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Klaewkla M, Wangpaiboon K, Pichyangkura R, Charoenwongpaiboon T. Unraveling the role of flexible coil near calcium binding site of levansucrase on thermostability and product profile via proline substitution and molecular dynamics simulations. Proteins 2024; 92:170-178. [PMID: 37753539 DOI: 10.1002/prot.26592] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 08/18/2023] [Accepted: 09/07/2023] [Indexed: 09/28/2023]
Abstract
Due to its bioactivity and versatile applications, levan has appeared as a promising biomaterial. Levansucrase is responsible for the conversion of sucrose into levan. With the goal of enhancing levan production, the strategy for enhancing the stability of levansucrase is being intensively studied. To make proteins more stable under high temperatures, proline, the most rigid residue, can be introduced into previously flexible regions. Herein, G249, D250, N251, and H252 on the flexible coil close to the calcium binding site of Bacillus licheniformis levansucrase were replaced with proline. Mutations at G249P greatly enhance both the enzyme's thermodynamic and kinetic stability, while those at H252P improve solely the enzyme's kinetic stability. GPC analysis revealed that G249P synthesize more levan, but H252P generate primarily oligosaccharides. Molecular dynamics simulations (MD) and MM/GBSA analysis revealed that G249P mutation increased not only the stability of levansucrase, but also affinity toward fructan.
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Affiliation(s)
| | - Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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2
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Charoenwongpaiboon T, Klaewkla M, Chaiyen P, Tongsook C. Mechanistic Insights into Roseoflavin Synthesis by N, N-8-Demethyl-8-aminoriboflavin Dimethyltransferase (RosA): Molecular Dynamics Simulations and Residue Conservation Analysis. J Chem Inf Model 2023. [PMID: 37310018 DOI: 10.1021/acs.jcim.3c00655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
8-Demethyl-8-dimethylaminoriboflavin (Roseoflavin or RoF) is a natural riboflavin analogue found in Streptomyces davaonensis and Streptomyces cinnabarinus. RoF displays potent antibiotic properties because it affects FMN riboswitches and flavoproteins of cellular targets. N,N-8-Demethyl-8-aminoriboflavin dimethyltransferase (RosA) is an enzyme that catalyzes the last step of RoF biosynthesis, a consecutive dimethylation of 8-demethyl-8-aminoriboflavin (AF) to generate RoF. Thus, understanding mechanistic insights into RosA structures and mechanisms could lead to the improvement of the RoF product yield. Herein, mechanistic insights into roseoflavin synthesis by RosA were evaluated using molecular dynamics simulations. The obtained results revealed that RosA possibly catalyzes the reaction by positioning the substrate binding to have proper distance and orientation to the methyl group donor, S-adenosylmethionine. No direct participation of catalytic residues in the reaction was identified. The enzyme's active site structures change drastically to accommodate the ligand binding. On the basis of the MM/GBSA calculations and conservation analysis, the amino acid residues involved in substrate binding were identified. The structural information obtained from this study could be beneficial in designing RosA to efficiently produce roseoflavin.
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Affiliation(s)
| | | | - Pimchai Chaiyen
- School of Biomolecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology (VISTEC), Rayong 21210, Thailand
| | - Chanakan Tongsook
- Department of Chemistry, Faculty of Science, Silpakorn University, Nakorn Pathom 73000, Thailand
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3
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Wangpaiboon K, Charoenwongpaiboon T, Klaewkla M, Field RA, Panpetch P. Cassava pullulanase and its synergistic debranching action with isoamylase 3 in starch catabolism. Front Plant Sci 2023; 14:1114215. [PMID: 36778707 PMCID: PMC9911869 DOI: 10.3389/fpls.2023.1114215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Pullulanase (EC 3.2.1.41, PUL), a debranching enzyme belonging to glycoside hydrolase family 13 subfamily 13, catalyses the cleavage of α-1,6 linkages of pullulan and β-limit dextrin. The present work studied PUL from cassava Manihot esculenta Crantz (MePUL) tubers, an important economic crop. The Mepul gene was successfully cloned and expressed in E. coli and rMePUL was biochemically characterised. MePUL was present as monomer and homodimer, as judged by apparent mass of ~ 84 - 197 kDa by gel permeation chromatography analysis. Optimal pH and temperature were at pH 6.0 and 50 °C, and enzyme activity was enhanced by the addition of Ca2+ ions. Pullulan is the most favourable substrate for rMePUL, followed by β-limit dextrin. Additionally, maltooligosaccharides were potential allosteric modulators of rMePUL. Interestingly, short-chain maltooligosaccharides (DP 2 - 4) were significantly revealed at a higher level when rMePUL was mixed with cassava isoamylase 3 (rMeISA3), compared to that of each single enzyme reaction. This suggests that MePUL and MeISA3 debranch β-limit dextrin in a synergistic manner, which represents a major starch catabolising process in dicots. Additionally, subcellular localisation suggested the involvement of MePUL in starch catabolism, which normally takes place in plastids.
