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Yilmaz F, Karageorgiou C, Kim K, Pajic P, Scheer K, Beck CR, Torregrossa AM, Lee C, Gokcumen O. Paleolithic Gene Duplications Primed Adaptive Evolution of Human Amylase Locus Upon Agriculture. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.27.568916. [PMID: 38077078 PMCID: PMC10705236 DOI: 10.1101/2023.11.27.568916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Starch digestion is a cornerstone of human nutrition. The amylase genes code for the starch-digesting amylase enzyme. Previous studies suggested that the salivary amylase (AMY1) gene copy number increased in response to agricultural diets. However, the lack of nucleotide resolution of the amylase locus hindered detailed evolutionary analyses. Here, we have resolved this locus at nucleotide resolution in 98 present-day humans and identified 30 distinct haplotypes, revealing that the coding sequences of all amylase gene copies are evolving under negative selection. The phylogenetic reconstruction suggested that haplotypes with three AMY1 gene copies, prevalent across all continents and constituting about 70% of observed haplotypes, originated before the out-of-Africa migrations of ancestral modern humans. Using thousands of unique 25 base pair sequences across the amylase locus, we showed that additional AMY1 gene copies existed in the genomes of four archaic hominin genomes, indicating that the initial duplication of this locus may have occurred as far back 800,000 years ago. We similarly analyzed 73 ancient human genomes dating from 300 - 45,000 years ago and found that the AMY1 copy number variation observed today existed long before the advent of agriculture (~10,000 years ago), predisposing this locus to adaptive increase in the frequency of higher amylase copy number with the spread of agriculture. Mechanistically, the common three-copy haplotypes seeded non-allelic homologous recombination events that appear to be occurring at one of the fastest rates seen for tandem repeats in the human genome. Our study provides a comprehensive population-level understanding of the genomic structure of the amylase locus, identifying the mechanisms and evolutionary history underlying its duplication and copy number variability in relation to the onset of agriculture.
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Li Z, Liu S, Gao Z, Ji L, Jiao J, Zheng N, Li X, Wang G, Qin J, Wang Y. Dynamic Proteomic Changes in Tumor and Immune Organs Reveal Systemic Immune Response to Tumor Development. Mol Cell Proteomics 2024; 23:100756. [PMID: 38554776 PMCID: PMC11060955 DOI: 10.1016/j.mcpro.2024.100756] [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: 09/05/2023] [Revised: 03/20/2024] [Accepted: 03/27/2024] [Indexed: 04/02/2024] Open
Abstract
In orthotopic mouse tumor models, tumor progression is a complex process, involving interactions among tumor cells, host cell-derived stromal cells, and immune cells. Much attention has been focused on the tumor and its tumor microenvironment, while the host's macroenvironment including immune organs in response to tumorigenesis is poorly understood. Here, we report a temporal proteomic analysis on a subcutaneous tumor and three immune organs (LN, MLN, and spleen) collected on Days 0, 3, 7, 10, 14, and 21 after inoculation of mouse forestomach cancer cells in a syngeneic mouse model. Bioinformatics analysis identified key biological processes during distinct tumor development phases, including an initial acute immune response, the attack by the host immune system, followed by the adaptive immune activation, and the build-up of extracellular matrix. Proteomic changes in LN and spleen largely recapitulated the dynamics of the immune response in the tumor, consistent with an acute defense response on D3, adaptive immune response on D10, and immune evasion by D21. In contrast, the immune response in MLN showed a gradual and sustained activation, suggesting a delayed response from a distal immune organ. Combined analyses of tumors and host immune organs allowed the identification of potential therapeutic targets. A proof-of-concept experiment demonstrated that significant growth reduction can be achieved by dual inhibition of MEK and DDR2. Together, our temporal proteomic dataset of tumors and immune organs provides a useful resource for understanding the interaction between tumors and the immune system and has the potential for identifying new therapeutic targets for cancer treatment.
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Affiliation(s)
- Zhike Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Shuwen Liu
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Zhouyong Gao
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical University, Tianjin, China; Department of Child Health Care, Kunshan Maternity and Child Health Care Institute, Kunshan, China
| | - Linlin Ji
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical University, Tianjin, China; Department of Thoracic Surgery, Weifang People's Hospital, Weifang, China
| | - Jiaqi Jiao
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Nairen Zheng
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Xianju Li
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Guangshun Wang
- Department of Thoracic Surgery, Baodi Clinical College, Tianjin Medical University, Tianjin, China
| | - Jun Qin
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China
| | - Yi Wang
- State Key Laboratory of Medical Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, China.
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Cao L, Lin M, Ning J, Meng X, Pu X, Zhang R, Wu Q, Huang Z, Zhou J. Critical Roles of Acidic Residues in Loop Regions of the Structural Surface for the Salt Tolerance of a GH39 β-d-Xylosidase. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:5805-5815. [PMID: 38451212 DOI: 10.1021/acs.jafc.3c07957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Xylan is the main component of hemicellulose. Complete hydrolysis of xylan requires synergistically acting xylanases, such as β-d-xylosidases. Salt-tolerant β-d-xylosidases have significant application benefits, but few reports have explored the critical amino acids affecting the salt tolerance of xylosidases. Herein, the site-directed mutation was used to demonstrate that negative electrostatic potentials generated by 19 acidic residues in the loop regions of the structural surface positively correlated with the improved salt tolerance of GH39 β-d-xylosidase JB13GH39P28. These mutants showed reduced negative potentials on structural surfaces as well as a 13-43% decrease in stability in 3.0-30.0% (w/v) NaCl. Six key residue sites, D201, D259, D297, D377, D395, and D474, were confirmed to influence both the stability and activity of GH39 β-d-xylosidase. The activity of the GH39 β-d-xylosidase was found promoting by SO42- and inhibiting by NO3-. Values of Km and Kcat/Km decreased aggravatedly in 30.0% (w/v) NaCl when mutation operated on residues E179 and D182 in the loop regions of the catalytic domain. Taken together, mutation on acidic residues in loop regions from catalytic and noncatalytic domains may cause the deformation of catalytic pocket and aggregation of protein particles then decrease the stability, binding affinity, and catalytic efficiency of the β-d-xylosidase.
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Affiliation(s)
- Lijuan Cao
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Mingyue Lin
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Juan Ning
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Xin Meng
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Xiong Pu
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Rui Zhang
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Qian Wu
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Zunxi Huang
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
| | - Junpei Zhou
- College of Life Sciences, Yunnan Normal University, Kunming 650500, People's Republic of China
- Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Yunnan Normal University, Kunming 650500, People's Republic of China
- Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, Yunnan 650500, People's Republic of China
- Key Laboratory of Yunnan Provincial Education Department for Plateau Characteristic Food Enzymes, Yunnan Normal University, Kunming 650500, People's Republic of China
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Zhang Y, Chen Y, Chen C, Zhu Y, Liu M, Chen J. The enhancement mechanisms of mucin and lactoferrin on α-amylase activity in saliva: Exploring the interactions using QCM-D and molecular docking. Int J Biol Macromol 2024; 257:128710. [PMID: 38101660 DOI: 10.1016/j.ijbiomac.2023.128710] [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: 08/22/2023] [Revised: 11/12/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
α-Amylase activity differs between individuals and is influenced by dietary behavior and salivary constituents, but limited information is available on the relationship between α-amylase activity and saliva components. This study investigated the impact of salivary proteins on α-amylase activity, their various correlations, the effect of mucin (MUC5B and MUC7) and lactoferrin on the enzymatic kinetics of α-amylase, and the mechanisms of these interactions using the quartz crystal microbalance with dissipation (QCM-D) technique and molecular docking. The results showed that α-amylase activity was significantly correlated with the concentrations of MUC5B (R2 = 0.42, p < 0.05), MUC7 (R2 = 0.35, p < 0.05), and lactoferrin (R2 = 0.35, p < 0.05). An in vitro study demonstrated that α-amylase activity could be significantly increased by mucins and lactoferrin by decreasing the Michaelis constant (Km) of α-amylase. Moreover, the results from the QCM-D and molecule docking suggested that mucin and lactoferrin could interact with α-amylase to form stable α-amylase-mucin and α-amylase-lactoferrin complexes through hydrophobic interactions, electrostatic interactions, Van der Waals forces, and hydrogen bonds. In conclusion, these findings indicated that the salivary α-amylase activity depended not only on the α-amylase content, but also could be enhanced by the interactions of mucin/lactoferrin with α-amylase.
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Affiliation(s)
- Yufeng Zhang
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Yong Chen
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China.
| | - Chen Chen
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Yang Zhu
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Ming Liu
- Fujian Provincial Key Laboratory of Terahertz Functional Devices and Intelligent Sensing, School of Mechanical Engineering and Automation, Fuzhou University - Qishan Campus, Fuzhou, Fujian 350108, China
| | - Jianshe Chen
- Laboratory of Food Oral Processing, School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
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Azhagesan A, Rajendran D, Varghese RP, George Priya Doss C, Chandrasekaran N. Assessment of polystyrene nano plastics effect on human salivary α-amylase structural alteration: Insights from an in vitro and in silico study. Int J Biol Macromol 2024; 257:128650. [PMID: 38065455 DOI: 10.1016/j.ijbiomac.2023.128650] [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: 08/16/2023] [Revised: 11/19/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
The study found that the enzyme activity of human salivary α-amylase (α-AHS) was competitively inhibited by nanoplastic polystyrene (PS-NPs), with a half-inhibitory concentration (IC50) of 92 μg/mL, while the maximum reaction rate (Vmax) remained unchanged at 909 μg/mL•min. An increase in the concentration of PS-NPs led to a quenching of α-AHS fluorescence with a slight red shift, indicating a static mechanism. The binding constant (Ka) and quenching constant (Kq) were calculated to be 2.92 × 1011 M-1 and 1.078 × 1019 M-1• S-1 respectively, with a hill coefficient (n) close to one and an apparent binding equilibrium constant (KA) of 1.54 × 1011 M-1. Molecular docking results suggested that the interaction between α-AHS and PS-NPs involved π-anion interactions between the active site Asp197, Asp300 residues, and van der Waals force interactions affecting the Tyr, Trp, and other residues. Fourier transform infrared (FT-IR) and circular dichroism (CD) analyses revealed conformational changes in α-AHS, including a loss of secondary structure α-helix and β-sheet. The study concludes that the interaction between α-AHS and PS-NPs leads to structural and functional changes in α-AHS, potentially impacting human health. This research provides a foundation for further toxicological analysis of MPs/NPs in the human digestive system.
