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Tütüncü HE, Durmuş N, Sürmeli Y. Unraveling the potential of uninvestigated thermoalkaliphilic lipases by molecular docking and molecular dynamic simulation: an in silico characterization study. 3 Biotech 2024; 14:179. [PMID: 38882640 PMCID: PMC11176153 DOI: 10.1007/s13205-024-04023-5] [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: 11/17/2023] [Accepted: 05/29/2024] [Indexed: 06/18/2024] Open
Abstract
Thermoalkaliphilic lipase enzymes are mostly favored for use in the detergent industry. While there has been considerable research on Geobacillus lipases, a significant portion of these enzymes remains unexplored or undocumented in the scientific literature. This work performed in silico phylogeny, sequence alignment, structural and enzyme-substrate interaction analyses of the five thermoalkaliphilic lipases belonging to different Geobacillus species (Geobacillus stearothermophilus lipase = GsLip, Geobacillus sp. B4113_201601 lipase = Gb4Lip, Geobacillus kaustophilus HTA426 lipase = GkLip, Geobacillus sp. SP22 lipase = GspLip, Geobacillus sp. NTU 03 lipase = GntLip). For this purpose, unreviewed enzyme sequences of five Geobacillus thermoalkaliphilic lipases were analyzed at sequence and phylogeny levels. 3D homology enzyme models were built, validated, and investigated by different bioinformatics tools. The ligand interactions screening using seven para-nitrophenyl (pNP) esters and enzyme-ligand interactions were analyzed on Gb4Lip:pNP-C12 and BTL2:pNP-C12 by MD simulation. Biophysicochemical characteristic analysis showed that Gb4Lip had a theoretical T m value of above 65 ºC, and a higher aliphatic index indicating greater thermal stability. Sequence alignment showed a hydrophilic threonine in the α6 helix of Gb4Lip, indicating high enzymatic activity. A normalized temperature factor B (B'-factor) analysis showed that the lid domains of five lipases significantly possessed lower B'-factor values, compared to G. thermocatenulatus lipase 2 (BTL2), indicating that they had higher rigidity. Molecular docking results indicated that the five lipases had the highest binding affinity toward pNP-C12. The RMSF investigation revealed that the thermostability of Gb4Lip is influenced by specific molecular elements: D202-S203 within the αB region of the lid domain, and E274-Q275 within the b3 strand, as well as W278 in the b3-b4 loop, and H282 in the b4 strand of the Ca2+-binding region. MD simulation analysis showed that catalytic residue S114 and at least one oxyanion hole residue (F17 and/or Q114) in Gb4Lip frequently formed hydrogen bonds with the pNP-C12 ligand at 343 K and 348 K throughout the simulation process, indicating that Gb4Lip might catalyze relatively long-chain ligand pNP-C12 with high performance. In conclusion, Gb4Lip might be a more suitable candidate as the detergent additive. In addition, this investigation can offer valuable perspectives on Family I.5 lipases such as Gb4Lip for future exploration in the field of protein engineering. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-024-04023-5.
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Affiliation(s)
- Havva Esra Tütüncü
- Department of Nutrition and Dietetics, Malatya Turgut Özal University, 44210 Malatya, Turkey
| | - Naciye Durmuş
- Department of Molecular Biology and Genetics, İstanbul Technical University, 34485 Istanbul, Turkey
| | - Yusuf Sürmeli
- Department of Agricultural Biotechnology, Tekirdağ Namık Kemal University, 59030 Tekirdağ, Turkey
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Soni S. Trends in lipase engineering for enhanced biocatalysis. Biotechnol Appl Biochem 2022; 69:265-272. [PMID: 33438779 DOI: 10.1002/bab.2105] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/08/2021] [Indexed: 01/19/2023]
Abstract
Lipases, also known as triacylglycerol hydrolases (E.C.No. 3.1.1.3), are considered as leading biocatalysts in the lipid modification business. With properties like ease of availability, capability to work in heterogeneous media, stability in organic solvents, property of catalyzing at the lipid-water interface and even in nonaqueous conditions, have made them a versatile choice for applications in the food, flavor, detergent, pharmaceutical, leather, textile, cosmetic, and paper industries [1]. The increasing alertness toward sustainable technologies, lesser waste generation and solvent usage and minimization of energy input has brought light toward the production and usage of recombinant/improved lipases. For example, Novozym 435, a broadly used recombinant lipase isolated from Candida antarctica, dominates the lipase industry and has even created a supplier bias in the market. This shows that there is a desperate need for novel, low-cost lipases with better properties. For this, mining of existing extremophilic genomes seems more rewarding. But considering the diversity of industrial requirements such as types of solvents used or carrier systems employed for enzyme immobilization, tailor-designed enzymes are an unrealized pressing priority. Therefore, protein engineering strategies in collaboration with the discovery of new lipases can serve as a vital tool to obtain tailor-made enzymes with specific characteristics.
