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Salas-Bruggink D, Guzmán H, Espina G, Blamey JM. Recombinant Expression and Characterization of a Novel Thermo-Alkaline Lipase with Increased Solvent Stability from the Antarctic Thermophilic Bacterium Geobacillus sp. ID17. Int J Mol Sci 2024; 25:7928. [PMID: 39063171 PMCID: PMC11277018 DOI: 10.3390/ijms25147928] [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: 06/01/2024] [Revised: 07/10/2024] [Accepted: 07/15/2024] [Indexed: 07/28/2024] Open
Abstract
Lipases are enzymes that hydrolyze long-chain carboxylic esters, and in the presence of organic solvents, they catalyze organic synthesis reactions. However, the use of solvents in these processes often results in enzyme denaturation, leading to a reduction in enzymatic activity. Consequently, there is significant interest in identifying new lipases that are resistant to denaturing conditions, with extremozymes emerging as promising candidates for this purpose. Lip7, a lipase from Geobacillus sp. ID17, a thermophilic microorganism isolated from Deception Island, Antarctica, was recombinantly expressed in E. coli C41 (DE3) in functional soluble form. Its purification was achieved with 96% purity and 23% yield. Enzymatic characterization revealed Lip7 to be a thermo-alkaline enzyme, reaching a maximum rate of 3350 U mg-1 at 50 °C and pH 11.0, using p-nitrophenyl laurate substrate. Notably, its kinetics displayed a sigmoidal behavior, with a higher kinetic efficiency (kcat/Km) for substrates of 12-carbon atom chain. In terms of thermal stability, Lip7 demonstrates stability up to 60 °C at pH 8.0 and up to 50 °C at pH 11.0. Remarkably, it showed high stability in the presence of organic solvents, and under certain conditions even exhibited enzymatic activation, reaching up to 2.5-fold and 1.35-fold after incubation in 50% v/v ethanol and 70% v/v isopropanol, respectively. Lip7 represents one of the first lipases from the bacterial subfamily I.5 and genus Geobacillus with activity and stability at pH 11.0. Its compatibility with organic solvents makes it a compelling candidate for future research in biocatalysis and various biotechnological applications.
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Affiliation(s)
| | - Hardy Guzmán
- Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Santiago 9170022, Chile;
| | - Giannina Espina
- Fundación Biociencia, José Domingo Cañas 2280, Santiago 7750132, Chile;
| | - Jenny M. Blamey
- Fundación Biociencia, José Domingo Cañas 2280, Santiago 7750132, Chile;
- Facultad de Química y Biología, Universidad de Santiago de Chile, Alameda 3363, Santiago 9170022, Chile;
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2
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Shehata M, Ünlü A, Iglesias-Fernández J, Osuna S, Sezerman OU, Timucin E. Brave new surfactant world revisited by thermoalkalophilic lipases: computational insights into the role of SDS as a substrate analog. Phys Chem Chem Phys 2023; 25:2234-2247. [PMID: 36594810 DOI: 10.1039/d2cp05093e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Non-ionic surfactants were shown to stabilize the active conformation of thermoalkalophilic lipases by mimicking the lipid substrate while the catalytic interactions formed by anionic surfactants have not been well characterized. In this study, we combined μs-scale molecular dynamics (MD) simulations and lipase activity assays to analyze the effect of ionic surfactant, sodium dodecyl sulfate (SDS), on the structure and activity of thermoalkalophilic lipases. Both the open and closed lipase conformations that differ in geometry were recruited to the MD analysis to provide a broader understanding of the molecular effect of SDS on the lipase structure. Simulations at 298 K showed the potential of SDS for maintaining the active lipase through binding to the sn-1 acyl-chain binding pocket in the open conformation or transforming the closed conformation to an open-like state. Consistent with MD findings, experimental analysis showed increased lipase activity upon SDS incubation at ambient temperature. Notably, the lipase cores stayed intact throughout 2 μs regardless of an increase in the simulation temperature or SDS concentration. However, the surface structures were unfolded in the presence of SDS and at elevated temperature for both conformations. Simulations of the dimeric lipase were also carried out and showed reduced flexibility of the surface structures which were unfolded in the monomer, indicating the insulating role of dimer interactions against SDS. Taken together, this study provides insights into the possible substrate mimicry by the ionic surfactant SDS for the thermoalkalophilic lipases without temperature elevation, underscoring SDS's potential for interfacial activation at ambient temperatures.