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Affiliation(s)
- Ananthaselvam Azhagesan
- Centre for Nanobiotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - Durgalakshmi Rajendran
- Centre for Nanobiotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - Rinku Polachirakkal Varghese
- Department of Integrative Biology, School of BioSciences & Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - C George Priya Doss
- Department of Integrative Biology, School of BioSciences & Technology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India
| | - Natarajan Chandrasekaran
- Centre for Nanobiotechnology, Vellore Institute of Technology (VIT), Vellore, Tamil Nadu 632 014, India.
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Llopiz A, Ramírez-Martínez MA, Olvera L, Xolalpa-Villanueva W, Pastor N, Saab-Rincon G. The Role of a Loop in the Non-catalytic Domain B on the Hydrolysis/Transglycosylation Specificity of the 4-α-Glucanotransferase from Thermotoga maritima. Protein J 2023; 42:502-518. [PMID: 37464145 PMCID: PMC10480278 DOI: 10.1007/s10930-023-10136-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/27/2023] [Indexed: 07/20/2023]
Abstract
The mechanism by which glycoside hydrolases control the reaction specificity through hydrolysis or transglycosylation is a key element embedded in their chemical structures. The determinants of reaction specificity seem to be complex. We looked for structural differences in domain B between the 4-α-glucanotransferase from Thermotoga maritima (TmGTase) and the α-amylase from Thermotoga petrophila (TpAmylase) and found a longer loop in the former that extends towards the active site carrying a W residue at its tip. Based on these differences we constructed the variants W131G and the partial deletion of the loop at residues 120-124/128-131, which showed a 11.6 and 11.4-fold increased hydrolysis/transglycosylation (H/T) ratio relative to WT protein, respectively. These variants had a reduction in the maximum velocity of the transglycosylation reaction, while their affinity for maltose as the acceptor was not substantially affected. Molecular dynamics simulations allow us to rationalize the increase in H/T ratio in terms of the flexibility near the active site and the conformations of the catalytic acid residues and their associated pKas.
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Affiliation(s)
- Alexey Llopiz
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62209, Cuernavaca, Morelos, Mexico
| | - Marco A Ramírez-Martínez
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, 62209, Cuernavaca, Morelos, Mexico
| | - Leticia Olvera
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62209, Cuernavaca, Morelos, Mexico
| | - Wendy Xolalpa-Villanueva
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62209, Cuernavaca, Morelos, Mexico
| | - Nina Pastor
- Centro de Investigación en Dinámica Celular, IICBA, Universidad Autónoma del Estado de Morelos, 62209, Cuernavaca, Morelos, Mexico
| | - Gloria Saab-Rincon
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62209, Cuernavaca, Morelos, Mexico.
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Rhimi M, Da Lage JL, Haser R, Feller G, Aghajari N. Structural and Functional Characterization of Drosophila melanogaster α-Amylase. Molecules 2023; 28:5327. [PMID: 37513201 PMCID: PMC10384113 DOI: 10.3390/molecules28145327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/03/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
Insects rely on carbohydrates such as starch and glycogen as an energy supply for growth of larvae and for longevity. In this sense α-amylases have essential roles under extreme conditions, e.g., during nutritional or temperature stress, thereby contributing to survival of the insect. This makes them interesting targets for combating insect pests. Drosophila melanogaster α-amylase, DMA, which belongs to the glycoside hydrolase family 13, sub family 15, has been studied from an evolutionary, biochemical, and structural point of view. Our studies revealed that the DMA enzyme is active over a broad temperature and pH range, which is in agreement with the fluctuating environmental changes with which the insect is confronted. Crystal structures disclosed a new nearly fully solvated metal ion, only coordinated to the protein via Gln263. This residue is only conserved in the subgroup of D. melanogaster and may thus contribute to the enzyme adaptive response to large temperature variations. Studies of the effect of plant inhibitors and the pseudo-tetrasaccharide inhibitor acarbose on DMA activity, allowed us to underline the important role of the so-called flexible loop on activity/inhibition, but also to suggest that the inhibition modes of the wheat inhibitors WI-1 and WI-3 on DMA, are likely different.
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Affiliation(s)
- Moez Rhimi
- Molecular Microbiology and Structural Biochemistry, UMR5086, CNRS, University of Lyon 1, 7 Passage du Vercors, F-69367 Lyon, CEDEX 07, France
| | - Jean-Luc Da Lage
- Evolution, Génomes, Comportement, Ecologie, UMR 9191 University Paris-Saclay-CNRS-IRD, F-91190 Gif-sur-Yvette, France
| | - Richard Haser
- Molecular Microbiology and Structural Biochemistry, UMR5086, CNRS, University of Lyon 1, 7 Passage du Vercors, F-69367 Lyon, CEDEX 07, France
| | - Georges Feller
- Laboratory of Biochemistry, Center for Protein Engineering-InBioS, Institute of Chemistry B6a, University of Liège, B-4000 Liège, Belgium
| | - Nushin Aghajari
- Molecular Microbiology and Structural Biochemistry, UMR5086, CNRS, University of Lyon 1, 7 Passage du Vercors, F-69367 Lyon, CEDEX 07, France
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Sun Y, Liu G, Liu G, Tang H, Sun C, Zhang W, Chen L. The novel amylase function of the carboxyl terminal domain of Amy63. Biochem Biophys Res Commun 2023; 671:10-17. [PMID: 37290279 DOI: 10.1016/j.bbrc.2023.05.071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/18/2023] [Indexed: 06/10/2023]
Abstract
α-amylase plays a crucial role in regulating metabolism and health by hydrolyzing of starch and glycogen. Despite comprehensive studies of this classic enzyme spanning over a century, the function of its carboxyl terminal domain (CTD) with a conserved eight β-strands is still not fully understood. Amy63, identified from a marine bacterium, was reported as a novel multifunctional enzyme with amylase, agarase and carrageenase activities. In this study, the crystal structure of Amy63 was determined at 1.8 Å resolution, revealing high conservation with some other amylases. Interestingly, the independent amylase activity of the carboxyl terminal domain of Amy63 (Amy63_CTD) was newly discovered by the plate-based assay and mass spectrometry. To date, the Amy63_CTD alone could be regarded as the smallest amylase subunit. Moreover, the significant amylase activity of Amy63_CTD was measured over a wide range of temperature and pH, with optimal activity at 60 °C and pH 7.5. The Small-angle X-ray scattering (SAXS) data showed that the high-order oligomeric assembly gradually formed with increasing concentration of Amy63_CTD, implying the novel catalytic mechanism as revealed by the assembly structure. Therefore, the discovery of the novel independent amylase activity of Amy63_CTD suggests a possible missing step or a new perspective in the complex catalytic process of Amy63 and other related α-amylases. This work may shed light on the design of nanozymes to process marine polysaccharides efficiently.
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Affiliation(s)
- Yufan Sun
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China; Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; The Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Ge Liu
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Guangfeng Liu
- National Center for Protein Science Shanghai, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201204, China
| | - Haixu Tang
- Luddy School of Informatics, Computing, and Engineering, Indiana University Bloomington, IN 47408, USA
| | - Chaomin Sun
- CAS Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Wen Zhang
- Fudan University Pudong Medical Center, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China; The Department of Systems Biology for Medicine, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
| | - Li Chen
- Department of Medical Microbiology, Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China.
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Musiał N, Bogucka A, Tretiakow D, Skorek A, Ryl J, Czaplewska P. Proteomic analysis of sialoliths from calcified, lipid and mixed groups as a source of potential biomarkers of deposit formation in the salivary glands. Clin Proteomics 2023; 20:11. [PMID: 36949424 PMCID: PMC10035263 DOI: 10.1186/s12014-023-09402-3] [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: 01/12/2023] [Accepted: 03/08/2023] [Indexed: 03/24/2023] Open
Abstract
Salivary stones, also known as sialoliths, are formed in a pathological situation in the salivary glands. So far, neither the mechanism of their formation nor the factors predisposing to their formation are known despite several hypotheses. While they do not directly threaten human life, they significantly deteriorate the patient's quality of life. Although this is not a typical research material, attempts are made to apply various analytical tools to characterise sialoliths and search for the biomarkers in their proteomes. In this work, we used mass spectrometry and SWATH-MS qualitative and quantitative analysis to investigate the composition and select proteins that may contribute to solid deposits in the salivary glands. Twenty sialoliths, previously characterized spectroscopically and divided into the following groups: calcified (CAL), lipid (LIP) and mixed (MIX), were used for the study. Proteins unique for each of the groups were found, including: for the CAL group among them, e.g. proteins from the S100 group (S100 A8/A12 and P), mucin 7 (MUC7), keratins (KRT1/2/4/5/13), elastase (ELANE) or stomatin (STOM); proteins for the LIP group-transthyretin (TTR), lactotransferrin (LTF), matrix Gla protein (MPG), submandibular gland androgen-regulated protein 3 (SMR3A); mixed stones had the fewest unique proteins. Bacterial proteins present in sialoliths have also been identified. The analysis of the results indicates the possible role of bacterial infections, disturbances in calcium metabolism and neutrophil extracellular traps (NETs) in the formation of sialoliths.