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Affiliation(s)
- Karan Wangpaiboon
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Methus Klaewkla
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Robert A. Field
- Department of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, Manchester, United Kingdom
| | - Pawinee Panpetch
- Center of Excellence in Structural and Computational Biology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Klaewkla M, Prousoontorn J, Charoenwongpaiboon T. A theoretical study on binding and stabilization of galactose and novel galactose analogues to the human α-galactosidase A variant causing Fabry disease. Biophys Chem 2023; 292:106915. [PMID: 36334502 DOI: 10.1016/j.bpc.2022.106915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/15/2022] [Accepted: 10/23/2022] [Indexed: 12/14/2022]
Abstract
α-galactosidase A (α-Gal A) catalyzes the hydrolysis of terminal α-galactosyl moieties from globotriaosylceramide, and mutations in this enzyme lead to the lipid metabolism disorder "Fabry disease". Mutation in α-Gal A possibly causes the protein misfolding, which reduces catalytic activity and stability of the enzyme. A recent study demonstrated that the binding of galactose on the α-Gal A catalytic site significantly increases its stability. Herein, the effect of mutation on secondary structure, structural energy, and galactose affinity of α-Gal A (wild type and A143T variant) was investigated using molecular dynamics simulations and free energy calculations based on MM/GBSA method. The results showed that A143T mutation caused the formation of unusual H-bonds that induced the change in secondary structure and binding affinities toward galactose. The amino acid residues involved in galactose binding were identified. The molecular binding mechanism obtained from this study could be helpful for optimizations and designs of new galactose analogs as pharmacological chaperones against Fabry disease.
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Chanvijit S, Phuagkhaopong S, Mahalapbutr P, Klaewkla M, Chavasiri W, Wonganan P. Allyl ether of mansonone G as a potential anticancer agent for colorectal cancer. Sci Rep 2022; 12:19668. [PMID: 36385303 PMCID: PMC9668903 DOI: 10.1038/s41598-022-23997-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 11/08/2022] [Indexed: 11/17/2022] Open
Abstract
Mansonone G (MG), a 1,2-naphthoquinone isolated from the heartwood of Mansonia gagei Drumm, exhibited several pharmacological activities such as anti-bacterial, anti-estrogenic and anti-adipogenic effect. This study evaluated the cytotoxicity of MG and its derivatives as well as determined the mechanism(s) underlying the cytotoxic activity of the most potent MG derivative on two CRC cell lines, HCT-116 cells carrying p53 wild-type and HT-29 cells carrying p53 mutant. We found that MG and its derivatives could inhibit viability of HCT-116 and HT-29 cells in a concentration-dependent manner. Of all semi-synthetic derivatives of MG, allyl ether mansonone G (MG7) was the most potent cytotoxic agent toward cancer cells and less toxic to normal cells. MG7 could induce ROS generation which was associated with cytotoxicity and apoptosis in both HCT-116 and HT-29 cells. Western blot analysis revealed that MG7 downregulated the expression of Bcl-2 and Bcl-xL proteins in both CRC cell lines and upregulated the expression of BAK protein in HT-29 cells. Moreover, MG7 inhibited AKT signaling pathway in both CRC cell lines and modulated ERK1/2 signaling pathway by inhibiting ERK1/2 phosphorylation in HCT-116 cells and activating ERK1/2 phosphorylation in HT-29 cells. Molecular docking revealed that MG7 could bind to the ATP-binding pocket of AKT and ERK1 via hydrophobic interactions.