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Affiliation(s)
- Mohamed Shehata
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
| | - Aişe Ünlü
- Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | | | - Sílvia Osuna
- CompBioLab Group, Institut de Química Computacional i Catàlisi (IQCC) and Department de Química, Universitat de Girona, c/Maria Aurèlia Capmany 69, 17003 Girona, Spain.,ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - O Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
| | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem University, Istanbul 34752, Turkey.
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Godoy CA, Pardo-Tamayo JS, Barbosa O. Microbial Lipases and Their Potential in the Production of Pharmaceutical Building Blocks. Int J Mol Sci 2022; 23:9933. [PMID: 36077332 PMCID: PMC9456414 DOI: 10.3390/ijms23179933] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 08/19/2022] [Accepted: 08/23/2022] [Indexed: 11/17/2022] Open
Abstract
Processes involving lipases in obtaining active pharmaceutical ingredients (APIs) are crucial to increase the sustainability of the industry. Despite their lower production cost, microbial lipases are striking for their versatile catalyzing reactions beyond their physiological role. In the context of taking advantage of microbial lipases in reactions for the synthesis of API building blocks, this review focuses on: (i) the structural origins of the catalytic properties of microbial lipases, including the results of techniques such as single particle monitoring (SPT) and the description of its selectivity beyond the Kazlauskas rule as the "Mirror-Image Packing" or the "Key Region(s) rule influencing enantioselectivity" (KRIE); (ii) immobilization methods given the conferred operative advantages in industrial applications and their modulating capacity of lipase properties; and (iii) a comprehensive description of microbial lipases use as a conventional or promiscuous catalyst in key reactions in the organic synthesis (Knoevenagel condensation, Morita-Baylis-Hillman (MBH) reactions, Markovnikov additions, Baeyer-Villiger oxidation, racemization, among others). Finally, this review will also focus on a research perspective necessary to increase microbial lipases application development towards a greener industry.
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Affiliation(s)
- César A. Godoy
- Laboratorio de Investigación en Biocatálisis y Biotransformaciones (LIBB), Grupo de Investigación en Ingeniería de los Procesos Agroalimentarios y Biotecnológicos (GIPAB), Departamento de Química, Universidad del Valle, Cali 76001, Colombia
| | - Juan S. Pardo-Tamayo
- Laboratorio de Investigación en Biocatálisis y Biotransformaciones (LIBB), Grupo de Investigación en Ingeniería de los Procesos Agroalimentarios y Biotecnológicos (GIPAB), Departamento de Química, Universidad del Valle, Cali 76001, Colombia
| | - Oveimar Barbosa
- Grupo de Investigación de Materiales Porosos (GIMPOAT), Departamento de Química, Universidad del Tolima, Ibague 730001, Colombia
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Biocatalysts Synthesized with Lipase from Pseudomonas cepacia on Glycol-Modified ZIF-8: Characterization and Utilization in the Synthesis of Green Biodiesel. Molecules 2022; 27:molecules27175396. [PMID: 36080163 PMCID: PMC9458167 DOI: 10.3390/molecules27175396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/16/2022] [Accepted: 08/19/2022] [Indexed: 11/16/2022] Open
Abstract
This research presents results on the production of biodiesel from the transesterification of acylglycerides present in palm oil, using the biocatalysts ZIF-8-PCL and Gly@ZIF-8-PCL synthesized by immobilization of Pseudomonas Cepacia Lipase as catalytic materials and using pure ZIF-8 and Gly@ZIF-8 (modified ZIF-8) as supports. The Gly@ZIF-8 carbonaceous material was prepared by wet impregnation of ZIF-8 with ethylene glycol as the carbon source, and then thermally modified. The calcination conditions were 900 °C for two hours with a heating rate of 7 °C/min in an inert atmosphere. A textural characterization was performed, and results showed superficial changes of materials at the microporous and mesoporous levels for the Gly@ZIF-8 material. Both the starting materials and biocatalysts were characterized by infrared spectroscopy (FTIR) and Raman spectroscopy. During the transesterification, using the two biocatalysts (ZIF-8-PCL and Gly@ZIF-8-PCL), two supernatant liquids were generated which were characterized by infrared spectroscopy (FTIR), gas chromatography coupled to mass spectrometry (GC-MS), and nuclear magnetic resonance (NMR). The results show that the two routes of synthesis of supports from ZIF-8 will be configured as effective methods for the generation of effective biocatalysts for biodiesel production.
