1
|
Mészáros Z, Kulik N, Petrásková L, Bojarová P, Texidó M, Planas A, Křen V, Slámová K. Three-Step Enzymatic Remodeling of Chitin into Bioactive Chitooligomers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:15613-15623. [PMID: 38978453 PMCID: PMC11261597 DOI: 10.1021/acs.jafc.4c03077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 07/01/2024] [Accepted: 07/03/2024] [Indexed: 07/10/2024]
Abstract
Here we describe a complex enzymatic approach to the efficient transformation of abundant waste chitin, a byproduct of the food industry, into valuable chitooligomers with a degree of polymerization (DP) ranging from 6 to 11. This method involves a three-step process: initial hydrolysis of chitin using engineered variants of a novel fungal chitinase from Talaromyces flavus to generate low-DP chitooligomers, followed by an extension to the desired DP using the high-yielding Y445N variant of β-N-acetylhexosaminidase from Aspergillus oryzae, achieving yields of up to 57%. Subsequently, enzymatic deacetylation of chitooligomers with DP 6 and 7 was accomplished using peptidoglycan deacetylase from Bacillus subtilis BsPdaC. The innovative enzymatic procedure demonstrates a sustainable and feasible route for converting waste chitin into unavailable bioactive chitooligomers potentially applicable as natural pesticides in ecological and sustainable agriculture.
Collapse
Affiliation(s)
- Zuzana Mészáros
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Natalia Kulik
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Lucie Petrásková
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Pavla Bojarová
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Mònica Texidó
- Laboratory
of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, ES 08017 Barcelona, Spain
| | - Antoni Planas
- Laboratory
of Biochemistry, Institut Químic de Sarrià, University Ramon Llull, ES 08017 Barcelona, Spain
| | - Vladimír Křen
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| | - Kristýna Slámová
- Institute
of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, CZ 14200, Prague 4, Czech Republic
| |
Collapse
|
2
|
Catassi G, Aloi M, Giorgio V, Gasbarrini A, Cammarota G, Ianiro G. The Role of Diet and Nutritional Interventions for the Infant Gut Microbiome. Nutrients 2024; 16:400. [PMID: 38337684 PMCID: PMC10857663 DOI: 10.3390/nu16030400] [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: 12/14/2023] [Revised: 01/14/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024] Open
Abstract
The infant gut microbiome plays a key role in the healthy development of the human organism and appears to be influenced by dietary practices through multiple pathways. First, maternal diet during pregnancy and infant nutrition significantly influence the infant gut microbiota. Moreover, breastfeeding fosters the proliferation of beneficial bacteria, while formula feeding increases microbial diversity. The timing of introducing solid foods also influences gut microbiota composition. In preterm infants the gut microbiota development is influenced by multiple factors, including the time since birth and the intake of breast milk, and interventions such as probiotics and prebiotics supplementation show promising results in reducing morbidity and mortality in this population. These findings underscore the need for future research to understand the long-term health impacts of these interventions and for further strategies to enrich the gut microbiome of formula-fed and preterm infants.
Collapse
Affiliation(s)
- Giulia Catassi
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, Umberto I Hospital, 00161 Rome, Italy;
| | - Marina Aloi
- Pediatric Gastroenterology and Liver Unit, Sapienza University of Rome, Umberto I Hospital, 00161 Rome, Italy;
| | - Valentina Giorgio
- Department of Woman and Child Health and Public Health, UOC Pediatria, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy;
| | - Antonio Gasbarrini
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Giovanni Cammarota
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| | - Gianluca Ianiro
- Department of Translational Medicine and Surgery, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (G.C.); (A.G.); (G.C.)