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Affiliation(s)
- Surabhi Soni
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
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3
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Thermostable lipases and their dynamics of improved enzymatic properties. Appl Microbiol Biotechnol 2021; 105:7069-7094. [PMID: 34487207 DOI: 10.1007/s00253-021-11520-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 07/29/2021] [Accepted: 07/31/2021] [Indexed: 10/20/2022]
Abstract
Thermal stability is one of the most desirable characteristics in the search for novel lipases. The search for thermophilic microorganisms for synthesising functional enzyme biocatalysts with the ability to withstand high temperature, and capacity to maintain their native state in extreme conditions opens up new opportunities for their biotechnological applications. Thermophilic organisms are one of the most favoured organisms, whose distinctive characteristics are extremely related to their cellular constituent particularly biologically active proteins. Modifications on the enzyme structure are critical in optimizing the stability of enzyme to thermophilic conditions. Thermostable lipases are one of the most favourable enzymes used in food industries, pharmaceutical field, and actively been studied as potential biocatalyst in biodiesel production and other biotechnology application. Particularly, there is a trade-off between the use of enzymes in high concentration of organic solvents and product generation. Enhancement of the enzyme stability needs to be achieved for them to maintain their enzymatic activity regardless the environment. Various approaches on protein modification applied since decades ago conveyed a better understanding on how to improve the enzymatic properties in thermophilic bacteria. In fact, preliminary approach using advanced computational analysis is practically conducted before any modification is being performed experimentally. Apart from that, isolation of novel extremozymes from various microorganisms are offering great frontier in explaining the crucial native interaction within the molecules which could help in protein engineering. In this review, the thermostability prospect of lipases and the utility of protein engineering insights into achieving functional industrial usefulness at their high temperature habitat are highlighted. Similarly, the underlying thermodynamic and structural basis that defines the forces that stabilize these thermostable lipase is discussed. KEY POINTS: • The dynamics of lipases contributes to their non-covalent interactions and structural stability. • Thermostability can be enhanced by well-established genetic tools for improved kinetic efficiency. • Molecular dynamics greatly provides structure-function insights on thermodynamics of lipase.
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Temperature-resistant and solvent-tolerant lipases as industrial biocatalysts: Biotechnological approaches and applications. Int J Biol Macromol 2021; 187:127-142. [PMID: 34298046 DOI: 10.1016/j.ijbiomac.2021.07.101] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/14/2021] [Accepted: 07/15/2021] [Indexed: 12/21/2022]
Abstract
The development of new biocatalytic systems to replace the chemical catalysts, with suitable characteristics in terms of efficiency, stability under high temperature reactions and in the presence of organic solvents, reusability, and eco-friendliness is considered a very important step to move towards the green processes. From this basis, the use of lipase as a catalyst is highly desired for many industrial applications because it offers the reactions in which could be used, stability in harsh conditions, reusability and a greener process. Therefore, the introduction of temperature-resistant and solvent-tolerant lipases have become essential and ideal for industrial applications. Temperature-resistant and solvent-tolerant lipases have been involved in many large-scale applications including biodiesel, detergent, food, pharmaceutical, organic synthesis, biosensing, pulp and paper, textile, animal feed, cosmetics, and leather industry. So, the present review provides a comprehensive overview of the industrial use of lipase. Moreover, special interest in biotechnological and biochemical techniques for enhancing temperature-resistance and solvent-tolerance of lipases to be suitable for the industrial uses.