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Kılınç E, Can Timucin A, Selim Cinaroglu S, Timucin E. Modeling and dynamical analysis of the full-length structure of factor XII with zinc. J Mol Model 2022; 28:129. [PMID: 35469101 DOI: 10.1007/s00894-022-05113-y] [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: 10/12/2021] [Accepted: 04/05/2022] [Indexed: 11/24/2022]
Abstract
Zinc (II), the second most abundant transition metal in blood, binds to the initiator of the contact pathway, factor XII (FXII). This binding induces conformational changes in the structure of FXII eventually leading to its activation. Despite many in vitro and in vivo studies on zinc-mediated activation of FXII, its molecular mechanism remains elusive mainly due to absence of a full-length structural model of FXII. To this end, this study investigated the role of zinc in the structure and dynamics of the full-length structure FXII that was obtained through molecular modeling. We have used four structural templates covering more than 70% of the FXII sequence and the remaining interconnecting regions were built by loop modeling. The resulting full-length structure of FXII contained disordered regions, but in comparison to the AlphaFold (AF) prediction, our full-length model represented a more realistic structure because of the disordered regions which were modeled to yield a more compact full-length structure in our model than the AF structure. Other than the disordered regions, our model and AF prediction were highly similar. The resulting full-length FXII structure was used to generate different systems representing the zinc-bound form (holo). Further to assess the contribution of the disulfide bridges, we also analyzed the apo and holo FXII structures with oxidized or reduced cysteine side-chains. Simulations suggested zinc binding conferred rigidity to the structure, particularly to the light chain of FXII. Zinc binding alone was sufficient to limit the backbone flexibility while 15 disulfide bonds, which were scattered throughout the structure, made a less significant contribution to the backbone rigidity. Altogether our results provide insights into the first realistic full-length structure of FXII focusing on the impact of structural zinc and disulfide bridges in the dynamics of this structure.
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Affiliation(s)
- Evren Kılınç
- Department of Biophysics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, 34752, Turkey
| | - Ahmet Can Timucin
- Department of Molecular Biology and Genetics, Faculty of Arts and Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul, 34752, Turkey
| | | | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, 34752, Turkey.
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Shehata M, Timucin E, Venturini A, Sezerman OU. Understanding thermal and organic solvent stability of thermoalkalophilic lipases: insights from computational predictions and experiments. J Mol Model 2020; 26:122. [PMID: 32383051 DOI: 10.1007/s00894-020-04396-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 04/28/2020] [Indexed: 11/25/2022]
Abstract
Bacillus thermocatenulatus lipase (BTL2), a member of the isolated lipase family known as thermoalkalophilic lipases, carries potential for industrial applications owing to its ability to catalyze versatile reactions under extreme conditions. This study investigates the molecular effects of distinct solvents on the stability of BTL2 at different temperatures, aiming to contribute to lipase use in industrial applications. Initially, molecular dynamic (MD) simulations were carried out to address for the molecular impacts of distinct solvents on the structural stability of BTL2 at different temperatures. Two lipase conformations representing the active and inactive forms were simulated in 5 solvents including water, ethanol, methanol, cyclohexane, and toluene. Low temperature simulations showed that polar solvents led to enhanced lid fluctuations compared with non-polar solvents reflecting a more dynamic equilibrium between active and inactive lipase conformations in polar solvents including water, while the overall structure of the lipase in both forms became more rigid in non-polar solvents than they were in polar solvent. Notably, the native lipase fold was maintained in non-polar solvents even at high temperatures, indicating an enhancement of lipase's thermostability in non-polar organic solvents. Next, we conducted experiments for which BTL2 was expressed in a heterologous host and purified to homogeneity, and its thermostability in different solvents was assessed. Parallel to the computational findings, experimental results suggested that non-polar organic solvents contributed to BTL2's thermostability at concentrations as high as 70% (v/v). Altogether, this study provides beneficial insights to the lipase use under extreme conditions. Graphical Abstract.