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Affiliation(s)
- Savinee Chanvijit
- grid.7922.e0000 0001 0244 7875Interdisciplinary Program in Pharmacology, Graduate School, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Suttinee Phuagkhaopong
- grid.7922.e0000 0001 0244 7875Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Pathumwan, Bangkok, 10330 Thailand
| | - Panupong Mahalapbutr
- grid.9786.00000 0004 0470 0856Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002 Thailand
| | - Methus Klaewkla
- Future Health Innovation Technology Co., Ltd., Bangkok, 10170 Thailand
| | - Warinthorn Chavasiri
- grid.7922.e0000 0001 0244 7875Center of Excellence in Natural Products Chemistry, Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330 Thailand
| | - Piyanuch Wonganan
- grid.7922.e0000 0001 0244 7875Department of Pharmacology, Faculty of Medicine, Chulalongkorn University, 1873 Rama IV Road, Pathumwan, Bangkok, 10330 Thailand
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Detarya M, Lert-Itthiporn W, Mahalapbutr P, Klaewkla M, Sorin S, Sawanyawisuth K, Silsirivanit A, Seubwai W, Wongkham C, Araki N, Wongkham S. Emerging roles of GALNT5 on promoting EGFR activation in cholangiocarcinoma: a mechanistic insight. Am J Cancer Res 2022; 12:4140-4159. [PMID: 36225633 PMCID: PMC9548001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 08/23/2022] [Indexed: 06/16/2023] Open
Abstract
Cholangiocarcinoma (CCA) is a lethal cancer in that the incidence is now increasing worldwide. N-acetylgalactosaminyltransferase 5 (GALNT5), an enzyme that initiates the first step of mucin type-O glycosylation, has been reported to promote aggressiveness of CCA cells via the epithelial to the mesenchymal transition (EMT) process, and Akt/Erk activation. In this study, the clinical and biological relevance of GALNT5 and the molecular mechanisms by which GALNT5 modulated EGFR in promoting CCA progression were examined. Using publicly available datasets, upregulation of GALNT5 in patient CCA tissues and its correlation with EGFR expression was noted. High levels of GALNT5 were significantly associated with the short survival of patients, suggesting a prognostic marker of GALNT5 for CCA. GALNT5 modulated EGFR expression as shown in CCA cell lines. Upregulation of GALNT5 significantly increased EGFR mRNA and protein in GALNT5 overexpressing cells, whereas suppression of GALNT5 expression gave the opposite results. The molecular dynamics simulations and MM/PB(GB)SA-based free energy calculations showed that O-glycosylation on the EGFR extracellular domain enhanced the structural stability, compactness, and H-bond formation of the EGF/GalNAc-EGFR complex compared with those of EGF/EGFR. This stabilized the growth factor binding site and fostered stronger interactions between EGF and EGFR. Using the EGF-induced EGFR activation model, GALNT5 was shown to mediate EGFR stability via a decreased rate of EGFR degradation and enhanced EGFR activity by increasing the binding affinity of EGF/EGFR that consequently increasing the activation of EGFR and its downstream effectors Akt and Erk. In summary, GALNT5 was upregulated in CCA tissues and associated with a worse prognosis. The study identified for the first time the impacts of GALNT5 on EGFR activity by increasing: 1) EGFR expression via a transcriptional-dependent mechanism, 2) EGFR stability by reducing EGFR degradation, and 3) EGFR activation through an increased binding affinity of EGF/EGFR which all together fostered the activation of EGFR. These results expanded the understanding of the molecular mechanism of how GALNT5 impacted CCA progression and suggested GALNT5 as a new target for therapeutic intervention against metastatic CCA.