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Affiliation(s)
- Natalia Musiał
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland.
| | - Aleksandra Bogucka
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland
- Institute of Biochemistry, Medical Faculty, Justus Liebig University of Giessen, Friedrichstrasse 24, 35392, Giessen, Germany
| | - Dmitry Tretiakow
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Andrzej Skorek
- Department of Otolaryngology, Faculty of Medicine, Medical University of Gdańsk, Smoluchowskiego 17, 80-214, Gdańsk, Poland
| | - Jacek Ryl
- Division of Electrochemistry and Surface Physical Chemistry, Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, G. Narutowicza 11/12, 80-233, Gdańsk, Poland
| | - Paulina Czaplewska
- Intercollegiate Faculty of Biotechnology UG&MUG, University of Gdańsk, Abrahama 58, 80-307, Gdańsk, Poland.
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Su H, Sun J, Guo C, Jia Z, Mao X. New Insights into Bifunctional Chitosanases with Hydrolysis Activity toward Chito- and Cello-Substrates. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:6168-6176. [PMID: 35549271 DOI: 10.1021/acs.jafc.2c01577] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In the present study, we carried out a comprehensive investigation of glycoside hydrolase (GH) 46 model-chitosanases based on cleavage specificity classification to understand their unknown bifunctional activity. We for the first time show that GH46 chitosanase CsnMHK1 from Bacillus circulans MH-K1, which was previously thought to be strictly exclusive to chitosan, can hydrolyze both chito- and cello-substrates. We determined the digestion direction of bifunctional chitosanase CsnMHK1 from class III and compared it with class II chitosanase belonging to GH8, providing insight into unique substrate specificities and a new perspective on its reclassification. The results lead us to challenge the current understanding of chitosanase substrate specificity based on GH taxonomy classification and suggest that the prevalence from the common bifunctional activity may have occurred. Altogether, these data contribute to the understanding of chitosanase recognition and hydrolysis toward chito- and cello-substrates, which is valuable for future studies on chitosanases.
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Affiliation(s)
- Haipeng Su
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Jianan Sun
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Chaoran Guo
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Zhenrong Jia
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
| | - Xiangzhao Mao
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
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11
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Hámori C, Kandra L, Gyémánt G. LDAmy, an α-amylase from Colorado potato beetle ( Leptinotarsa decemlineata) with transglycosylation activity. BIOCATAL BIOTRANSFOR 2022. [DOI: 10.1080/10242422.2022.2050707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Csaba Hámori
- Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Lili Kandra
- Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
| | - Gyöngyi Gyémánt
- Department of Inorganic and Analytical Chemistry, Faculty of Science and Technology, University of Debrecen, Debrecen, Hungary
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12
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Purification and Characterization of Trehalase From Acyrthosiphon pisum, a Target for Pest Control. Protein J 2021; 41:189-200. [PMID: 34845557 DOI: 10.1007/s10930-021-10032-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2021] [Indexed: 10/19/2022]
Abstract
Insect trehalases are glycoside hydrolases essential for trehalose metabolism and stress resistance. We here report the extraction and purification of Acyrthosiphon pisum soluble trehalase (ApTreh-1), its biochemical and structural characterization, as well as the determination of its kinetic properties. The protein has been purified by ammonium sulphate precipitation, first followed by an anion-exchange and then by an affinity chromatography. The SDS-PAGE shows a main band at 70 kDa containing two isoforms of ApTreh-1 (X1 and X2), identified by mass spectrometry and slightly contrasting in the C-terminal region. A phylogenetic tree, a multiple sequence alignment, as well as a modelled 3D-structure were constructed and they all reveal the ApTreh-1 similarity to other insect trehalases, i.e. the two signature motifs 179PGGRFRELYYWDTY192 and 479QWDFPNAWPP489, a glycine-rich region 549GGGGEY554, and the catalytic residues Asp336 and Glu538. The optimum enzyme activity occurs at 45 °C and pH 5.0, with Km and Vmax values of ~ 71 mM and ~ 126 µmol/min/mg, respectively. The present structural and functional characterization of soluble A. pisum trehalase enters the development of new strategies to control the aphids pest without significant risk for non-target organisms and human health.
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13
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Tsukamoto K, Ariki S, Nakazawa M, Sakamoto T, Ueda M. Novel cold-adapted raw-starch digesting α-amylases from Eisenia fetida: Gene cloning, expression, and characterization. BIOTECHNOLOGY REPORTS 2021; 31:e00662. [PMID: 34557389 PMCID: PMC8446577 DOI: 10.1016/j.btre.2021.e00662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/01/2021] [Accepted: 07/28/2021] [Indexed: 11/25/2022]
Abstract
There have been few reports about gene cloning and expression of α-amylases from E. fetida. Ef-Amy I and II were shown to 89% identity of amino acid sequences. The catalytically important residues of α-amylase of GH family 13 were conserved in Ef-amy I and II. The substrate specificities of rEf-Amy I and II were dissimilar. It found that rEf-Amy I and II could be possible use for simultaneous saccharification and fermentation process.
We identified the raw-starch-digesting α-amylase genes a earthworm Eisenia fetid α amylase I and II (Ef-Amy I and Ef-Amy II). Each gene consists of 1,530 base pairs (bp) that encode proteins of 510 amino acids, as indicated by the corresponding mRNA sequences. Ef-Amy I and II showed an 89% amino acid identity. The amino acid sequences of Ef-Amy I and II were similar to those of the α-amylases from porcine pancreas, human pancreas, Tenebrio molitor, Oryctolagus cuniculus, and Xenopus (Silurana) tropicalis. Each gene encoding mature Ef-Amy I and II was expressed in the GS115 strain of Pichia pastoris. The molecular masses of the recombinant Ef-Amy I and II were 57 kDa each, and catalytically important residues of α-amylases of the GH family 13 were conserved in both proteins. These amylases exhibited raw-starch-digesting activity at 4 °C. The substrate specificities of rEf-Amy I and II were dissimilar. rEf-Amy I and II were shown to be active even in 40% ethanol, 4 M NaCl, and 4 M KCl.
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14
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Feller G, Bonneau M, Da Lage JL. Amyrel, a novel glucose-forming α-amylase from Drosophila with 4-α-glucanotransferase activity by disproportionation and hydrolysis of maltooligosaccharides. Glycobiology 2021; 31:1134-1144. [PMID: 33978737 DOI: 10.1093/glycob/cwab036] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 11/12/2022] Open
Abstract
The α-amylase paralogue Amyrel present in true flies (Diptera Muscomorpha) has been classified as a glycoside hydrolase in CAZy family GH13 on the basis of its primary structure. Here we report that, in fact, Amyrel is currently unique amongst Animals as it possesses both the hydrolytic α-amylase activity (EC 3.2.1.1) and a 4-α-glucanotransferase (EC 2.4.1.25) transglycosylation activity. Amyrel reacts specifically on α-(1-4) glycosidic bonds of starch and related polymers but produces a complex mixture of maltooligosaccharides, in sharp contrast with canonical animal α-amylases. With model maltooligosaccharides G2 (maltose) to G7, the Amyrel reaction starts by a disproportionation leading to Gn-1 and Gn + 1 products, which become themselves substrates for new disproportionation cycles. As a result, all detectable odd- and even-numbered maltooligosaccharides at least up to G12 were observed. However, hydrolysis of these products proceeds simultaneously, as shown by p-nitrophenyl-tagged oligosaccharides and microcalorimetry, and upon prolonged reaction, glucose is the major end product followed by maltose. The main structural determinant of these atypical activities was found to be a Gly-His-Gly-Ala deletion in the so-called flexible loop bordering the active site. Indeed, engineering this deletion in pig pancreatic and D. melanogaster α-amylases results in reaction patterns similar to those of Amyrel. It is proposed that this deletion provides more freedom to the substrate for subsites occupancy and allows a less constrained action pattern resulting in versatile activities at the active site.
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Affiliation(s)
- Georges Feller
- Laboratory of Biochemistry, Center for Protein Engineering-InBioS, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - Magalie Bonneau
- UMR 9191 Evolution, Génomes, Comportement et Ecologie, CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, F-91198 Gif-sur-Yvette, France
| | - Jean-Luc Da Lage
- Laboratory of Biochemistry, Center for Protein Engineering-InBioS, University of Liège, B-4000 Liège-Sart Tilman, Belgium.,UMR 9191 Evolution, Génomes, Comportement et Ecologie, CNRS, IRD, Université Paris-Sud, Université Paris-Saclay, F-91198 Gif-sur-Yvette, France
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15
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Lakshmi SA, Shafreen RB, Priyanga A, Shiburaj S, Pandian SK. A highly divergent α-amylase from Streptomyces spp.: An evolutionary perspective. Int J Biol Macromol 2020; 163:2415-2428. [PMID: 32961188 DOI: 10.1016/j.ijbiomac.2020.09.103] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 08/01/2020] [Accepted: 09/15/2020] [Indexed: 11/18/2022]
Abstract
The present study deals with the genetic changes observed in the protein sequence of an α-amylase from Streptomyces spp. and its structural homologs from Pseudoalteromonas haloplanktis, invertebrates and mammals. The structural homologs are renowned for their important features such as chloride binding triad and a serine-protease like catalytic triad (a triad which is reported to be strictly conserved in all chloride-dependent α-amylases). These conserved regions are essential for allosteric activation of enzyme and conformational stability, respectively. An evaluation of these distinctive features in Streptomyces α-amylases revealed the role of mutations in conserved regions and evolution of chloride-independent α-amylases in Streptomyces spp. Besides, the study also discovers a highly divergent α-amylase from Streptomyces spp. which varies greatly even within the homologs of the same genus. Another very important feature is the number of disulfide bridges in which the structural homologs own eight Cys residues to form four disulfide bridges whereas Streptomyces α-amylases possess only seven Cys to form three disulfide bridges. The study also highlights the unique evolution of carbohydrate binding module 20 domain (CBM20 also known as raw starch binding domain or E domain) in Streptomyces α-amylases which is completely absent in α-amylases of other structural homologs.