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Single Residue Substitution at N-Terminal Affects Temperature Stability and Activity of L2 Lipase. Molecules 2020; 25:molecules25153433. [PMID: 32731608 PMCID: PMC7435863 DOI: 10.3390/molecules25153433] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/26/2020] [Accepted: 07/01/2020] [Indexed: 11/24/2022] Open
Abstract
Rational design is widely employed in protein engineering to tailor wild-type enzymes for industrial applications. The typical target region for mutation is a functional region like the catalytic site to improve stability and activity. However, few have explored the role of other regions which, in principle, have no evident functionality such as the N-terminal region. In this study, stability prediction software was used to identify the critical point in the non-functional N-terminal region of L2 lipase and the effects of the substitution towards temperature stability and activity were determined. The results showed 3 mutant lipases: A8V, A8P and A8E with 29% better thermostability, 4 h increase in half-life and 6.6 °C higher thermal denaturation point, respectively. A8V showed 1.6-fold enhancement in activity compared to wild-type. To conclude, the improvement in temperature stability upon substitution showed that the N-terminal region plays a role in temperature stability and activity of L2 lipase.
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Ishak SNH, Kamarudin NHA, Ali MSM, Leow ATC, Rahman RNZRA. Ion-Pair Interaction and Hydrogen Bonds as Main Features of Protein Thermostability in Mutated T1 Recombinant Lipase Originating from Geobacillus zalihae. Molecules 2020; 25:E3430. [PMID: 32731607 PMCID: PMC7435748 DOI: 10.3390/molecules25153430] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 07/04/2020] [Accepted: 07/09/2020] [Indexed: 01/19/2023] Open
Abstract
A comparative structure analysis between space- and an Earth-grown T1 recombinant lipase from Geobacillus zalihae had shown changes in the formation of hydrogen bonds and ion-pair interactions. Using the space-grown T1 lipase validated structure having incorporated said interactions, the recombinant T1 lipase was re-engineered to determine the changes brought by these interactions to the structure and stability of lipase. To understand the effects of mutation on T1 recombinant lipase, five mutants were developed from the structure of space-grown T1 lipase and biochemically characterized. The results demonstrate an increase in melting temperature up to 77.4 °C and 76.0 °C in E226D and D43E, respectively. Moreover, the mutated lipases D43E and E226D had additional hydrogen bonds and ion-pair interactions in their structures due to the improvement of stability, as observed in a longer half-life and an increased melting temperature. The biophysical study revealed differences in β-Sheet percentage between less stable (T118N) and other mutants. As a conclusion, the comparative analysis of the tertiary structure and specific residues associated with ion-pair interactions and hydrogen bonds could be significant in revealing the thermostability of an enzyme with industrial importance.
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Affiliation(s)
- Siti Nor Hasmah Ishak
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Centre of Foundation Studies for Agricultural Science, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Adam Thean Chor Leow
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd. Rahman
- Enzyme and Microbial Technology Research Centre, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia; (S.N.H.I.); (N.H.A.K.); (M.S.M.A.); (A.T.C.L.)