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Affiliation(s)
- Marutpong Detarya
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Worachart Lert-Itthiporn
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Methus Klaewkla
- Future Health Innovation Technology Co., Ltd.Bangkok 10170, Thailand
| | - Supannika Sorin
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Kanlayanee Sawanyawisuth
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Atit Silsirivanit
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Wunchana Seubwai
- Department of Forensic Medicine, Faculty of Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Chaisiri Wongkham
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
| | - Norie Araki
- Department of Tumor Genetics and Biology, Graduate School of Medical Sciences, Faculty of Life Sciences, Kumamoto UniversityKumamoto 860-8556, Japan
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, and Center for Translational Medicine, Khon Kaen UniversityKhon Kaen 40002, Thailand
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Sitthiyotha T, Klaewkla M, Krusong K, Pichyangkura R, Chunsrivirot S. Computational design of Lactobacillus Acidophilus α-L-rhamnosidase to increase its structural stability. PLoS One 2022; 17:e0268953. [PMID: 35613129 PMCID: PMC9132286 DOI: 10.1371/journal.pone.0268953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 05/11/2022] [Indexed: 11/26/2022] Open
Abstract
α-L-rhamnosidase catalyzes hydrolysis of the terminal α-L-rhamnose from various natural rhamnoglycosides, including naringin and hesperidin, and has various applications such as debittering of citrus juices in the food industry and flavonoid derhamnosylation in the pharmaceutical industry. However, its activity is lost at high temperatures, limiting its usage. To improve Lactobacillus acidophilus α-L-rhamnosidase stability, we employed molecular dynamics (MD) to identify a highly flexible region, as evaluated by its root mean square fluctuation (RMSF) value, and computational protein design (Rosetta) to increase rigidity and favorable interactions of residues in highly flexible regions. MD results show that five regions have the highest flexibilities and were selected for design by Rosetta. Twenty-one designed mutants with the best ΔΔG at each position and ΔΔG < 0 REU were simulated at high temperature. Eight designed mutants with ΔRMSF of highly flexible regions lower than -10.0% were further simulated at the optimum temperature of the wild type. N88Q, N202V, G207D, Q209M, N211T and Y213K mutants were predicted to be more stable and could maintain their native structures better than the wild type due to increased hydrogen bond interactions of designed residues and their neighboring residues. These designed mutants are promising enzymes with high potential for stability improvement.
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Affiliation(s)
- Thassanai Sitthiyotha
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Methus Klaewkla
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Kuakarun Krusong
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
| | - Surasak Chunsrivirot
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok, Thailand
- * E-mail:
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Mahalapbutr P, Klaewkla M, Charoenwongpaiboon T. Unraveling the effect of A143T, P205T and D244N mutations in α-galactosidase A on its catalytic activity and susceptibility to globotriaosylceramide and iminosugar 1-deoxygalactonojirimycin chaperone. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.118790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Wangpaiboon K, Klaewkla M, Charoenwongpaiboon T, Vongkusolkit N, Panpetch P, Kuttiyawong K, Visessanguan W, Pichyangkura R. Synergistic enzyme cocktail between levansucrase and inulosucrase for superb levan-type fructooligosaccharide synthesis. Enzyme Microb Technol 2021; 154:109960. [PMID: 34923315 DOI: 10.1016/j.enzmictec.2021.109960] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/17/2021] [Accepted: 12/04/2021] [Indexed: 11/24/2022]
Abstract
Inulosucrase (ISC) and levansucrase (LSC) utilise sucrose and produce inulin- and levan-type fructans, respectively. This study aims to propose a new strategy to improve levan-type fructooligosaccharide (L-FOS) production. The effect of ISC/ LSC -mixed reaction was elucidated on L-FOS production. The presence of ISC in the LSC reaction significantly leads to the higher production of L-FOSs as the main products. Furthermore, the different ratios between ISC and LSC affected the distribution of L-FOSs. A greater amount of ISC compared to LSC promoted the synthesis of short-chain L-FOSs. Conversely, when LSC was increased, the synthesis of longer-chain L-FOSs was enhanced. The addition of trisaccharide mixtures obtained from either a single ISC or LSC reaction could enhance L-FOSs synthesis in the LSC reaction. Analysis of these trisaccharides revealed that most species of the oligosaccharides were similar, with 1-kestose being the major one. The supplement of only 1-kestose in the LSC reaction showed similar results to those of the reaction in the presence of trisaccharide mixtures. Moreover, the results were supported by molecular dynamics simulations. This work not only provides an improvement in L-FOS production but also revealed and supported some insights into the mechanism of fructansucrases.
