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Bouvier B. Substituted Oligosaccharides as Protein Mimics: Deep Learning Free Energy Landscapes. J Chem Inf Model 2024; 64:2195-2204. [PMID: 37040394 DOI: 10.1021/acs.jcim.3c00179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/12/2023]
Abstract
Protein-protein complexes power the majority of cellular processes. Interfering with the formation of such complexes using well-designed mimics is a difficult, yet actively pursued, research endeavor. Due to the limited availability of results on the conformational preferences of oligosaccharides compared to polypeptides, the former have been much less explored than the latter as protein mimics, despite interesting ADMET characteristics. In this work, the conformational landscapes of a series of 956 substituted glucopyranose oligomers of lengths 3 to 12 designed as protein interface mimics are revealed using microsecond-time-scale, enhanced-sampling molecular dynamics simulations. Deep convolutional networks are trained on these large conformational ensembles, to predict the stability of longer oligosaccharide structures from those of their constituent trimer motifs. Deep generative adversarial networks are then designed to suggest plausible conformations for oligosaccharide mimics of arbitrary length and substituent sequences that can subsequently be used as input to docking simulations. Analyzing the performance of the neural networks also yields insights into the intricate collective effects that dominate oligosaccharide conformational dynamics.
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Affiliation(s)
- Benjamin Bouvier
- Enzyme and Cell Engineering, CNRS UMR7025/Université de Picardie Jules Verne, 10, rue Baudelocque, 80039 Amiens Cedex, France
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2
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Gericke M, Amaral AJR, Budtova T, De Wever P, Groth T, Heinze T, Höfte H, Huber A, Ikkala O, Kapuśniak J, Kargl R, Mano JF, Másson M, Matricardi P, Medronho B, Norgren M, Nypelö T, Nyström L, Roig A, Sauer M, Schols HA, van der Linden J, Wrodnigg TM, Xu C, Yakubov GE, Stana Kleinschek K, Fardim P. The European Polysaccharide Network of Excellence (EPNOE) research roadmap 2040: Advanced strategies for exploiting the vast potential of polysaccharides as renewable bioresources. Carbohydr Polym 2024; 326:121633. [PMID: 38142079 DOI: 10.1016/j.carbpol.2023.121633] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/25/2023]
Abstract
Polysaccharides are among the most abundant bioresources on earth and consequently need to play a pivotal role when addressing existential scientific challenges like climate change and the shift from fossil-based to sustainable biobased materials. The Research Roadmap 2040 of the European Polysaccharide Network of Excellence (EPNOE) provides an expert's view on how future research and development strategies need to evolve to fully exploit the vast potential of polysaccharides as renewable bioresources. It is addressed to academic researchers, companies, as well as policymakers and covers five strategic areas that are of great importance in the context of polysaccharide related research: (I) Materials & Engineering, (II) Food & Nutrition, (III) Biomedical Applications, (IV) Chemistry, Biology & Physics, and (V) Skills & Education. Each section summarizes the state of research, identifies challenges that are currently faced, project achievements and developments that are expected in the upcoming 20 years, and finally provides outlines on how future research activities need to evolve.