- Department of Medical and Surgical Sciences, UOC Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
- Department of Medical and Surgical Sciences, UOC CEMAD Centro Malattie dell’Apparato Digerente, Medicina Interna e Gastroenterologia, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy
| |
Collapse
|
3
|
Bains RK, Nasseri SA, Liu F, Wardman JF, Rahfeld P, Withers SG. Characterization of a new family of 6-sulfo-N-acetylglucosaminidases. J Biol Chem 2023; 299:105214. [PMID: 37660924 PMCID: PMC10570127 DOI: 10.1016/j.jbc.2023.105214] [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: 06/15/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/05/2023] Open
Abstract
Sulfation is widespread in nature and plays an important role in modulating biological function. Among the strategies developed by microbes to access sulfated oligosaccharides as a nutrient source is the production of 6-sulfoGlcNAcases to selectively release 6-sulfoGlcNAc from target oligosaccharides. Thus far, all 6-sulfoGlcNAcases identified have belonged to the large GH20 family of β-hexosaminidases. Ηere, we identify and characterize a new, highly specific non-GH20 6-sulfoGlcNAcase from Streptococcus pneumoniae TIGR4, Sp_0475 with a greater than 110,000-fold preference toward N-acetyl-β-D-glucosamine-6-sulfate substrates over the nonsulfated version. Sp_0475 shares distant sequence homology with enzymes of GH20 and with the newly formed GH163 family. However, the sequence similarity between them is sufficiently low that Sp_0475 has been assigned as the founding member of a new glycoside hydrolase family, GH185. By combining results from site-directed mutagenesis with mechanistic studies and bioinformatics we provide insight into the substrate specificity, mechanism, and key active site residues of Sp_0475. Enzymes of the GH185 family follow a substrate-assisted mechanism, consistent with their distant homology to the GH20 family, but the catalytic residues involved are quite different. Taken together, our results highlight in more detail how microbes can degrade sulfated oligosaccharides for nutrients.
Collapse
Affiliation(s)
- Rajneesh K Bains
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Seyed A Nasseri
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Feng Liu
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jacob F Wardman
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Rahfeld
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G Withers
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada; Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
| |
Collapse
|
4
|
Alfonso-Prieto M, Cuxart I, Potocki-Véronèse G, André I, Rovira C. Substrate-Assisted Mechanism for the Degradation of N-Glycans by a Gut Bacterial Mannoside Phosphorylase. ACS Catal 2023. [DOI: 10.1021/acscatal.3c00451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Affiliation(s)
- Mercedes Alfonso-Prieto
- Departament de Química Inorgànica i Orgànica and Institute of Theoretical and Computational Chemistry (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Irene Cuxart
- Departament de Química Inorgànica i Orgànica and Institute of Theoretical and Computational Chemistry (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
| | - Gabrielle Potocki-Véronèse
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 04, France
| | - Isabelle André
- Toulouse Biotechnology Institute (TBI), Université de Toulouse, CNRS, INRAE, INSA, 135 Avenue de Rangueil, F-31077 Toulouse Cedex 04, France
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica and Institute of Theoretical and Computational Chemistry (IQTCUB), Universitat de Barcelona, Martí i Franquès 1, 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| |
Collapse
|
5
|
Yang W, Zhuang J, Li C, Cheng GJ. Unveiling the Methyl Transfer Mechanisms in the Epigenetic Machinery DNMT3A-3L: A Comprehensive Study Integrating Assembly Dynamics with Catalytic Reactions. Comput Struct Biotechnol J 2023; 21:2086-2099. [PMID: 36968013 PMCID: PMC10034213 DOI: 10.1016/j.csbj.2023.03.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Revised: 03/02/2023] [Accepted: 03/02/2023] [Indexed: 03/07/2023] Open
Abstract
In epigenetic mechanisms, DNA methyltransferase 3 alpha (DNMT3A) acts as an initiator for DNA methylation and prevents the downstream genes from expressing. Perturbations of DNMT3A functions may cause uncontrolled gene expression, resulting in pathogenic consequences such as cancers. It is, therefore, vitally important to understand the catalytic process of DNMT3A in its biological macromolecule assembly, viz., heterotetramer: (DNMT3A-3 L)dimer. In this study, we utilized molecular dynamics (MD) simulations, Markov State Models (MSM), and quantum mechanics/molecular mechanics simulations (QM/MM) to investigate the de novo methyl transfer process. We identified the dynamics of the key residues relevant to the insertion of the target cytosine (dC) into the catalytic domain of DNMT3A, and the detailed potential energy surface of the seven-step reaction referring to methyl transfer. Our calculated potential energy barrier (22.51 kcal/mol) approximates the former experimental data (23.12 kcal/mol). The conformational change of the 5-methyl-cytosine (5mC) intermediate was found necessary in forming a four-water chain for the elimination step, which is unique to the other DNMTs. The biological assembly facilitates the creation of such a water chain, and the elimination occurs in an asynchronized mechanism in the two catalytic pockets. We anticipate the findings can enable a better understanding of the general mechanisms of the de novo methyl transfer for fulfilling the key enzymatic functions in epigenetics. And the unique elimination of DNMT3A might ignite novel methods for designing anti-cancer and tumor inhibitors of DNMTs.
