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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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Ong SN, Kamarudin NHA, Shariff FM, Noor NDM, Ali MSM, Rahman RNZRA. Effects of alcohol concentration and temperature on the dynamics and stability of mutant Staphylococcal lipase. J Biomol Struct Dyn 2023:1-17. [PMID: 37968883 DOI: 10.1080/07391102.2023.2282177] [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: 08/07/2023] [Accepted: 11/03/2023] [Indexed: 11/17/2023]
Abstract
The stability and activity of lipase in organic media are important parameters in determining how quickly biocatalysis proceeds. This study aimed to examine the effects of two commonly used alcohols in industrial applications, methanol (MtOH) and ethanol (EtOH) on the conformational stability and catalytic activity of G210C lipase, a laboratory-evolved mutant of Staphylococcus epidermidis AT2 lipase. Simulation studies were performed using an open-form predicted structure under 30, 40 and 50% of MtOH and EtOH at 25 °C and 45 °C. The overall enzyme structure becomes more flexible with increasing concentration of MtOH and exhibited the highest flexibility in 40% EtOH. In EtOH, the movement of the lid was found to be temperature-dependent with a noticeable shift in the lid position at 45 °C. Lid opening was evidenced at 50% of MtOH and EtOH which was supported by the increase in SASA of hydrophobic residues of the lid and catalytic triad. The active site remained mostly intact. An open-closed lid transition was observed when the structure was re-simulated in water. Experimental evaluation of the lipase stability showed that the half-life reduced when the enzyme was treated with 40% (v/v) and 50% (v/v) of EtOH and MtOH respectively. The finding implies that a high concentration of alcohol and elevated temperature can induce the lid opening of lipase which could be essential for the activation of the enzyme, provided that the catalytic performance in the active site is not compromised.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shir Nee Ong
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Nor Hafizah Ahmad Kamarudin
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Centre for Foundation Studies in Science of Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Fairolniza Mohd Shariff
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Noor Dina Muhd Noor
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd Shukuri Mohamad Ali
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Raja Noor Zaliha Raja Abd Rahman
- Enzyme and Microbial Technology Research Center, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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Etemadi A, Karimi-Jafari MH, Negahdari B, Asgari Y, Reza Khorramizadeh M, Mohammadian F, Mazloomi M. Design of a dual-function agent by fusing a designed anti-VEGF-A binder and CPG-2 enzyme. J Biomol Struct Dyn 2023; 41:11463-11470. [PMID: 36629035 DOI: 10.1080/07391102.2022.2162584] [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: 06/29/2022] [Accepted: 12/19/2022] [Indexed: 01/12/2023]
Abstract
Anti-VEGF therapies are common for the treatment of cancer. Carboxypeptidase G (CPG-2) enzyme is a zinc-dependent metalloenzyme that metabolizes non-toxic synthetic 'benzoic mustard prodrugs' to cytotoxic moieties in tumor cells. In this study, we designed a dual-activity agent by combining a designed anti-VEGF- and CPG-2 enzyme to convert methotrexate (MTX). VEGF-A was docked against a set of scaffolds, and suitable inverse rotamers were made. Rosetta design was used for the interface design. The top 1200 binders were chosen by flow cytometry and displayed in yeast. The activity of CPG-2 enzyme was analyzed at different temperature conditions and in the presence of the substrate, MTX. Optimal binders were selected and protein was eluted using immobilized metal affinity chromatography and size-exclusion chromatography. Both, native PAGE and on-yeast flow cytometry confirmed the binding of the binder to VEGF-A. The activity of truncated enzymes was slightly lower than that of full-length enzymes linked to VEGF-A. The method should be generally useful as a dual-activity agent for targeting VEGF-A and combination therapy with the enzyme CPG-2 for metabolizing non-toxic prodrugs to cytotoxic moieties.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ali Etemadi
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | | | - Babak Negahdari
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Yazdan Asgari
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Mohammad Reza Khorramizadeh
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences (TUMS), Tehran, Iran
| | - Farideh Mohammadian
- Department of Medical Biotechnology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammadali Mazloomi
- Medical Biotechnology Department, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences (TUMS), Tehran, Iran
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Fang Y, Zhou Y, Xin Y, Shi Y, Guo Z, Li Y, Gu Z, Ding Z, Shi G, Zhang L. Preparation and characterization of a novel thermostable lipase from Thermomicrobium roseum. Catal Sci Technol 2021. [DOI: 10.1039/d1cy01486b] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
In this study, a hypothetical lipase gene from Thermomicrobium roseum DSM 5159 (GenBank: ACM04789.1) was recombinantly expressed in two system and characterized.
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Affiliation(s)
- Yakun Fang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Yanjie Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Yu Xin
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Yi Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Zitao Guo
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Youran Li
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Zhenghua Gu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Zhongyang Ding
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Guiyang Shi
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
| | - Liang Zhang
- Key Laboratory of Industrial Biotechnology, Ministry of Education, National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, Wuxi, 214122, Jiangsu, P.R. China
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