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Affiliation(s)
- Selvaraj Alagu Lakshmi
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630003, Tamil Nadu, India
| | | | - Appasamy Priyanga
- Department of Biotechnology, Alagappa University, Science Campus, Karaikudi 630003, Tamil Nadu, India
| | - Sugathan Shiburaj
- Division of Microbiology, Jawaharlal Nehru Tropical Botanic Garden and Research Institute, Palode, Thiruvananthapuram, Kerala 695562, India; Department of Botany, University of Kerala, Kariavattom, Thiruvananthapuram, Kerala 695581, India
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16
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Plaks JG, Brewer JA, Jacobsen NK, McKenna M, Uzarski JR, Lawton TJ, Filocamo SF, Kaar JL. Rosetta-Enabled Structural Prediction of Permissive Loop Insertion Sites in Proteins. Biochemistry 2020; 59:3993-4002. [PMID: 32970423 DOI: 10.1021/acs.biochem.0c00533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
While loop motifs frequently play a major role in protein function, our understanding of how to rationally engineer proteins with novel loop domains remains limited. In the absence of rational approaches, the incorporation of loop domains often destabilizes proteins, thereby requiring massive screening and selection to identify sites that can accommodate loop insertion. We developed a computational strategy for rapidly scanning the entire structure of a scaffold protein to determine the impact of loop insertion at all possible amino acid positions. This approach is based on the Rosetta kinematic loop modeling protocol and was demonstrated by identifying sites in lipase that were permissive to insertion of the LAP peptide. Interestingly, the identification of permissive sites was dependent on the contribution of the residues in the near-loop environment on the Rosetta score and did not correlate with conventional structural features (e.g., B-factors). As evidence of this, several insertion sites (e.g., following residues 17, 47-49, and 108), which were predicted and confirmed to be permissive, interrupted helices, while others (e.g., following residues 43, 67, 116, 119, and 121), which are situated in loop regions, were nonpermissive. This approach was further shown to be predictive for β-glucosidase and human phosphatase and tensin homologue (PTEN), and to facilitate the engineering of insertion sites through in silico mutagenesis. By enabling the design of loop-containing protein libraries with high probabilities of soluble expression, this approach has broad implications in many areas of protein engineering, including antibody design, improving enzyme activity, and protein modification.
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Affiliation(s)
- Joseph G Plaks
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Jeff A Brewer
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Nicole K Jacobsen
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Michael McKenna
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
| | - Joshua R Uzarski
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Timothy J Lawton
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Shaun F Filocamo
- U.S. Army Combat Capabilities Development Command Soldier Center, Natick, Massachusetts 01760, United States
| | - Joel L Kaar
- Department of Chemical and Biological Engineering, University of Colorado, Boulder, Boulder, Colorado 80309, United States
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17
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Hirano Y, Tsukamoto K, Ariki S, Naka Y, Ueda M, Tamada T. X-ray crystallographic structural studies of α-amylase I from Eisenia fetida. Acta Crystallogr D Struct Biol 2020; 76:834-844. [DOI: 10.1107/s2059798320010165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 07/23/2020] [Indexed: 11/11/2022] Open
Abstract
The earthworm Eisenia fetida possesses several cold-active enzymes, including α-amylase, β-glucanase and β-mannanase. E. fetida possesses two isoforms of α-amylase (Ef-Amy I and II) to digest raw starch. Ef-Amy I retains its catalytic activity at temperatures below 10°C. To identify the molecular properties of Ef-Amy I, X-ray crystal structures were determined of the wild type and of the inactive E249Q mutant. Ef-Amy I has structural similarities to mammalian α-amylases, including the porcine pancreatic and human pancreatic α-amylases. Structural comparisons of the overall structures as well as of the Ca2+-binding sites of Ef-Amy I and the mammalian α-amylases indicate that Ef-Amy I has increased structural flexibility and more solvent-exposed acidic residues. These structural features of Ef-Amy I may contribute to its observed catalytic activity at low temperatures, as many cold-adapted enzymes have similar structural properties. The structure of the substrate complex of the inactive mutant of Ef-Amy I shows that a maltohexaose molecule is bound in the active site and a maltotetraose molecule is bound in the cleft between the N- and C-terminal domains. The recognition of substrate molecules by Ef-Amy I exhibits some differences from that observed in structures of human pancreatic α-amylase. This result provides insights into the structural modulation of the recognition of substrates and inhibitors.
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18
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Lim J, Pullicin AJ. Oral carbohydrate sensing: Beyond sweet taste. Physiol Behav 2019; 202:14-25. [DOI: 10.1016/j.physbeh.2019.01.021] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/15/2019] [Accepted: 01/23/2019] [Indexed: 01/28/2023]
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19
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Cloning and characterization of trehalase: a conserved glycosidase from oriental midge, Chironomus ramosus. 3 Biotech 2018; 8:352. [PMID: 30105177 DOI: 10.1007/s13205-018-1376-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 07/27/2018] [Indexed: 12/14/2022] Open
Abstract
Insect trehalase is a multiferous enzyme, crucial for normal physiological functions as well as under stress conditions. In this report, we present a fundamental study of the trehalase gene segment (1587 bp) from Chironomus ramosus (CrTre) encoding for 529 amino acids, using appropriate bioinformatics tools. C. ramosus, a tropical midge is an emerging animal model to investigate the consequences of environmental stresses. We observed that CrTre belongs to GH family 37 in the CAZy database and possess 57-92% identity to dipteran trehalases. In silico characterization provided information regarding the structural, functional and evolutionary aspects of midge trehalase. In the phylogenetic tree, CrTre clustered with the soluble dipteran trehalases. Moreover, domain functional characterization of the deduced protein sequence by InterProScan (IPR001661), ProSite (PS00927 and PS00928) and Pfam (PF01204) indicated presence of highly conserved signature motifs which are important for the identification of trehalase superfamily. Furthermore, the instability index of CrTre was predicted to be < 40 suggesting its in vivo stability while, the high aliphatic index indicated towards its thermal stability (index value 71-81). The modelled 3D tertiary structure of CrTre depicts a (α/α)6 barrel toroidal core. The catalytic domain of the enzyme comprised Glu424 and Asp226 as the putative active site residues. Interestingly, the conserved motifs were observed to be formed by the flexible loopy regions in the tertiary structure. This study revealed essential sequence features of the midge trehalase and offers better insights into the structural aspects of this enzyme which can be correlated with its function.
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20
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Sun J, Dong S, Wu Y, Zhao H, Li X, Gao W. Inhibitor discovery from pomegranate rind for targeting human salivary α-amylase. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2164-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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21
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Villa-Rodriguez JA, Kerimi A, Abranko L, Tumova S, Ford L, Blackburn RS, Rayner C, Williamson G. Acute metabolic actions of the major polyphenols in chamomile: an in vitro mechanistic study on their potential to attenuate postprandial hyperglycaemia. Sci Rep 2018; 8:5471. [PMID: 29615674 PMCID: PMC5882934 DOI: 10.1038/s41598-018-23736-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 03/20/2018] [Indexed: 01/19/2023] Open
Abstract
Transient hyperglycaemia is a risk factor for type 2 diabetes and endothelial dysfunction, especially in subjects with impaired glucose tolerance. Nutritional interventions and strategies for controlling postprandial overshoot of blood sugars are considered key in preventing progress to the disease state. We have identified apigenin-7-O-glucoside, apigenin, and (Z) and (E)−2-hydroxy-4-methoxycinnamic acid glucosides as the active (poly)phenols in Chamomile (Matricaria recutita) able to modulate carbohydrate digestion and absorption in vitro as assessed by inhibition of α-amylase and maltase activities. The latter two compounds previously mistakenly identified as ferulic acid hexosides were purified and characterised and studied for their contribution to the overall bioactivity of chamomile. Molecular docking studies revealed that apigenin and cinnamic acids present totally different poses in the active site of human α-amylase. In differentiated Caco-2/TC7 cell monolayers, apigenin-7-O-glucoside and apigenin strongly inhibited D-[U-14C]-glucose and D-[U-14C]-sucrose transport, and less effectively D-[U-14C]-fructose transport. Inhibition of D-[U-14C]-glucose transport by apigenin was stronger under Na+-depleted conditions, suggesting interaction with the GLUT2 transporter. Competitive binding studies with molecular probes indicate apigenin interacts primarily at the exofacial-binding site of GLUT2. Taken together, the individual components of Chamomile are promising agents for regulating carbohydrate digestion and sugar absorption at the site of the gastrointestinal tract.
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Affiliation(s)
| | - Asimina Kerimi
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK
| | - Laszlo Abranko
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK.,Szent István University, Faculty of Food Science, Department of Applied Chemistry, 29-43 Villányi, Budapest, H-1118, Hungary
| | - Sarka Tumova
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK
| | - Lauren Ford
- School of Chemistry, University of Leeds, Leeds, LS2 9JT, UK.,School of Design, University of Leeds, Leeds, LS2 9JT, UK
| | | | | | - Gary Williamson
- School of Food Science and Nutrition, University of Leeds, Leeds, LS2 9JT, UK.