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
- Laboratory of Halal Science Research, Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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Development of a new Geobacillus lipase variant GDlip43 via directed evolution leading to identification of new activity-regulating amino acids. Int J Biol Macromol 2020; 151:1194-1204. [DOI: 10.1016/j.ijbiomac.2019.10.163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 10/25/2022]
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8
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Druteika G, Sadauskas M, Malunavicius V, Lastauskiene E, Statkeviciute R, Savickaite A, Gudiukaite R. New engineered Geobacillus lipase GD-95RM for industry focusing on the cleaner production of fatty esters and household washing product formulations. World J Microbiol Biotechnol 2020; 36:41. [DOI: 10.1007/s11274-020-02816-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 02/20/2020] [Indexed: 12/19/2022]
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Filling the Void: Introducing Aromatic Interactions into Solvent Tunnels To Enhance Lipase Stability in Methanol. Appl Environ Microbiol 2018; 84:AEM.02143-18. [PMID: 30217852 DOI: 10.1128/aem.02143-18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 09/12/2018] [Indexed: 12/17/2022] Open
Abstract
An enhanced stability of enzymes in organic solvents is desirable under industrial conditions. The potential of lipases as biocatalysts is mainly limited by their denaturation in polar alcohols. In this study, we focused on selected solvent tunnels in lipase from Geobacillus stearothermophilus T6 to improve its stability in methanol during biodiesel synthesis. Using rational mutagenesis, bulky aromatic residues were incorporated to occupy solvent channels and induce aromatic interactions leading to a better inner core packing. The chemical and structural characteristics of each solvent tunnel were systematically analyzed. Selected residues were replaced with Phe, Tyr, or Trp. Overall, 16 mutants were generated and screened in 60% methanol, from which 3 variants showed an enhanced stability up to 81-fold compared with that of the wild type. All stabilizing mutations were found in the longest tunnel detected in the "closed-lid" X-ray structure. The combination of Phe substitutions in an A187F/L360F double mutant resulted in an increase in unfolding temperature (Tm ) of 7°C in methanol and a 3-fold increase in biodiesel synthesis yield from waste chicken oil. A kinetic analysis with p-nitrophenyl laurate revealed that all mutants displayed lower hydrolysis rates (k cat), though their stability properties mostly determined the transesterification capability. Seven crystal structures of different variants were solved, disclosing new π-π or CH/π intramolecular interactions and emphasizing the significance of aromatic interactions for improved solvent stability. This rational approach could be implemented for the stabilization of other enzymes in organic solvents.IMPORTANCE Enzymatic synthesis in organic solvents holds increasing industrial opportunities in many fields; however, one major obstacle is the limited stability of biocatalysts in such a denaturing environment. Aromatic interactions play a major role in protein folding and stability, and we were inspired by this to redesign enzyme voids. The rational protein engineering of solvent tunnels of lipase from Geobacillus stearothermophilus is presented here, offering a promising approach to introduce new aromatic interactions within the enzyme core. We discovered that longer tunnels leading from the surface to the enzyme active site were more beneficial targets for mutagenesis for improving lipase stability in methanol during biodiesel biosynthesis. A structural analysis of the variants confirmed the generation of new interactions involving aromatic residues. This work provides insights into stability-driven enzyme design by targeting the solvent channel void.
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The molecular basis for lipase stereoselectivity. Appl Microbiol Biotechnol 2018; 102:3487-3495. [DOI: 10.1007/s00253-018-8858-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Revised: 02/11/2018] [Accepted: 02/12/2018] [Indexed: 01/13/2023]
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Javed S, Azeem F, Hussain S, Rasul I, Siddique MH, Riaz M, Afzal M, Kouser A, Nadeem H. Bacterial lipases: A review on purification and characterization. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 132:23-34. [DOI: 10.1016/j.pbiomolbio.2017.07.014] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Revised: 07/18/2017] [Accepted: 07/27/2017] [Indexed: 11/16/2022]
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Shahinyan G, Margaryan A, Panosyan H, Trchounian A. Identification and sequence analyses of novel lipase encoding novel thermophillic bacilli isolated from Armenian geothermal springs. BMC Microbiol 2017; 17:103. [PMID: 28464816 PMCID: PMC5414190 DOI: 10.1186/s12866-017-1016-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 04/26/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Among the huge diversity of thermophilic bacteria mainly bacilli have been reported as active thermostable lipase producers. Geothermal springs serve as the main source for isolation of thermostable lipase producing bacilli. Thermostable lipolytic enzymes, functioning in the harsh conditions, have promising applications in processing of organic chemicals, detergent formulation, synthesis of biosurfactants, pharmaceutical processing etc. RESULTS In order to study the distribution of lipase-producing thermophilic bacilli and their specific lipase protein primary structures, three lipase producers from different genera were isolated from mesothermal (27.5-70 °C) springs distributed on the territory of Armenia and Nagorno Karabakh. Based on phenotypic characteristics and 16S rRNA gene sequencing the isolates were identified as Geobacillus sp., Bacillus licheniformis and Anoxibacillus flavithermus strains. The lipase genes of isolates were sequenced by using initially designed primer sets. Multiple alignments generated from primary structures of the lipase proteins and annotated lipase protein sequences, conserved regions analysis and amino acid composition have illustrated the similarity (98-99%) of the lipases with true lipases (family I) and GDSL esterase family (family II). A conserved sequence block that determines the thermostability has been identified in the multiple alignments of the lipase proteins. CONCLUSIONS The results are spreading light on the lipase producing bacilli distribution in geothermal springs in Armenia and Nagorno Karabakh. Newly isolated bacilli strains could be prospective source for thermostable lipases and their genes.