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Affiliation(s)
- Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Methus Klaewkla
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | | | - Napas Vongkusolkit
- Department of Biology, Barnard College, Columbia University, New York, NY 10027, USA
| | - Pawinee Panpetch
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Kamontip Kuttiyawong
- Department of Chemistry, Faculty of Liberal Arts and Science, Kasetsart University Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand
| | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, 113 Paholayothin Road, Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
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Klaewkla M, Pichyangkura R, Chunsrivirot S. Computational Design of Oligosaccharide-Producing Levansucrase from Bacillus licheniformis RN-01 to Increase Its Stability at High Temperature. J Phys Chem B 2021; 125:5766-5774. [PMID: 34047564 DOI: 10.1021/acs.jpcb.1c02016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Levan-type fructooligosaccharides (LFOs) and levan can potentially be used as ingredients in prebiotics, skincare products, and antitumor agents. The Y246S mutant of Bacillus licheniformis RN-01 levansucrase (oligosaccharide-producing levansucrase, OPL) was reported to productively synthesize LFOs; however, OPL's thermostability is low at high temperatures. To enhance OPL structural stability, this study employed molecular dynamics (AMBER) to identify a highly flexible region, as measured by its average root-mean-square fluctuation (RMSF) value, on the OPL surface and computational protein design (Rosetta) to rigidify and increase favorable interactions to increase its structural stability. AMBER identified region nine (residues 277-317) as a highly flexible region that was selected for design because it has the highest number of residues and the second-highest average RMSF, and it is farthest from the active site. Rosetta designed 14 mutants with the best ΔΔG value in each position, where three mutants have better ΔG than OPL. To determine whether their flexibilities and stabilities are lower than those of OPL, all 14 designed mutants were simulated at high temperature (500 K), and we found that K296E, G309S, and A310W mutants were predicted to be more stable and could retain their native structures better than OPL. Our results suggest that enhanced structural stabilities of these mutants are caused by increased hydrogen bond strengths of the designed residues and their neighboring residues. This study designed K296E, G309S, and A310W mutants of OPL with high potential for stability improvement, and they could potentially be used for the effective production of LFOs.
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Affiliation(s)
- Methus Klaewkla
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Surasak Chunsrivirot
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.,Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
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Lorthongpanich C, Charoenwongpaiboon T, Supakun P, Klaewkla M, Kheolamai P, Issaragrisil S. Fisetin Inhibits Osteogenic Differentiation of Mesenchymal Stem Cells via the Inhibition of YAP. Antioxidants (Basel) 2021; 10:antiox10060879. [PMID: 34070903 PMCID: PMC8226865 DOI: 10.3390/antiox10060879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 05/27/2021] [Accepted: 05/27/2021] [Indexed: 12/12/2022] Open
Abstract
Mesenchymal stem cells (MSCs) are self-renewal and capable of differentiating to various functional cell types, including osteocytes, adipocytes, myoblasts, and chondrocytes. They are, therefore, regarded as a potential source for stem cell therapy. Fisetin is a bioactive flavonoid known as an active antioxidant molecule that has been reported to inhibit cell growth in various cell types. Fisetin was shown to play a role in regulating osteogenic differentiation in animal-derived MSCs; however, its molecular mechanism is not well understood. We, therefore, studied the effect of fisetin on the biological properties of human MSCs derived from chorion tissue and its role in human osteogenesis using MSCs and osteoblast-like cells (SaOs-2) as a model. We found that fisetin inhibited proliferation, migration, and osteogenic differentiation of MSCs as well as human SaOs-2 cells. Fisetin could reduce Yes-associated protein (YAP) activity, which results in downregulation of osteogenic genes and upregulation of fibroblast genes. Further analysis using molecular docking and molecular dynamics simulations suggests that fisetin occupied the hydrophobic TEAD pocket preventing YAP from associating with TEA domain (TEAD). This finding supports the potential application of flavonoids like fisetin as a protein–protein interaction disruptor and also suggesting an implication of fisetin in regulating human osteogenesis.
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Affiliation(s)
- Chanchao Lorthongpanich
- Siriraj Center of Excellence for Stem Cell Research, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (P.S.); (S.I.)
- Correspondence:
| | | | - Prapasri Supakun
- Siriraj Center of Excellence for Stem Cell Research, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (P.S.); (S.I.)
| | - Methus Klaewkla
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand;
| | - Pakpoom Kheolamai
- Division of Cell Biology, Faculty of Medicine, Thammasat University, Pathum Thani 10120, Thailand;
| | - Surapol Issaragrisil
- Siriraj Center of Excellence for Stem Cell Research, Department of Medicine, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand; (P.S.); (S.I.)