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Talungchit S, Buajeeb W, Lerdtripop C, Surarit R, Chairatvit K, Roytrakul S, Kobayashi H, Izumi Y, Khovidhunkit SOP. Putative salivary protein biomarkers for the diagnosis of oral lichen planus: a case-control study. BMC Oral Health 2018. [PMID: 29534707 PMCID: PMC5851270 DOI: 10.1186/s12903-018-0504-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Salivary protein biomarkers for screening and diagnosis of oral lichen planus (OLP) are not well-defined. The objective of this study was to identify putative protein biomarkers for OLP using proteomic approaches. METHODS Pooled unstimulated whole saliva was collected from five OLP patients and five healthy control participants. Saliva samples were then subjected to two-dimensional gel electrophoresis, followed by mass spectrometry to identify putative protein biomarkers. Subsequently, a subset of these putative biomarkers were validated in 24 OLP patients and 24 age-matched healthy control subjects, using an enzyme-linked immunosorbent assay (ELISA). Immunoblotting analyses were then performed in 3 pairs of age- and sex-matched OLP patients and healthy controls to confirm results from the ELISA study. RESULTS Thirty-one protein spots were identified, corresponding to 20 unique proteins. Notably, fibrinogen fragment D and complement component C3c exhibited increased expression in OLP patients, while cystatin SA exhibited decreased expression in OLP patients, compared with healthy control subjects. ELISA analyses indicated increased expression of fibrinogen fragment D and complement component C3c, and decreased expression of cystatin SA, in the saliva of OLP patients. Statistical differences in the expression of salivary complement C3c were observed between OLP patients and healthy control subjects. Immunoblotting analyses confirmed the results of our ELISA study. CONCLUSION Complement C3c, fibrinogen fragment D and cystatin SA may serve as salivary biomarkers for screening and/or diagnosis of OLP.
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Affiliation(s)
- Sineepat Talungchit
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand.,Department of Oral Surgery and Oral Medicine, Faculty of Dentistry, Srinakharinwirot University, Bangkok, Thailand
| | - Waranun Buajeeb
- Department of Oral Medicine and Periodontology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Chotima Lerdtripop
- Department of Advanced General Dentistry, Faculty of Dentistry, Mahidol University, 6 Yodhi St., Rajthewee, Bangkok, 10400, Thailand
| | - Rudee Surarit
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Kongthawat Chairatvit
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok, Thailand
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathumthani, Thailand
| | - Hiroaki Kobayashi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuichi Izumi
- Department of Periodontology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,Global Center of Excellence Program for Tooth and Bone Research, Tokyo Medical and Dental University, Tokyo, Japan
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23
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Vahidi SH, Bozorgmehr MR, Morsali A, Beyramabadi SA. Does high pressure have any effect on the structure of alpha amylase and its ability to binding to the oligosaccharides having 3-7 residues? Molecular dynamics study. J Mol Graph Model 2018; 80:85-94. [PMID: 29328994 DOI: 10.1016/j.jmgm.2018.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 01/02/2018] [Accepted: 01/04/2018] [Indexed: 10/18/2022]
Abstract
Studies have shown that deletion of amino acids from the C-terminus of amylase do not alter its amylolytic activity. Although high pressure is used to modify the structure and function of this enzyme, the effects of high pressures on the structures of the wild-type and truncated amylases have not yet been understood at the molecular level. Using molecular dynamic simulations and docking, we studied the structures of wild-type and truncated Taka-amylases at high pressures (1000-4000 bar). To construct the truncated Taka-amylase, 50 and 100 C-terminal residues were removed in two separate steps. Results of simulation showed that, although the overall shape partly agglomerates with rise in pressure, high pressure fails to modify the structure of the barrel-like region of the β-sheet in the wild-type and truncated enzymes. A comparison of contact graphs revealed that the changes at the N-terminus were less extensive than those at the C-terminus. Further analysis showed that 10 regions of the secondary structures changed due to pressure change in wild-type amylase, of which 6 regions were associated with the loops and 4 with helix, while the structure of β-sheets remained unchanged. The docking of maltotriose, maltotetraose, maltopentaose, maltohexaose, and maltoheptaose with the averaged structures obtained from different simulations was conducted to characterize the influence of pressure on the activities of the wild-type and truncated enzymes. The results showed that maltoheptaose made hydrophobic contacts with residues Tyr238-Asp117-Tyr82-Leu166-Leu232-Tyr155 and hydrogen contacts with residues Asp233-Gly234-Asp206-Arg204-His296-Glu230. Similar results were obtained for other malto-oligosaccharides.
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Affiliation(s)
- S Hooman Vahidi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | | | - Ali Morsali
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
| | - S Ali Beyramabadi
- Department of Chemistry, Mashhad Branch, Islamic Azad University, Mashhad, Iran
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24
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Sun J, Dong S, Wu Y, Zhao H, Li X, Gao W. Oleanolic acid and ursolic acid as potential inhibitors of human salivary α-amylase: insights from in vitro assays and in silico simulations. J Mol Model 2017; 23:248. [PMID: 28766112 DOI: 10.1007/s00894-017-3416-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 07/12/2017] [Indexed: 11/24/2022]
Abstract
It is known that inhibiting α-amylase, an important enzyme in digestion of starch and glycogen, is a useful strategy for treating disorders in carbohydrate uptake. Two natural components distributed in many fruits and plants, oleanolic acid and ursolic acid, are endowed with important pharmacological activities and wide therapeutic possibilities. Until now, only a tiny fraction of their applications have been identified and exploited. Our in vitro inhibition studies demonstrated that oleanolic acid and ursolic acid non-competitively inhibit the activity and function of human salivary α-amylase. The molecular simulations revealed that oleanolic acid and ursolic acid interact with amino acid residues within the binding pocket of human salivary α-amylase, among which the side chain of Arg195 and Asp 197 was supposed to be important in imparting the inhibitory activity of triterpenoids. The present work will provide meaningful information for future development of functional drugs for the treatment of disorders in carbohydrate metabolism. Graphical abstract This work is valuable for providing a deeper insight into the interaction mechanism of oleanolic acid and ursolic acid with α-amylase.
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Affiliation(s)
- Jiachen Sun
- Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Shengjie Dong
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Yueting Wu
- Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China
| | - Hui Zhao
- Department of Physics, Tianjin Normal University, Tianjin, 300387, China
| | - Xia Li
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
| | - Wenyuan Gao
- Tianjin University of Traditional Chinese Medicine, Tianjin, 300193, China.
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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Shaik F, Kumar A. ZnO nanoparticles and their acarbose-capped nanohybrids as inhibitors for human salivary amylase. IET Nanobiotechnol 2017; 11:329-335. [PMID: 28476991 PMCID: PMC8676339 DOI: 10.1049/iet-nbt.2016.0115] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 07/30/2016] [Accepted: 08/15/2016] [Indexed: 04/05/2024] Open
Abstract
The authors report a controlled synthesis of biocompatible ZnO and acarbose-capped nanohybrids, and examined the inhibition activities of these nanosystems with human salivary α-amylase (HSA) activity. XRD measurements reveal ZnO present in wurtzite phase with hexagonal structure. The average size of ZnO particles for the two studied nanosystems was estimated to lie between 10 to 12 nm using Scherrer equation. These particles depict the onset of absorption at about 320 nm and the band-gap emission at about 370 nm, which are fairly blue shifted as compared with the bulk ZnO and have been understood due to the size quantisation effect. The inhibitory action of thioglycerol capped ZnO nanoparticles (SP1) and acarbose drug (used for diabetes type II) capped ZnO (SP2) for HSA was observed to 61 and72%, respectively. The inhibition activity of the SP1 alone was found to be very similar to that of acarbose and the coating of these particles with drug (SP2) demonstrated an enhancement in inhibition activity of the enzyme by about 30%. From the inhibition studies, it is confirmed that these nanosystems showed better inhibition activity at physiological temperature and pH. These nanosystems are projected to have potential applications in diabetes type II control.
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Affiliation(s)
- Firdoz Shaik
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore
| | - Anil Kumar
- Department of Chemistry, Indian Institute of Technology Roorkee, Roorkee 247 667, India.
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Molecular cloning and in silico studies of physiologically significant trehalase from Drosophila melanogaster. Int J Biol Macromol 2016; 92:282-292. [DOI: 10.1016/j.ijbiomac.2016.06.097] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Revised: 06/22/2016] [Accepted: 06/30/2016] [Indexed: 02/04/2023]
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Cockburn D, Wilkens C, Dilokpimol A, Nakai H, Lewińska A, Abou Hachem M, Svensson B. Using Carbohydrate Interaction Assays to Reveal Novel Binding Sites in Carbohydrate Active Enzymes. PLoS One 2016; 11:e0160112. [PMID: 27504624 PMCID: PMC4978508 DOI: 10.1371/journal.pone.0160112] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 07/13/2016] [Indexed: 01/23/2023] Open
Abstract
Carbohydrate active enzymes often contain auxiliary binding sites located either on independent domains termed carbohydrate binding modules (CBMs) or as so-called surface binding sites (SBSs) on the catalytic module at a certain distance from the active site. The SBSs are usually critical for the activity of their cognate enzyme, though they are not readily detected in the sequence of a protein, but normally require a crystal structure of a complex for their identification. A variety of methods, including affinity electrophoresis (AE), insoluble polysaccharide pulldown (IPP) and surface plasmon resonance (SPR) have been used to study auxiliary binding sites. These techniques are complementary as AE allows monitoring of binding to soluble polysaccharides, IPP to insoluble polysaccharides and SPR to oligosaccharides. Here we show that these methods are useful not only for analyzing known binding sites, but also for identifying new ones, even without structural data available. We further verify the chosen assays discriminate between known SBS/CBM containing enzymes and negative controls. Altogether 35 enzymes are screened for the presence of SBSs or CBMs and several novel binding sites are identified, including the first SBS ever reported in a cellulase. This work demonstrates that combinations of these methods can be used as a part of routine enzyme characterization to identify new binding sites and advance the study of SBSs and CBMs, allowing them to be detected in the absence of structural data.