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Affiliation(s)
- Martin Gericke
- Friedrich Schiller University of Jena, Institute of Organic Chemistry and Macromolecular Chemistry, Centre of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743 Jena, Germany
| | - Adérito J R Amaral
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Tatiana Budtova
- MINES Paris, PSL University, CEMEF - Center for Materials Forming, UMR CNRS 7635, CS 10207, rue Claude Daunesse, 06904 Sophia Antipolis, France
| | - Pieter De Wever
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Thomas Groth
- Department Biomedical Materials, Institute of Pharmacy, Martin Luther University Halle-Wittenberg, 06099 Halle (Saale), Germany
| | - Thomas Heinze
- Friedrich Schiller University of Jena, Institute of Organic Chemistry and Macromolecular Chemistry, Centre of Excellence for Polysaccharide Research, Humboldtstraße 10, D-07743 Jena, Germany
| | - Herman Höfte
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Anton Huber
- University Graz, Inst.f. Chem./PS&HC - Polysaccharides & Hydrocolloids, Heinrichstrasse 28, 8010 Graz, Austria
| | - Olli Ikkala
- Department of Applied Physics, Aalto University School of Science, FI-00076 Espoo, Finland
| | - Janusz Kapuśniak
- Jan Dlugosz University in Czestochowa, Faculty of Science and Technology, Department of Dietetics and Food Studies, Waszyngtona 4/8, 42-200 Czestochowa, Poland
| | - Rupert Kargl
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, A-8010 Graz, Austria
| | - João F Mano
- Department of Chemistry, CICECO-Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Már Másson
- Faculty of Pharmaceutical Sciences, School of Health Sciences, University of Iceland, Hofsvallagata 53, IS-107 Reykjavík, Iceland
| | - Pietro Matricardi
- Sapienza University of Rome, Department of Drug Chemistry and Technologies, P.le A. Moro 5, 00185 Rome, Italy
| | - Bruno Medronho
- MED-Mediterranean Institute for Agriculture, Environment and Development, CHANGE-Global Change and Sustainability Institute, Faculdade de Ciências e Tecnologia, Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal; Surface and Colloid Engineering, FSCN Research Center, Mid Sweden University, SE-851 70 Sundsvall, Sweden
| | - Magnus Norgren
- Surface and Colloid Engineering, FSCN Research Center, Mid Sweden University, SE-851 70 Sundsvall, Sweden
| | - Tiina Nypelö
- Chalmers University of Technology, Department of Chemistry and Chemical Engineering, 41296 Gothenburg, Sweden; Aalto University, Department of Bioproducts and Biosystems, 00076 Aalto, Finland
| | - Laura Nyström
- ETH Zurich, Department of Health Sciences and Technology, Schmelzbergstrasse 9, 8092 Zurich, Switzerland
| | - Anna Roig
- Institute of Materials Science of Barcelona (ICMAB-CSIC), 08193 Bellaterra, Spain
| | - Michael Sauer
- University of Natural Resources and Life Sciences, Vienna, Department of Biotechnology, Institute of Microbiology and Microbial Biotechnology, Muthgasse 18, 1190 Vienna, Austria
| | - Henk A Schols
- Laboratory of Food Chemistry, Wageningen University and Research, Bornse Weilanden 9, 6708WG Wageningen, the Netherlands
| | | | - Tanja M Wrodnigg
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, A-8010 Graz, Austria
| | - Chunlin Xu
- Åbo Akademi University, Laboratory of Natural Materials Technology, Henrikinkatu 2, Turku/Åbo, Finland
| | - Gleb E Yakubov
- Soft Matter Biomaterials and Biointerfaces, Food Structure and Biomaterials Group, School of Biosciences, University of Nottingham, Sutton Bonington LE12 5RD, United Kingdom
| | - Karin Stana Kleinschek
- Graz University of Technology, Institute of Chemistry and Technology of Biobased Systems, Stremayrgasse 9, A-8010 Graz, Austria.