Collapse
Affiliation(s)
- Wei Yang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Biotechnology, University of Science and Technology of China, Hefei 230026, China
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Jingyuan Zhuang
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chen Li
- Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Gui-Juan Cheng
- Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Shenzhen Key Laboratory of Steroid Drug Development, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China
- Corresponding author at: Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, China.
| |
Collapse
|
6
|
Yang L, Zhu Y, Zhang W, Mu W. Recent progress in health effects and biosynthesis of lacto- N-tetraose, the most dominant core structure of human milk oligosaccharide. Crit Rev Food Sci Nutr 2023; 64:6802-6811. [PMID: 36744615 DOI: 10.1080/10408398.2023.2175197] [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] [Indexed: 02/07/2023]
Abstract
Human milk oligosaccharides (HMOs), which are a group of complex carbohydrates highly abundant in human milk, have been recognized as critical functional biomolecules for infant health. Lacto-N-tetraose (LNT) is one of the most abundant HMO members and the most dominant core structure of HMO. The promising physiological effects of LNT have been well documented, including prebiotic property, antiadhesive antimicrobial activity, and antiviral effect. Its safety has been evaluated and it has been commercially added to infant formula as a functional ingredient. Because of great commercial importance of LNT, increasing attention has been paid to its highly efficient biological production. In particular, microbial synthesis based on metabolic engineering displays obvious advantages in large-scale production of LNT. This review contains important information about the recent progress in physiological effects, safety evaluation, and biosynthesis of LNT.
Collapse
Affiliation(s)
- Longhao Yang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yingying Zhu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenli Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wanmeng Mu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, China
- International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, China
| |
Collapse
|
7
|
Zhang Z, Dong M, Zallot R, Blackburn GM, Wang N, Wang C, Chen L, Baumann P, Wu Z, Wang Z, Fan H, Roth C, Jin Y, He Y. Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases. ACS Catal 2022. [DOI: 10.1021/acscatal.2c05405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Zhen Zhang
- Key Laboratory of Synthetic and Natural Functional Molecule, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Mochen Dong
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Rémi Zallot
- Institute of Life Sciences, Swansea University Medical School, Swansea SA2 8PP, U.K
| | - George Michael Blackburn
- School of Biosciences, University of Sheffield, Firth Court, Western Bank, Sheffield S10 2TN, U.K
| | - Nini Wang
- Key Laboratory of Synthetic and Natural Functional Molecule, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Chengjian Wang
- Glycobiology and Glycotechnology Research Center, College of Food Science and Technology, Northwest University, Xi’an 710069, P. R. China
| | - Long Chen
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Patrick Baumann
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Zuyan Wu
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Zhongfu Wang
- Glycobiology and Glycotechnology Research Center, College of Food Science and Technology, Northwest University, Xi’an 710069, P. R. China
| | - Haiming Fan
- Key Laboratory of Synthetic and Natural Functional Molecule, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Christian Roth
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Arnimallee 22, 14195 Berlin, German
| | - Yi Jin
- School of Chemistry, Cardiff University, Cardiff CF10 3AT, U.K
| | - Yuan He
- Key Laboratory of Synthetic and Natural Functional Molecule, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| |
Collapse
|
8
|
Li CC, Yi H, Wang YM, Tang XY, Zhu YB, Song YJ, Zhao NL, Huang Q, Mou XY, Luo GH, Liu TG, Yang GL, Zeng YJ, Wang LJ, Tang H, Fan G, Bao R. Nucleotide binding as an allosteric regulatory mechanism for Akkermansia muciniphila β- N-acetylhexosaminidase Am2136. Gut Microbes 2022; 14:2143221. [PMID: 36394293 PMCID: PMC9673926 DOI: 10.1080/19490976.2022.2143221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
β-N-acetylhexosaminidases (EC3.2.1.52), which belong to the glycosyl hydrolase family GH20, are important enzymes for oligosaccharides modification. Numerous microbial β-N-acetylhexosaminidases have been investigated for applications in biology, biomedicine and biotechnology. Akkermansia muciniphila is an anaerobic intestinal commensal bacterium which possesses specific β-N-acetylhexosaminidases for gut mucosal layer colonization and mucin degradation. In this study, we assessed the in vitro mucin glycan cleavage activity of the A. muciniphila β-N-acetylhexosaminidase Am2136 and demonstrated its ability that hydrolyzing the β-linkages joining N-acetylglucosamine to a wide variety of aglycone residues, which indicated that Am2136 may be a generalist β-N-acetylhexosaminidase. Structural and enzyme activity assay experiments allowed us to probe the essential function of the inter-domain interactions in β23-β33. Importantly, we revealed that the hydrolysis activity of Am2136 was enhanced by nucleotides. We further speculated that this activation mechanism might be associated with the conformational motions between domain III and IV. To our knowledge, this is the first report of nucleotide effector regulated β-N-acetylhexosaminidase, to reveal its novel biological functions. These findings contribute to understanding the distinct properties within the GH20 family and lay a certain foundation to develop controllable glycan hydrolyzing catalysts.Abbreviations: OD600 - optical cell densities at 600 nm; LB - Luria-Bertani; IPTG - isopropyl β-D-1-thiogalactopyranoside; PMSF - phenylmethanesulfonyl fluoride; rmsd - root mean square deviation; GlcNAc - N-acetyl-β-D-glucosamine; GalNAc - N-acetyl-β-D-galactosamine; Gal - galactose.