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Affiliation(s)
- Darrell Cockburn
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Casper Wilkens
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Adiphol Dilokpimol
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Hiroyuki Nakai
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Anna Lewińska
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Maher Abou Hachem
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
| | - Birte Svensson
- Enzyme and Protein Chemistry, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark
- * E-mail:
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28
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Claisse G, Feller G, Bonneau M, Da Lage JL. A single amino-acid substitution toggles chloride dependence of the alpha-amylase paralog amyrel in Drosophila melanogaster and Drosophila virilis species. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2016; 75:70-77. [PMID: 27312592 DOI: 10.1016/j.ibmb.2016.06.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 06/01/2016] [Accepted: 06/10/2016] [Indexed: 06/06/2023]
Abstract
In animals, most α-amylases are chloride-dependent enzymes. A chloride ion is required for allosteric activation and is coordinated by one asparagine and two arginine side chains. Whereas the asparagine and one arginine are strictly conserved, the main chloride binding arginine is replaced by a glutamine in some rare instances, resulting in the loss of chloride binding and activation. Amyrel is a distant paralogue of α-amylase in Diptera, which was not characterized biochemically to date. Amyrel shows both substitutions depending on the species. In Drosophila melanogaster, an arginine is present in the sequence but in Drosophila virilis, a glutamine occurs at this position. We have investigated basic enzymological parameters and the dependence to chloride of Amyrel of both species, produced in yeast, and in mutants substituting arginine to glutamine or glutamine to arginine. We found that the amylolytic activity of Amyrel is about thirty times weaker than the classical Drosophila α-amylase, and that the substitution of the arginine by a glutamine in D. melanogaster suppressed the chloride-dependence but was detrimental to activity. In contrast, changing the glutamine into an arginine rendered D. virilis Amyrel chloride-dependent, and interestingly, significantly increased its catalytic efficiency. These results show that the chloride ion is not mandatory for Amyrel but stimulates the reaction rate. The possible phylogenetic origin of the arginine/glutamine substitution is also discussed.
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Affiliation(s)
- Gaëlle Claisse
- UMR 9191 Evolution, Génomes, Comportement et Ecologie, CNRS, F-91198 Gif-sur-Yvette, France; Univ. Paris-Sud, F-91405 Orsay Cedex, France
| | - Georges Feller
- Laboratory of Biochemistry, Center for Protein Engineering, University of Liège, B-4000 Liège-Sart Tilman, Belgium
| | - Magalie Bonneau
- UMR 9191 Evolution, Génomes, Comportement et Ecologie, CNRS, F-91198 Gif-sur-Yvette, France; Univ. Paris-Sud, F-91405 Orsay Cedex, France
| | - Jean-Luc Da Lage
- UMR 9191 Evolution, Génomes, Comportement et Ecologie, CNRS, F-91198 Gif-sur-Yvette, France; Univ. Paris-Sud, F-91405 Orsay Cedex, France.
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Homoki JR, Nemes A, Fazekas E, Gyémánt G, Balogh P, Gál F, Al-Asri J, Mortier J, Wolber G, Babinszky L, Remenyik J. Anthocyanin composition, antioxidant efficiency, and α-amylase inhibitor activity of different Hungarian sour cherry varieties (Prunus cerasus L.). Food Chem 2016; 194:222-9. [DOI: 10.1016/j.foodchem.2015.07.130] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 07/27/2015] [Accepted: 07/28/2015] [Indexed: 11/26/2022]
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30
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Al-Asri J, Fazekas E, Lehoczki G, Perdih A, Görick C, Melzig MF, Gyémánt G, Wolber G, Mortier J. From carbohydrates to drug-like fragments: Rational development of novel α-amylase inhibitors. Bioorg Med Chem 2015; 23:6725-32. [DOI: 10.1016/j.bmc.2015.09.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Revised: 08/31/2015] [Accepted: 09/03/2015] [Indexed: 12/21/2022]
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31
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Commin C, Aumont-Nicaise M, Claisse G, Feller G, Da Lage JL. Enzymatic characterization of recombinant α-amylase in the Drosophila melanogaster species subgroup: is there an effect of specialization on digestive enzyme? Genes Genet Syst 2014; 88:251-9. [PMID: 24463528 DOI: 10.1266/ggs.88.251] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
We performed a comparative study on the enzymological features of purified recombinant α-amylase of three species belonging to the Drosophila melanogaster species subgroup: D. melanogaster, D. erecta and D. sechellia. D. erecta and D. sechellia are specialist species, with host plant Pandanus candelabrum (Pandanaceae) and Morinda citrifolia (Rubiaceae), respectively. The temperature optima were around 57-60℃ for the three species. The pH optima were 7.2 for D. melanogaster, 8.2 for D. erecta and 8.5 for D. sechellia. The kcat and Km were also estimated for each species with different substrates. The specialist species D. erecta and D. sechellia display a higher affinity for starch than D. melanogaster. α-Amylase activity is higher on starch than on glycogen in all species. α-Amylases of D. erecta and D. sechellia have a higher activity on maltooligosaccharides (G6 and G7) than on starch, contrary to D. melanogaster. Such differences in the enzymological features between the species might reflect adaptation to different ecological niches and feeding habits.
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Affiliation(s)
- Céline Commin
- UPR 9034 Evolution, Génomes et Spéciation, CNRS, F-91198 Gif-sur-Yvette, France and Université Paris-Sud
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Ochiai A, Sugai H, Harada K, Tanaka S, Ishiyama Y, Ito K, Tanaka T, Uchiumi T, Taniguchi M, Mitsui T. Crystal structure of α-amylase from Oryza sativa: molecular insights into enzyme activity and thermostability. Biosci Biotechnol Biochem 2014; 78:989-97. [PMID: 25036124 DOI: 10.1080/09168451.2014.917261] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
AmyI-1 is an α-amylase from Oryza sativa (rice) and plays a crucial role in degrading starch in various tissues and at various growth stages. This enzyme is a glycoprotein with an N-glycosylated carbohydrate chain, a unique characteristic among plant α-amylases. In this study, we report the first crystal structure of AmyI-1 at 2.2-Å resolution. The structure consists of a typical (β/α)8-barrel, which is well-conserved among most α-amylases in the glycoside hydrolase family-13. Structural superimposition indicated small variations in the catalytic domain and carbohydrate-binding sites between AmyI-1 and barley α-amylases. By contrast, regions around the N-linked glycosylation sites displayed lower conservation of amino acid residues, including Asn-263, Asn-265, Thr-307, Asn-342, Pro-373, and Ala-374 in AmyI-1, which are not conserved in barley α-amylases, suggesting that these residues may contribute to the construction of the structure of glycosylated AmyI-1. These results increase the depths of our understanding of the biological functions of AmyI-1.
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Affiliation(s)
- Akihito Ochiai
- a Faculty of Engineering, Department of Materials Science and Technology , Niigata University , Niigata , Japan
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Funane K, Ishii T, Terasawa K, Yamamoto T, Kobayashi M. Construction of Chimeric Glucansucrases for Analyzing Substrate-binding Regions That Affect the Structure of Glucan Products. Biosci Biotechnol Biochem 2014; 68:1912-20. [PMID: 15388967 DOI: 10.1271/bbb.68.1912] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A gene that encodes dextransucrase S (dsrS) from Leuconostoc mesenteroides NRRL B-512F encodes a glucansucrase dextransucrase S (DSRS) which mainly produces water-soluble glucan (dextran), while the dsrT5 gene derived from dsrT of the B-512F strain encodes an enzyme dextransucrase T5 (DSRT5), which mainly produces water-insoluble glucan. Tyr340-Asn510 of DSRS and Tyr307-Asn477 of DSRT5 (Site 1), Lys696-Gly768 of DSRS and Lys668-Gly740 of DSRT5 (Site 2), and Asn917-Lys1131 of DSRS and Asn904-Lys1118 of DSRT5 (Site 3) were exchanged and six different chimeric enzymes were constructed. Water-soluble glucan produced by recombinant DSRS was composed of 64% 6-linked glucopyranoside (Glcp), 9% 3,6-linked Glcp, and 13% 4-linked Glcp. Water-insoluble glucan produced by recombinant DSRT5 was composed of 47% 6-linked Glcp and 43% 3-linked Glcp. All of the chimeric enzymes produced glucans different from the ones produced by their parental enzymes. Some of the glucans produced by chimeric enzymes were extremely changed. The Site 1 chimeric enzyme of DSRS (STS1) produced water-soluble glucan composed mostly of 6-linked Glcp. That of DSRT5 (TST1) produced water-insoluble glucan composed mostly of 4-linked Glcp. The Site 3 chimeric enzyme of DSRS (STS3) produced mainly water-insoluble glucan, DSRT5 (TST3) produced mainly water-soluble glucans, and all of the glucan fractions consisted of 3-Glcp, 4-Glcp, and 6-Glcp. The amounts of the three linkages in the water-soluble glucan produced by TST3 were about 1:1:1. Site 1 was assumed to be important for making or avoiding making alpha-1,4 linkages, while Site 3 was assumed to be important for determining the kinds of glucosyl linkages made.
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Affiliation(s)
- Kazumi Funane
- National Food Research Institute, Tsukuba, Ibaraki, Japan.