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Affiliation(s)
- Mohamed Shehata
- Institute of Health Science, Department of Medical Biotechnology, Acibadem Mehmet Ali Aydınlar University, Atasehir, Istanbul, Turkey.
| | - Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydınlar University, Atasehir, Istanbul, Turkey
| | - Alessandro Venturini
- Institute of Organic Synthesis and Photoreactivity, National Research Council of Italy, Via P. Gobetti 101, 40129, Bologna, Italy
| | - Osman Uğur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydınlar University, Atasehir, Istanbul, Turkey
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Godoy CA, Klett J, Di Geronimo B, Hermoso JA, Guisán JM, Carrasco-López C. Disulfide Engineered Lipase to Enhance the Catalytic Activity: A Structure-Based Approach on BTL2. Int J Mol Sci 2019; 20:ijms20215245. [PMID: 31652673 PMCID: PMC6862113 DOI: 10.3390/ijms20215245] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/16/2019] [Accepted: 09/23/2019] [Indexed: 12/15/2022] Open
Abstract
Enhancement, control, and tuning of hydrolytic activity and specificity of lipases are major goals for the industry. Thermoalkaliphilic lipases from the I.5 family, with their native advantages such as high thermostability and tolerance to alkaline pHs, are a target for biotechnological applications. Although several strategies have been applied to increase lipases activity, the enhancement through protein engineering without compromising other capabilities is still elusive. Lipases from the I.5 family suffer a unique and delicate double lid restructuration to transition from a closed and inactive state to their open and enzymatically active conformation. In order to increase the activity of the wild type Geobacillus thermocatenulatus lipase 2 (BTL2) we rationally designed, based on its tridimensional structure, a mutant (ccBTL2) capable of forming a disulfide bond to lock the open state. ccBTL2 was generated replacing A191 and F206 to cysteine residues while both wild type C64 and C295 were mutated to serine. A covalently immobilized ccBTL2 showed a 3.5-fold increment in esterase activity with 0.1% Triton X-100 (2336 IU mg−1) and up to 6.0-fold higher with 0.01% CTAB (778 IU mg−1), both in the presence of oxidizing sulfhydryl agents, when compared to BTL2. The remarkable and industrially desired features of BTL2 such as optimal alkaliphilic pH and high thermal stability were not affected. The designed disulfide bond also conferred reversibility to the enhancement, as the increment on activity observed for ccBTL2 was controlled by redox pretreatments. MD simulations suggested that the most stable conformation for ccBTL2 (with the disulfide bond formed) was, as we predicted, similar to the open and active conformation of this lipase.
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Affiliation(s)
- César A Godoy
- Departamento de Química (LIBB), Grupo de Investigación en Ingeniería de los Procesos Agroalimentarios y Biotecnológicos (GIPAB), Universidad del Valle, C.P. 76001 Cali, Colombia.
| | - Javier Klett
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro 3, E-28029 Madrid, Spain.
| | - Bruno Di Geronimo
- Experimental Therapeutics Programme, Spanish National Cancer Research Centre (CNIO), C/Melchor Fernández Almagro 3, E-28029 Madrid, Spain.
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Rocasolano" (IQFR-CSIC), E_28006 Madrid, Spain.
| | - José M Guisán
- Departamento de Biocatálisis. Instituto de Catálisis. CSIC. Campus UAM. Cantoblanco. C.P. 28049 Madrid, Spain.
| | - César Carrasco-López
- Department of Chemical and Biological Engineering, Hoyt Laboratory, Princeton University, Princeton, NJ 08544, USA.