Collapse
Affiliation(s)
- Chang-Cheng Li
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Huan Yi
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Yan-Mei Wang
- Institute of traditional Chinese medicine, Sichuan College of traditional Chinese Medicine (Sichuan Second Hospital of TCM), Chengdu, China
| | - Xin-Yue Tang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Yi-Bo Zhu
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ying-Jie Song
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ning-Lin Zhao
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Qin Huang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Xing-Yu Mou
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Gui-Hua Luo
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Tong-Gen Liu
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Gang-Long Yang
- School of Biotechnology, Jiangnan University, Chengdu, China
| | - Yu-Jiao Zeng
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Li-Jie Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Hong Tang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China,Hong Tang Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University. Chengdu. China
| | - Gang Fan
- State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine, Chengdu, China,Gang Fan State Key Laboratory of Southwestern Chinese Medicine Resources, College of Ethnic Medicine, Chengdu University of Traditional Chinese Medicine. Chengdu. China
| | - Rui Bao
- Division of Infectious Diseases, State Key Laboratory of Biotherapy and Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China,CONTACT Rui Bao
| |
Collapse
|
9
|
Neves RPP, Fernandes PA, Ramos MJ. Role of Enzyme and Active Site Conformational Dynamics in the Catalysis by α-Amylase Explored with QM/MM Molecular Dynamics. J Chem Inf Model 2022; 62:3638-3650. [PMID: 35880954 PMCID: PMC9778734 DOI: 10.1021/acs.jcim.2c00691] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
We assessed enzyme:substrate conformational dynamics and the rate-limiting glycosylation step of a human pancreatic α-amylase:maltopentose complex. Microsecond molecular dynamics simulations suggested that the distance of the catalytic Asp197 nucleophile to the anomeric carbon of the buried glucoside is responsible for most of the enzyme active site fluctuations and that both Asp197 and Asp300 interact the most with the buried glucoside unit. The buried glucoside binds either in a 4C1 chair or 2SO skew conformations, both of which can change to TS-like conformations characteristic of retaining glucosidases. Starting from four distinct enzyme:substrate complexes, umbrella sampling quantum mechanics/molecular mechanics simulations (converged within less than 1 kcal·mol-1 within a total simulation time of 1.6 ns) indicated that the reaction occurrs with a Gibbs barrier of 13.9 kcal·mol -1, in one asynchronous concerted step encompassing an acid-base reaction with Glu233 followed by a loose SN2-like nucleophilic substitution by the Asp197. The transition state is characterized by a 2H3 half-chair conformation of the buried glucoside that quickly changes to the E3 envelope conformation preceding the attack of the anomeric carbon by the Asp197 nucleophile. Thermodynamic analysis of the reaction supported that a water molecule tightly hydrogen bonded to the glycosidic oxygen of the substrate at the reactant state (∼1.6 Å) forms a short hydrogen bond with Glu233 at the transition state (∼1.7 Å) and lowers the Gibbs barrier in over 5 kcal·mol-1. The resulting Asp197-glycosyl was mostly found in the 4C1 conformation, although the more endergonic B3,O conformation was also observed. Altogether, the combination of short distances for the acid-base reaction with the Glu233 and for the nucleophilic attack by the Asp197 nucleophile and the availability of water within hydrogen bonding distance of the glycosidic oxygen provides a reliable criteria to identify reactive conformations of α-amylase complexes.
Collapse
|