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34
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Janeček Š, Svensson B, MacGregor EA. α-Amylase: an enzyme specificity found in various families of glycoside hydrolases. Cell Mol Life Sci 2014; 71:1149-70. [PMID: 23807207 PMCID: PMC11114072 DOI: 10.1007/s00018-013-1388-z] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 05/27/2013] [Accepted: 05/27/2013] [Indexed: 10/26/2022]
Abstract
α-Amylase (EC 3.2.1.1) represents the best known amylolytic enzyme. It catalyzes the hydrolysis of α-1,4-glucosidic bonds in starch and related α-glucans. In general, the α-amylase is an enzyme with a broad substrate preference and product specificity. In the sequence-based classification system of all carbohydrate-active enzymes, it is one of the most frequently occurring glycoside hydrolases (GH). α-Amylase is the main representative of family GH13, but it is probably also present in the families GH57 and GH119, and possibly even in GH126. Family GH13, known generally as the main α-amylase family, forms clan GH-H together with families GH70 and GH77 that, however, contain no α-amylase. Within the family GH13, the α-amylase specificity is currently present in several subfamilies, such as GH13_1, 5, 6, 7, 15, 24, 27, 28, 36, 37, and, possibly in a few more that are not yet defined. The α-amylases classified in family GH13 employ a reaction mechanism giving retention of configuration, share 4-7 conserved sequence regions (CSRs) and catalytic machinery, and adopt the (β/α)8-barrel catalytic domain. Although the family GH57 α-amylases also employ the retaining reaction mechanism, they possess their own five CSRs and catalytic machinery, and adopt a (β/α)7-barrel fold. These family GH57 attributes are likely to be characteristic of α-amylases from the family GH119, too. With regard to family GH126, confirmation of the unambiguous presence of the α-amylase specificity may need more biochemical investigation because of an obvious, but unexpected, homology with inverting β-glucan-active hydrolases.
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Affiliation(s)
- Štefan Janeček
- Laboratory of Protein Evolution, Institute of Molecular Biology, Slovak Academy of Sciences, Dúbravská cesta 21, 84551, Bratislava, Slovakia,
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35
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Housaindokht MR, Bozorgmehr MR, Hosseini HE, Jalal R, Asoodeh A, Saberi M, Haratipour Z, Monhemi H. Structural properties of the truncated and wild types of Taka-amylase: A molecular dynamics simulation and docking study. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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36
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GOUVEIA NEIREMDE, ALBUQUERQUE CIBELELDE, ESPINDOLA LAILAS, ESPINDOLA FOUEDS. Pouteria ramiflora extract inhibits salivary amylolytic activity and decreases glycemic level in mice. AN ACAD BRAS CIENC 2013; 85:1141-8. [DOI: 10.1590/s0001-37652013000300016] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Accepted: 02/27/2013] [Indexed: 12/12/2022] Open
Abstract
In this study, extracts of plant species from the Cerrado biome were assessed in order to find potential inhibitors of human salivary alpha-amylase. The plants were collected and extracts were obtained from leaves, bark, and roots. We performed a preliminary phytochemical analysis and a screening for salivar alpha-amylase inhibitory activity. Only three botanical families (Sapotaceae, Sapindaceae and Flacourtiaceae) and 16 extracts showed a substantial inhibition (>75%) of alpha-amylase. The ethanolic extracts of Pouteria ramiflora obtained from stem barks and root barks decreased amylolytic activity above 95% at a final concentration of 20 µg/mL. Thus, adult male Swiss mice were treated orally with P. ramiflora in acute toxicity and glycemic control studies. Daily administration with 25, 50 and 100 mg/kg of aqueous extract of P. ramiflora for eight days can reduce significantly body weight and blood glucose level in mice. These data suggest that the crude polar extract of P. ramiflora decreases salivary amylolytic activity while lowering the blood levels of glucose.
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37
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Fraccalvieri D, Tiberti M, Pandini A, Bonati L, Papaleo E. Functional annotation of the mesophilic-like character of mutants in a cold-adapted enzyme by self-organising map analysis of their molecular dynamics. MOLECULAR BIOSYSTEMS 2013; 8:2680-91. [PMID: 22802143 DOI: 10.1039/c2mb25192b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple comparison of the Molecular Dynamics (MD) trajectories of mutants in a cold-adapted α-amylase (AHA) could be used to elucidate functional features required to restore mesophilic-like activity. Unfortunately it is challenging to identify the different dynamic behaviors and correctly relate them to functional activity by routine analysis. We here employed a previously developed and robust two-stage approach that combines Self-Organising Maps (SOMs) and hierarchical clustering to compare conformational ensembles of proteins. Moreover, we designed a novel strategy to identify the specific mutations that more efficiently convert the dynamic signature of the psychrophilic enzyme (AHA) to that of the mesophilic counterpart (PPA). The SOM trained on AHA and its variants was used to classify a PPA MD ensemble and successfully highlighted the relationships between the flexibilities of the target enzyme and of the different mutants. Moreover the local features of the mutants that mostly influence their global flexibility in a mesophilic-like direction were detected. It turns out that mutations of the cold-adapted enzyme to hydrophobic and aromatic residues are the most effective in restoring the PPA dynamic features and could guide the design of more mesophilic-like mutants. In conclusion, our strategy can efficiently extract specific dynamic signatures related to function from multiple comparisons of MD conformational ensembles. Therefore, it can be a promising tool for protein engineering.
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38
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Forcella M, Mozzi A, Bigi A, Parenti P, Fusi P. Molecular cloning of soluble trehalase from Chironomus riparius larvae, its heterologous expression in Escherichia coli and bioinformatic analysis. ARCHIVES OF INSECT BIOCHEMISTRY AND PHYSIOLOGY 2012; 81:77-89. [PMID: 22851493 DOI: 10.1002/arch.21041] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Trehalase is involved in the control of trehalose concentration, the main blood sugar in insects. Here, we describe the molecular cloning of the cDNA encoding for the soluble form of the trehalase from the midge larvae of Chironomus riparius, a well-known bioindicator of the quality of freshwater environments. Molecular cloning was achieved through multiple alignment of Diptera trehalase sequences, allowing the synthesis of internal homology-based primers; the complete open reading frame(ORF) was subsequently obtained through RACE-PCR(where RACE is rapid amplification of cDNA ends). The cDNA contained the 5' untranslated region (UTR), the 3' UTR including a poly(A) tail and the ORF of 1,725 bp consisting of 574 amino acid residues with a predicted molecular mass of 65,778 Da. Recombinant trehalase was successfully expressed in Escherichia coli as a His-tagged protein and purified on Ni-NTA affinity chromatography. Primary structure analysis showed a series of characteristic features shared by all insect trehalases, while three-dimensional structure prediction yielded the typical glucosidase fold, the two key residues involved in the catalytic mechanism being conserved. Production of recombinant insect trehalases opens the way to structural characterizations of the catalytic site, which might represent, among others, an element for reconsidering the enzyme as a target in pest insects' control.
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Affiliation(s)
- Matilde Forcella
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza, Milan, Italy
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39
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Arab-Jaziri F, Bissaro B, Barbe S, Saurel O, Débat H, Dumon C, Gervais V, Milon A, André I, Fauré R, O’Donohue MJ. Functional roles of H98 and W99 and β2α2 loop dynamics in the α-l
-arabinofuranosidase from Thermobacillus xylanilyticus. FEBS J 2012; 279:3598-3611. [DOI: 10.1111/j.1742-4658.2012.08720.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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40
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Papaleo E, Pasi M, Tiberti M, De Gioia L. Molecular dynamics of mesophilic-like mutants of a cold-adapted enzyme: insights into distal effects induced by the mutations. PLoS One 2011; 6:e24214. [PMID: 21915299 PMCID: PMC3168468 DOI: 10.1371/journal.pone.0024214] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2011] [Accepted: 08/02/2011] [Indexed: 11/18/2022] Open
Abstract
Networks and clusters of intramolecular interactions, as well as their "communication" across the three-dimensional architecture have a prominent role in determining protein stability and function. Special attention has been dedicated to their role in thermal adaptation. In the present contribution, seven previously experimentally characterized mutants of a cold-adapted α-amylase, featuring mesophilic-like behavior, have been investigated by multiple molecular dynamics simulations, essential dynamics and analyses of correlated motions and electrostatic interactions. Our data elucidate the molecular mechanisms underlying the ability of single and multiple mutations to globally modulate dynamic properties of the cold-adapted α-amylase, including both local and complex unpredictable distal effects. Our investigation also shows, in agreement with the experimental data, that the conversion of the cold-adapted enzyme in a warm-adapted variant cannot be completely achieved by the introduction of few mutations, also providing the rationale behind these effects. Moreover, pivotal residues, which are likely to mediate the effects induced by the mutations, have been identified from our analyses, as well as a group of suitable candidates for protein engineering. In fact, a subset of residues here identified (as an isoleucine, or networks of mesophilic-like salt bridges in the proximity of the catalytic site) should be considered, in experimental studies, to get a more efficient modification of the features of the cold-adapted enzyme.
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Affiliation(s)
- Elena Papaleo
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Milan, Italy.
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41
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Vieira DS, Ward RJ. Conformation analysis of a surface loop that controls active site access in the GH11 xylanase A from Bacillus subtilis. J Mol Model 2011; 18:1473-9. [PMID: 21785938 DOI: 10.1007/s00894-011-1172-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2011] [Accepted: 06/29/2011] [Indexed: 11/29/2022]
Abstract
Xylanases (EC 3.2.1.8 endo-1,4-glycosyl hydrolase) catalyze the hydrolysis of xylan, an abundant hemicellulose of plant cell walls. Access to the catalytic site of GH11 xylanases is regulated by movement of a short β-hairpin, the so-called thumb region, which can adopt open or closed conformations. A crystallographic study has shown that the D11F/R122D mutant of the GH11 xylanase A from Bacillus subtilis (BsXA) displays a stable "open" conformation, and here we report a molecular dynamics simulation study comparing this mutant with the native enzyme over a range of temperatures. The mutant open conformation was stable at 300 and 328 K, however it showed a transition to the closed state at 338 K. Analysis of dihedral angles identified thumb region residues Y113 and T123 as key hinge points which determine the open-closed transition at 338 K. Although the D11F/R122D mutations result in a reduction in local inter-intramolecular hydrogen bonding, the global energies of the open and closed conformations in the native enzyme are equivalent, suggesting that the two conformations are equally accessible. These results indicate that the thumb region shows a broader degree of energetically permissible conformations which regulate the access to the active site region. The R122D mutation contributes to the stability of the open conformation, but is not essential for thumb dynamics, i.e., the wild type enzyme can also adapt to the open conformation.