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Shift in Bacillus sp. JR3 esterase LipJ activity profile after addition of essential residues from family I.5 thermophilic lipases. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.01.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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9
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Structural basis of the correct subunit assembly, aggregation, and intracellular degradation of nylon hydrolase. Sci Rep 2018; 8:9725. [PMID: 29950566 PMCID: PMC6021441 DOI: 10.1038/s41598-018-27860-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 06/12/2018] [Indexed: 11/09/2022] Open
Abstract
Nylon hydrolase (NylC) is initially expressed as an inactive precursor (36 kDa). The precursor is cleaved autocatalytically at Asn266/Thr267 to generate an active enzyme composed of an α subunit (27 kDa) and a β subunit (9 kDa). Four αβ heterodimers (molecules A-D) form a doughnut-shaped quaternary structure. In this study, the thermostability of the parental NylC was altered by amino acid substitutions located at the A/D interface (D122G/H130Y/D36A/L137A) or the A/B interface (E263Q) and spanned a range of 47 °C. Considering structural, biophysical, and biochemical analyses, we discuss the structural basis of the stability of nylon hydrolase. From the analytical centrifugation data obtained regarding the various mutant enzymes, we conclude that the assembly of the monomeric units is dynamically altered by the mutations. Finally, we propose a model that can predict whether the fate of the nascent polypeptide will be correct subunit assembly, inappropriate protein-protein interactions causing aggregation, or intracellular degradation of the polypeptide.
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Timucin E, Sezerman OU. Thermostability of the PYL–PP2C Heterodimer Is Dependent on Magnesium: In Silico Insights into the Link between Heat Stress Response and Magnesium Deficiency in Plants. J Chem Inf Model 2018; 58:661-672. [DOI: 10.1021/acs.jcim.7b00655] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Emel Timucin
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, 34752, Istanbul Turkey
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Atasehir, 34752, Istanbul Turkey
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Romero O, de las Rivas B, Lopez-Tejedor D, Palomo JM. Effect of Site-Specific Peptide-Tag Labeling on the Biocatalytic Properties of Thermoalkalophilic Lipase from Geobacillus thermocatenulatus. Chembiochem 2018; 19:369-378. [DOI: 10.1002/cbic.201700466] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Indexed: 12/19/2022]
Affiliation(s)
- Oscar Romero
- Department of Biocatalysis; Institute of Catalysis (CSIC); Marie Curie 2 Cantoblanco CampusUAM 28049 Madrid Spain
| | - Blanca de las Rivas
- Laboratorio de Biotecnología Microbiana; Instituto de Ciencia y Tecnología de alimentos y Nutrición (ICTAN-CSIC); José Antonio Novais, 10 28040 Madrid Spain
| | - David Lopez-Tejedor
- Department of Biocatalysis; Institute of Catalysis (CSIC); Marie Curie 2 Cantoblanco CampusUAM 28049 Madrid Spain
| | - Jose M. Palomo
- Department of Biocatalysis; Institute of Catalysis (CSIC); Marie Curie 2 Cantoblanco CampusUAM 28049 Madrid Spain
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Timucin E, Cousido-Siah A, Mitschler A, Podjarny A, Sezerman OU. Probing the roles of two tryptophans surrounding the unique zinc coordination site in lipase family I.5. Proteins 2015; 84:129-42. [DOI: 10.1002/prot.24961] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/09/2015] [Accepted: 11/06/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Emel Timucin
- Faculty of Engineering and Natural Sciences, Molecular Biology, Genetics and Bioengineering; Sabanci University; Istanbul 34956 Turkey
| | - Alexandra Cousido-Siah
- Department of Integrative Biology; Institut De Génétique Et De Biologie Moléculaire Et Cellulaire, CNRS, INSERM, UdS; 1 Rue Laurent Fries, 67404 Illkirch Cedex France
| | - André Mitschler
- Department of Integrative Biology; Institut De Génétique Et De Biologie Moléculaire Et Cellulaire, CNRS, INSERM, UdS; 1 Rue Laurent Fries, 67404 Illkirch Cedex France
| | - Alberto Podjarny
- Department of Integrative Biology; Institut De Génétique Et De Biologie Moléculaire Et Cellulaire, CNRS, INSERM, UdS; 1 Rue Laurent Fries, 67404 Illkirch Cedex France
| | - Osman Ugur Sezerman
- Department of Biostatistics and Medical Informatics, School of Medicine; Acibadem University; Atasehir Istanbul 34742 Turkey
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