lipolytica lipase Lip8p. A total of 21 mutant lipases exhibited significant shifts in substrate specificity. Cp128, the most active enzyme mutant, showed higher catalytic activity (14.5-fold) and higher affinity (4.6-fold) (decreased K m) to p-nitrophenyl-myristate (pNP-C14) than wild type (WT). Based on the three-dimensional (3D) structure model of the Lip8p, we found that most of the functional mutation occurred in the surface-exposed loop region in close proximity to the lid domain (S112–F122), which implies the steric effect of the lid on lipase activity and substrate specificity. The temperature properties of Cp128 were also investigated. In contrast to the optimal temperature of 45 °C for the WT enzyme, Cp128 exhibited the maximal activity at 37 °C. But it is noteworthy that there is no change in thermostability.
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48
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Cheng M, Angkawidjaja C, Koga Y, Kanaya S. Calcium-independent opening of lid1 of a family I.3 lipase by a single Asp to Arg mutation at the calcium-binding site. Protein Eng Des Sel 2014; 27:169-76. [DOI: 10.1093/protein/gzu009] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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49
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Yu XW, Zhu SS, Xiao R, Xu Y. Conversion of a Rhizopus chinensis lipase into an esterase by lid swapping. J Lipid Res 2014; 55:1044-51. [PMID: 24670990 DOI: 10.1194/jlr.m043950] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Indexed: 11/20/2022] Open
Abstract
In an effort to explore the feasibility of converting a lipase into an esterase by modifying the lid region, we designed and characterized two novel Rhizopus chinensis lipase variants by lid swapping. The substrate specificity of an R. chinensis lipase was successfully modified toward water-soluble substrates, that is, turned into an esterase, by replacing the hydrophobic lid with a hydrophilic lid from ferulic acid esterase from Aspergillus niger Meanwhile, as a comparison, the lid of R. chinensis lipase was replaced by a hydrophobic lid from Rhizomucor miehei lipase, which did not alter its substrate specificity but led to a 5.4-fold higher catalytic efficiency (k*cat/K*m) toward p-nitrophenyl laurate. Based on the analysis of structure-function relationships, it suggests that the amphipathic nature of the lid is very important for the substrate specificity. This study provides new insight into the structural basis of lipase specificities and a way to tune the substrate preference of lipases.
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Affiliation(s)
- Xiao-Wei Yu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
| | - Shan-Shan Zhu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology
| | - Rong Xiao
- Center for Advanced Biotechnology and Medicine, Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854
| | - Yan Xu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, Jiangsu, China
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50
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Ferrario V, Ebert C, Svendsen A, Besenmatter W, Gardossi L. An integrated platform for automatic design and screening of virtual mutants based on 3D-QSAR analysis. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2013.12.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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