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Affiliation(s)
- Grigor Shahinyan
- Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia
| | - Armine Margaryan
- Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia.,Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia
| | - Hovik Panosyan
- Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia
| | - Armen Trchounian
- Research Institute of Biology, Yerevan State University, 0025, Yerevan, Armenia. .,Department of Biochemistry, Microbiology and Biotechnology, Faculty of Biology, Yerevan State University, 0025, Yerevan, Armenia.
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Samoylova YV, Piligaev AV, Sorokina KN, Parmon VN. Enzymatic interesterification of sunflower oil and hydrogenated soybean oil with the immobilized bacterial recombinant lipase from Geobacillus stearothermophilus G3. CATALYSIS IN INDUSTRY 2017. [DOI: 10.1134/s2070050417010123] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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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: 209] [Impact Index Per Article: 29.9] [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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Mandelli F, Gonçalves TA, Gandin CA, Oliveira ACP, Oliveira Neto M, Squina FM. Characterization and Low-Resolution Structure of an Extremely Thermostable Esterase of Potential Biotechnological Interest from Pyrococcus furiosus. Mol Biotechnol 2016; 58:757-766. [DOI: 10.1007/s12033-016-9975-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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16
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Kotogán A, Kecskeméti A, Szekeres A, Papp T, Chandrasekaran M, Kadaikunnan S, Alharbi NS, Vágvölgyi C, Takó M. Characterization of transesterification reactions by Mucoromycotina lipases in non-aqueous media. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.molcatb.2016.02.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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17
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Analysis of Comparative Sequence and Genomic Data to Verify Phylogenetic Relationship and Explore a New Subfamily of Bacterial Lipases. PLoS One 2016; 11:e0149851. [PMID: 26934700 PMCID: PMC4774917 DOI: 10.1371/journal.pone.0149851] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 02/06/2016] [Indexed: 12/01/2022] Open
Abstract
Thermostable and organic solvent-tolerant enzymes have significant potential in a wide range of synthetic reactions in industry due to their inherent stability at high temperatures and their ability to endure harsh organic solvents. In this study, a novel gene encoding a true lipase was isolated by construction of a genomic DNA library of thermophilic Aneurinibacillus thermoaerophilus strain HZ into Escherichia coli plasmid vector. Sequence analysis revealed that HZ lipase had 62% identity to putative lipase from Bacillus pseudomycoides. The closely characterized lipases to the HZ lipase gene are from thermostable Bacillus and Geobacillus lipases belonging to the subfamily I.5 with ≤ 57% identity. The amino acid sequence analysis of HZ lipase determined a conserved pentapeptide containing the active serine, GHSMG and a Ca2+-binding motif, GCYGSD in the enzyme. Protein structure modeling showed that HZ lipase consisted of an α/β hydrolase fold and a lid domain. Protein sequence alignment, conserved regions analysis, clustal distance matrix and amino acid composition illustrated differences between HZ lipase and other thermostable lipases. Phylogenetic analysis revealed that this lipase represented a new subfamily of family I of bacterial true lipases, classified as family I.9. The HZ lipase was expressed under promoter Plac using IPTG and was characterized. The recombinant enzyme showed optimal activity at 65°C and retained ≥ 97% activity after incubation at 50°C for 1h. The HZ lipase was stable in various polar and non-polar organic solvents.