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12
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Charoenwongpaiboon T, Punnatin P, Klaewkla M, Pramoj Na Ayutthaya P, Wangpaiboon K, Chunsrivirot S, Field RA, Pichyangkura R. Conserved Calcium-Binding Residues at the Ca-I Site Involved in Fructooligosaccharide Synthesis by Lactobacillus reuteri 121 Inulosucrase. ACS Omega 2020; 5:28001-28011. [PMID: 33163783 PMCID: PMC7643167 DOI: 10.1021/acsomega.0c03521] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 10/07/2020] [Indexed: 06/11/2023]
Abstract
Inulosucrase is an enzyme that synthesizes inulin-type β-2,1-linked fructooligosaccharides (IFOS) from sucrose. Previous studies have shown that calcium is important for the activity and stability of Lactobacillus reuteri 121 inulosucrase (LrInu). Here, mutational analyses of four conserved calcium-binding site I (Ca-I) residues of LrInu, Asp418, Gln449, Asn488, and Asp520 were performed. Alanine substitution for these residues not only reduced the stability and activity of LrInu, but also modulated the pattern of the IFOS produced. Circular dichroism spectroscopy and molecular dynamics simulation indicated that these mutations had limited impact on the overall conformation of the enzyme. One of Ca-I residues most critical for controlling LrInu-mediated polymerization of IFOS, Asp418, was also subjected to mutagenesis, generating D418E, D418H, D418L, D418N, D418S, and D418W. The activity of these mutants demonstrated that the IFOS chain length could be controlled by a single mutation at the Ca-I site.
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Affiliation(s)
| | - Panachai Punnatin
- Structural
and Computational Biology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Methus Klaewkla
- Structural
and Computational Biology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
- Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Pathumwan, Bangkok 10330, Thailand
| | | | - Karan Wangpaiboon
- Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Pathumwan, Bangkok 10330, Thailand
| | - Surasak Chunsrivirot
- Structural
and Computational Biology Research Unit, Department of Biochemistry,
Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
- Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Pathumwan, Bangkok 10330, Thailand
| | - Robert A. Field
- Department
of Chemistry and Manchester Institute of Biotechnology, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.
| | - Rath Pichyangkura
- Department
of Biochemistry, Faculty of Science, Chulalongkorn
University, Pathumwan, Bangkok 10330, Thailand
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13
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Klaewkla M, Pichyangkura R, Charoenwongpaiboon T, Wangpaiboon K, Chunsrivirot S. Computational design of oligosaccharide producing levansucrase from Bacillus licheniformis RN-01 to improve its thermostability for production of levan-type fructooligosaccharides from sucrose. Int J Biol Macromol 2020; 160:252-263. [PMID: 32439436 DOI: 10.1016/j.ijbiomac.2020.05.102] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/27/2022]
Abstract
Levansucrase catalyzes production of levan and levan-type fructooligosaccharides (LFOs) with potential applications in food and pharmaceutical industries such as prebiotics and anti-tumor agents. Previous study found that Y246S mutant of Bacillus licheniformis RN-01 levansucrase (oligosaccharide producing levansucrase, OPL) could effectively produce LFOs but its thermostability is limited at high temperature. In this study, molecular dynamics (MD) and computational protein design were used to create mutants with higher thermostability than OPL by rigidifying highly flexible residues on enzyme surface. MD results show that highly flexible residues suitable for design are K82, N83, D179, and Q308. Two approaches were employed to improve their interactions by allowing them to be amino acids that could potentially form favorable interactions with their neighboring residues or natural amino acids except G, P and C. Flexibilities of designed residues of K82H, N83R, Q308S and K82H/N83R mutants are lower than those of OPL. Experimental results show that characteristics and product patterns of designed mutants are relatively similar to those of OPL. K82H/N83R mutant has higher thermostability than OPL with 1.7-fold increase in t1/2. Circular dichroism result suggests that designed mutations do not drastically affect secondary structures. This study shows how computational technique can engineer enzyme for thermostability improvement.
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Affiliation(s)
- Methus Klaewkla
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand; Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | | | - Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand
| | - Surasak Chunsrivirot
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand; Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Pathumwan, Bangkok 10330, Thailand.