| | - Pedro Fardim
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), Celestijnenlaan 200F, 3001 Leuven, Belgium
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Tetrault T, Meredith RJ, Zhang W, Carmichael I, Serianni AS. One-Bond 13C- 1H and 13C- 13C Spin-Coupling Constants as Constraints in MA'AT Analysis of Saccharide Conformation. J Phys Chem B 2022; 126:9506-9515. [PMID: 36356177 DOI: 10.1021/acs.jpcb.2c04986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
MA'AT analysis uses ensembles of redundant experimental NMR spin-coupling constants, parametrized J-coupling equations obtained from density functional theory (DFT) calculations, and circular statistics to produce probability distributions of molecular torsion angles in solution and information on librational motions about these angles (Meredith et al., J. Chem. Info. Model. 2022, 62, 3135-3141). Current DFT methods give nearly quantitative two- and three-bond JHH, JCH, and 1JCC values for use in MA'AT analysis of saccharides. In contrast, the accuracy of DFT-calculated one-bond 1JCH and 1JCC values is more difficult to determine, preventing their use in MA'AT modeling. This report describes experimental and computational studies that address this problem using two approaches (Strategies 1 and 2). Differences [1JCHcalc - 1JCHexp] (Strategy 1) ranged from -1.2 to 2.5 Hz, giving an average difference of 0.8 ± 1.7 Hz. Percent differences ranged from -0.8% to 1.6%, giving an average % difference of 0.5 ± 1.1%. In comparison, [1JCHMA'AT - 1JCHexp] (Strategy 2) ranged from -1.8 to 0.2 Hz, giving an average difference of -1.2 ± 0.7 Hz. Percent differences ranged from -1.2% to 0.1%, giving an average % difference of -0.8 ± 0.5%. Strategy 1 gave an average difference of 2.1 Hz between calculated and experimental 1JCC values, with an average % difference of 5.1 ± 0.2%. Calculated 1JCC values were consistently larger than experimental values. Strategy 2 also gave calculated 1JCC values that were larger than the experimental values, with an average difference of 2.3 ± 0.6 Hz, and an average % difference of 5.6 ± 1.6%. The findings of both strategies are similar and indicate that 1JCH values in saccharides can be calculated nearly quantitatively, but 1JCC values appear to be consistently overestimated by ∼5% using current DFT methods.
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Affiliation(s)
| | | | - Wenhui Zhang
- Omicron Biochemicals, Inc., South Bend, Indiana 46617, United States
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Meredith R, Carmichael I, Serianni AS. Nonconventional NMR Spin-Coupling Constants in Oligosaccharide Conformational Modeling: Structural Dependencies Determined from Density Functional Theory Calculations. ACS OMEGA 2022; 7:23950-23966. [PMID: 35847250 PMCID: PMC9280969 DOI: 10.1021/acsomega.2c02793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Nonconventional NMR spin-coupling constants were investigated to determine their potential as conformational constraints in MA'AT modeling of the O-glycosidic linkages of oligosaccharides. Four (1 J C1',H1', 1 J C1',C2', 2 J C1',H2', and 2 J C2',H1') and eight (1 J C4,H4, 1 J C3,C4, 1 J C4,C5, 2 J C3,H4, 2 J C4,H3, 2 J C5,H4, 2 J C4,H5, and 2 J C3,C5) spin-couplings in methyl β-d-galactopyranosyl-(1→4)-β-d-glucopyranoside (methyl β-lactoside) were calculated using density functional theory (DFT) to determine their dependencies on O-glycosidic linkage C-O torsion angles, ϕ and ψ, respectively. Long-range 4 J H1',H4 was also examined as a potential conformational constraint of either ϕ or ψ. Secondary effects of exocyclic (hydroxyl) C-O bond rotation within or proximal to these coupling pathways were investigated. Based on the findings of methyl β-lactoside, analogous J-couplings were studied in five additional two-bond O-glycosidic linkages [βGlcNAc-(1→4)-βMan, 2-deoxy-βGlc-(1→4)-βGlc, αMan-(1→3)-βMan, αMan-(1→2)-αMan, and βGlcNAc(1→2)-αMan] to determine whether the coupling behaviors observed in methyl β-lactoside were more broadly observed. Of the 13 nonconventional J-couplings studied, 7 exhibit properties that may be useful in future MA'AT modeling of O-glycosidic linkages, none of which involve coupling pathways that include the linkage C-O bonds. The findings also provide new insights into the general effects of exocyclic C-O bond conformation on the magnitude of experimental spin-couplings in saccharides and other hydroxyl-containing molecules.
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Affiliation(s)
- Reagan
J. Meredith
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556-5670, United States
| | - Ian Carmichael
- Radiation
Laboratory, University of Notre Dame, Notre Dame, Indiana 46556-5670, United States
| | - Anthony S. Serianni
- Department
of Chemistry and Biochemistry, University
of Notre Dame, Notre
Dame, Indiana 46556-5670, United States
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