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Farrokh P, Yakhchali B, Karkhane AA. Rational Design of K173A Substitution Enhances Thermostability Coupled with Catalytic Activity of Enterobacter sp. Bn12 Lipase. J Mol Microbiol Biotechnol 2014; 24:262-9. [DOI: 10.1159/000365890] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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19
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Improved thermostability of esterase from Aspergillus fumigatus by site-directed mutagenesis. Enzyme Microb Technol 2014; 64-65:11-6. [PMID: 25152411 DOI: 10.1016/j.enzmictec.2014.06.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 06/03/2014] [Accepted: 06/20/2014] [Indexed: 11/23/2022]
Abstract
A 1.020-bp esterase gene, estQ, encoding for a protein of 339 amino acids, was cloned from Aspergillus fumigatus and expressed in E. coli. EstQ exhibited the optimal activity around 40 °C and pH 9.0. In order to obtain more thermostable esterases, three mutants (A134T, V160T, A134T-V160T) were constructed by site-directed mutagenesis and also characterized for further research. Compared to A134T and V160T displaying their optimum activity at 40 °C, A134T-V160T exhibited a 5 °C higher optimal temperature and a longer half-life more than 24 times than that of WT at 50 °C. All the mutants displayed favorable effects on thermostability and retained 53-76% activity after pre-incubation for 30 min at 45 °C, about 20-40% higher than that of the WT. With an increase in Km of the three mutants, a decrease in catalytic efficiency in kcat/Km was observed in mutant V160T and A134T-V160T against p-nitrophenyl butyrate. Homology models of WT and A134T-V160T were built to understand the structure-function relationship. The analysis results showed that the improved thermostability may be due to the favorable interaction and additional hydrogen bonds formed in the mutants by substitution of hydrophobic residues with hydrophilic residues. This study provide useful theoretical reference for enzyme evolution in vitro.
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Hwang HT, Qi F, Yuan C, Zhao X, Ramkrishna D, Liu D, Varma A. Lipase-catalyzed process for biodiesel production: Protein engineering and lipase production. Biotechnol Bioeng 2013; 111:639-53. [PMID: 24284881 DOI: 10.1002/bit.25162] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2013] [Revised: 10/16/2013] [Accepted: 11/20/2013] [Indexed: 01/05/2023]
Affiliation(s)
- Hyun Tae Hwang
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Feng Qi
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Chongli Yuan
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Xuebing Zhao
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Doraiswami Ramkrishna
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
| | - Dehua Liu
- Department of Chemical Engineering; Institute of Applied Chemistry; Tsinghua University; Beijing China
| | - Arvind Varma
- School of Chemical Engineering; Purdue University; 480 Stadium Mall Drive West Lafayette Indiana 47907
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Kumar R, Singh R, Kaur J. Characterization and molecular modelling of an engineered organic solvent tolerant, thermostable lipase with enhanced enzyme activity. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.09.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Singh RK, Tiwari MK, Singh R, Lee JK. From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes. Int J Mol Sci 2013; 14:1232-77. [PMID: 23306150 PMCID: PMC3565319 DOI: 10.3390/ijms14011232] [Citation(s) in RCA: 268] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Revised: 11/14/2012] [Accepted: 12/24/2012] [Indexed: 11/16/2022] Open
Abstract
Enzymes found in nature have been exploited in industry due to their inherent catalytic properties in complex chemical processes under mild experimental and environmental conditions. The desired industrial goal is often difficult to achieve using the native form of the enzyme. Recent developments in protein engineering have revolutionized the development of commercially available enzymes into better industrial catalysts. Protein engineering aims at modifying the sequence of a protein, and hence its structure, to create enzymes with improved functional properties such as stability, specific activity, inhibition by reaction products, and selectivity towards non-natural substrates. Soluble enzymes are often immobilized onto solid insoluble supports to be reused in continuous processes and to facilitate the economical recovery of the enzyme after the reaction without any significant loss to its biochemical properties. Immobilization confers considerable stability towards temperature variations and organic solvents. Multipoint and multisubunit covalent attachments of enzymes on appropriately functionalized supports via linkers provide rigidity to the immobilized enzyme structure, ultimately resulting in improved enzyme stability. Protein engineering and immobilization techniques are sequential and compatible approaches for the improvement of enzyme properties. The present review highlights and summarizes various studies that have aimed to improve the biochemical properties of industrially significant enzymes.
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Affiliation(s)
- Raushan Kumar Singh
- Department of Chemical Engineering, Konkuk University, 1 Hwayang-Dong, Gwangjin-Gu, Seoul 143-701, Korea.
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