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14
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Phengnoi P, Charoenwongpaiboon T, Wangpaiboon K, Klaewkla M, Nakapong S, Visessanguan W, Ito K, Pichyangkura R, Kuttiyawong K. Levansucrase from Bacillus amyloliquefaciens KK9 and Its Y237S Variant Producing the High Bioactive Levan-Type Fructooligosaccharides. Biomolecules 2020; 10:E692. [PMID: 32365662 PMCID: PMC7277640 DOI: 10.3390/biom10050692] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/25/2020] [Accepted: 04/27/2020] [Indexed: 12/29/2022] Open
Abstract
Levan-typed fructooligosaccharide (LFOS), a β-2,6 linked oligofructose, displays the potential application as a prebiotic and therapeutic dietary supplement. In the present study, LFOS was synthesized using levansucrase from Bacillus amyloliquefaciens KK9 (LsKK9). The wild-type LsKK9 was cloned and expressed in E. coli, and purified by cation exchanger chromatography. Additionally, Y237S variant of LsKK9 was constructed based on sequence alignment and structural analysis to enhance the LFOS production. High-performance anion-exchange chromatography coupled with pulsed amperometric detection (HPAEC-PAD) analysis indicated that Y237S variant efficiently produced a higher amount of short-chain LFOS than wild type. Also, the concentration of enzyme and sucrose in the reactions was optimized. Finally, prebiotic activity assay demonstrated that LFOS produced by Y237S variant had higher prebiotic activity than that of the wild-type enzyme, making the variant enzyme attractive for food biotechnology.
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Affiliation(s)
- Pongsakorn Phengnoi
- Department of Chemistry, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
| | | | - Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (K.W.); (M.K.); (R.P.)
| | - Methus Klaewkla
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (K.W.); (M.K.); (R.P.)
| | - Santhana Nakapong
- Department of Chemistry, Faculty of Science, Ramkhamhaeng University, Bangkok 10240, Thailand;
| | - Wonnop Visessanguan
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani 12120, Thailand;
| | - Kazuo Ito
- Graduate School of Science, Osaka City University, Osaka 558-8585, Japan;
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand; (K.W.); (M.K.); (R.P.)
| | - Kamontip Kuttiyawong
- Department of Chemistry, Faculty of Liberal Arts and Science, Kasetsart University, Kamphaeng Saen Campus, Nakhon Pathom 73140, Thailand;
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15
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Charoenwongpaiboon T, Klaewkla M, Chunsrivirot S, Wangpaiboon K, Pichyangkura R, Field RA, Prousoontorn MH. Rational re-design of Lactobacillus reuteri 121 inulosucrase for product chain length control. RSC Adv 2019; 9:14957-14965. [PMID: 35516339 PMCID: PMC9064246 DOI: 10.1039/c9ra02137j] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 05/07/2019] [Indexed: 11/21/2022] Open
Abstract
Fructooligosaccharides (FOSs) are well-known prebiotics that are widely used in the food, beverage and pharmaceutical industries. Inulosucrase (E.C. 2.4.1.9) can potentially be used to synthesise FOSs from sucrose. In this study, inulosucrase from Lactobacillus reuteri 121 was engineered by site-directed mutagenesis to change the FOS chain length. Three variants (R483F, R483Y and R483W) were designed, and their binding free energies with 1,1,1-kestopentaose (GF4) were calculated with the Rosetta software. R483F and R483Y were predicted to bind with GF4 better than the wild type, suggesting that these engineered enzymes should be able to effectively extend GF4 by one residue and produce a greater quantity of GF5 than the wild type. MALDI-TOF MS analysis showed that R483F, R483Y and R483W variants could synthesise shorter chain FOSs with a degree of polymerization (DP) up to 11, 10, and 10, respectively, while wild type produced longer FOSs and in polymeric form. Although the decrease in catalytic activity and the increase of hydrolysis/transglycosylation activity ratio was observed, the variants could effectively synthesise FOSs with the yield up to 73% of substrate. Quantitative analysis demonstrated that these variants produced a larger quantity of GF5 than wild type, which was in good agreement with the predicted binding free energy results. Our findings demonstrate the success of using aromatic amino acid residues, at position D418, to block the oligosaccharide binding track of inulosucrase in controlling product chain length.
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Affiliation(s)
| | - Methus Klaewkla
- Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
| | - Surasak Chunsrivirot
- Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
- Structural and Computational Biology Research Unit, Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
| | - Karan Wangpaiboon
- Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
| | - Rath Pichyangkura
- Department of Biochemistry, Faculty of Science, Chulalongkorn University Pathumwan Bangkok 10330 Thailand
| | - Robert A Field
- Department of Biological Chemistry, John Innes Centre Norwich Research Park Norwich NR4 7UH UK
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