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Affiliation(s)
- Davi Serradella Vieira
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto - Universidade de São Paulo, Avenida dos Bandeirantes, 3900 - 14040-90 Ribeirão Preto, SP, Brazil.
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Cuyvers S, Dornez E, Delcour JA, Courtin CM. Occurrence and functional significance of secondary carbohydrate binding sites in glycoside hydrolases. Crit Rev Biotechnol 2011; 32:93-107. [DOI: 10.3109/07388551.2011.561537] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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43
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Park S, Hyun S, Yu J. Selective α-glucosidase substrates and inhibitors containing short aromatic peptidyl moieties. Bioorg Med Chem Lett 2011; 21:2441-4. [DOI: 10.1016/j.bmcl.2011.02.062] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 02/11/2011] [Accepted: 02/15/2011] [Indexed: 10/18/2022]
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Cuyvers S, Dornez E, Rezaei MN, Pollet A, Delcour JA, Courtin CM. Secondary substrate binding strongly affects activity and binding affinity of Bacillus subtilis and Aspergillus niger GH11 xylanases. FEBS J 2011; 278:1098-111. [PMID: 21261814 DOI: 10.1111/j.1742-4658.2011.08023.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The secondary substrate binding site (SBS) of Bacillus subtilis and Aspergillus niger glycoside hydrolase family 11 xylanases was studied by site-directed mutagenesis and evaluation of activity and binding properties of mutant enzymes on different substrates. Modification of the SBS resulted in an up to three-fold decrease in the relative activity of the enzymes on polymeric versus oligomeric substrates and highlighted the importance of several amino acids in the SBS forming hydrogen bonds or hydrophobic stacking interactions with substrates. Weakening of the SBS increased K(d) values by up to 70-fold in binding affinity tests using natural substrates. The impact that modifications in the SBS have both on activity and on binding affinity towards polymeric substrates clearly shows that such structural elements can increase the efficiency of these single domain enzymes on their natural substrates.
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Affiliation(s)
- Sven Cuyvers
- Laboratory of Food Chemistry and Biochemistry & Leuven Food Science and Nutrition Research Centre (LFoRCe), Katholieke Universiteit Leuven, Leuven, Belgium
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45
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Computer-aided subsite mapping of α-amylases. Carbohydr Res 2011; 346:410-5. [DOI: 10.1016/j.carres.2010.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Revised: 11/30/2010] [Accepted: 12/03/2010] [Indexed: 11/19/2022]
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46
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Pasi M, Riccardi L, Fantucci P, De Gioia L, Papaleo E. Dynamic properties of a psychrophilic alpha-amylase in comparison with a mesophilic homologue. J Phys Chem B 2009; 113:13585-95. [PMID: 19775158 DOI: 10.1021/jp900790n] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cold-active, chloride-dependent alpha-amylase from Pseudoalteromonas haloplanktis (AHA) is one of the best characterized psychrophilic enzymes, and shares high sequence and structural similarity with its mesophilic porcine counterpart (PPA). An atomic detail comparative analysis was carried out by performing more than 60 ns of multiple-replica explicit-solvent molecular dynamics simulations on the two enzymes in order to characterize the differences in ensemble properties and dynamics in solution between the two homologues. We find in both enzymes high flexibility clusters in the surroundings of the substrate-binding groove, primarily involving the long loops that protrude from the main domain's barrel structure. These loops are longer in PPA and extend further away from the core of the barrel, where the active site is located: essential fluctuations in PPA mainly affect the highly solvent-accessible portions of these loops, whereas AHA is characterized by greater flexibility in the immediate surroundings of the active site. Furthermore, detailed analysis of active-site dynamics has revealed that elements previously identified through X-ray crystallography as involved in substrate binding in both enzymes undergo concerted motions that may be linked to catalysis.
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Affiliation(s)
- Marco Pasi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, P.za della Scienza 2, 20126 Milan, Italy
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Pollet A, Vandermarliere E, Lammertyn J, Strelkov SV, Delcour JA, Courtin CM. Crystallographic and activity-based evidence for thumb flexibility and its relevance in glycoside hydrolase family 11 xylanases. Proteins 2009; 77:395-403. [PMID: 19422059 DOI: 10.1002/prot.22445] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Enzyme intramolecular mobility and conformational changes of loops in particular play a significant role in biocatalysis. In this respect, the highly conserved thumb loop of glycoside hydrolase family (GH) 11 xylanases is an intriguing and characteristic structural element, of which the true dynamic nature and function in catalysis is still unknown. Crystallographic analysis of the structure of a Bacillus subtilis xylanase A mutant, found as a dimer in an asymmetric unit, revealed that the thumb region can adopt an extended conformation, which is stabilized in the crystal lattice through intermolecular contacts. In contrast to the closed thumb conformation of GH11 xylanases and the previously observed small conformational changes upon substrate binding, a relocation of the tip of the thumb of more than 15 A was observed. Site-directed mutagenesis of five thumb residues, including putative hinge point residues, and enzyme kinetics assays showed that Arg112, Asn114, and Thr126 play a role in the open-close thumb movement. Replacement of Arg112 by glycine or proline caused a strong decrease of turnover numbers and elevated Michaelis constants on xylan. Mutant N114P hindered thumb movement, provoking a fourfold decrease of turnover numbers and a sharp rise in Michaelis constants, whereas the proline mutant of Thr126 displayed an increase in specific activity. The observation that extensive thumb opening is possible combined with the kinetic data suggests that the thumb plays a crucial role in both binding of substrate and release of product from the active site.
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Affiliation(s)
- Annick Pollet
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre, Katholieke Universiteit Leuven, Kasteelpark Arenberg, B-3001 Leuven, Belgium
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48
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Gyémánt G, Zajácz Á, Bécsi B, Ragunath C, Ramasubbu N, Erdődi F, Batta G, Kandra L. Evidence for pentagalloyl glucose binding to human salivary α-amylase through aromatic amino acid residues. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:291-6. [DOI: 10.1016/j.bbapap.2008.10.012] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2008] [Revised: 09/22/2008] [Accepted: 10/23/2008] [Indexed: 12/01/2022]
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49
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Ragunath C, Manuel SG, Venkataraman V, Sait HB, Kasinathan C, Ramasubbu N. Probing the role of aromatic residues at the secondary saccharide-binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding. J Mol Biol 2008; 384:1232-48. [PMID: 18951906 PMCID: PMC2644404 DOI: 10.1016/j.jmb.2008.09.089] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2008] [Revised: 09/28/2008] [Accepted: 09/30/2008] [Indexed: 10/21/2022]
Abstract
Human salivary alpha-amylase (HSAmy) has three distinct functions relevant to oral health: (1) hydrolysis of starch, (2) binding to hydroxyapatite (HA), and (3) binding to bacteria (e.g., viridans streptococci). Although the active site of HSAmy for starch hydrolysis is well-characterized, the regions responsible for bacterial binding are yet to be defined. Since HSAmy possesses several secondary saccharide-binding sites in which aromatic residues are prominently located, we hypothesized that one or more of the secondary saccharide-binding sites harboring the aromatic residues may play an important role in bacterial binding. To test this hypothesis, the aromatic residues at five secondary binding sites were mutated to alanine to generate six mutants representing either single (W203A, Y276A, and W284A), double (Y276A/W284A and W316A/W388A), or multiple [W134A/W203A/Y276A/W284A/W316A/W388A; human salivary alpha-amylase aromatic residue multiple mutant (HSAmy-ar)] mutations. The crystal structure of HSAmy-ar as an acarbose complex was determined at a resolution of 1.5 A and compared with the existing wild-type acarbose complex. The wild-type and the mutant enzymes were characterized for their abilities to exhibit enzyme activity, starch-binding activity, HA-binding activity, and bacterial binding activity. Our results clearly showed that (1) mutation of aromatic residues does not alter the overall conformation of the molecule; (2) single or double mutants showed either moderate or minimal changes in both starch-binding activity and bacterial binding activity, whereas HSAmy-ar showed significant reduction in these activities; (3) starch-hydrolytic activity was reduced by 10-fold in HSAmy-ar; (4) oligosaccharide-hydrolytic activity was reduced in all mutants, but the action pattern was similar to that of the wild-type enzyme; and (5) HA binding was unaffected in HSAmy-ar. These results clearly show that the aromatic residues at the secondary saccharide-binding sites in HSAmy play a critical role in bacterial binding and in starch-hydrolytic functions of HSAmy.
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Affiliation(s)
- Chandran Ragunath
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Suba G.A. Manuel
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Venkat Venkataraman
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Hameetha B.R. Sait
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Chinnasamy Kasinathan
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
| | - Narayanan Ramasubbu
- Department of Oral Biology, University of Medicine and Dentistry of New Jersey, 185 South Orange Ave, Newark NJ 07103
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50
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An enzyme family reunion — similarities, differences and eccentricities in actions on α-glucans. Biologia (Bratisl) 2008. [DOI: 10.2478/s11756-008-0164-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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