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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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Abstract
Glycoscience assembles all the scientific disciplines involved in studying various molecules and macromolecules containing carbohydrates and complex glycans. Such an ensemble involves one of the most extensive sets of molecules in quantity and occurrence since they occur in all microorganisms and higher organisms. Once the compositions and sequences of these molecules are established, the determination of their three-dimensional structural and dynamical features is a step toward understanding the molecular basis underlying their properties and functions. The range of the relevant computational methods capable of addressing such issues is anchored by the specificity of stereoelectronic effects from quantum chemistry to mesoscale modeling throughout molecular dynamics and mechanics and coarse-grained and docking calculations. The Review leads the reader through the detailed presentations of the applications of computational modeling. The illustrations cover carbohydrate-carbohydrate interactions, glycolipids, and N- and O-linked glycans, emphasizing their role in SARS-CoV-2. The presentation continues with the structure of polysaccharides in solution and solid-state and lipopolysaccharides in membranes. The full range of protein-carbohydrate interactions is presented, as exemplified by carbohydrate-active enzymes, transporters, lectins, antibodies, and glycosaminoglycan binding proteins. A final section features a list of 150 tools and databases to help address the many issues of structural glycobioinformatics.
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Affiliation(s)
- Serge Perez
- Centre de Recherche sur les Macromolecules Vegetales, University of Grenoble-Alpes, Centre National de la Recherche Scientifique, Grenoble F-38041, France
| | - Olga Makshakova
- FRC Kazan Scientific Center of Russian Academy of Sciences, Kazan Institute of Biochemistry and Biophysics, Kazan 420111, Russia
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Grachev AA, Gerbst AG, Gening ML, Titov DV, Yudina ON, Tsvetkov YE, Shashkov AS, Pier GB, Nifantiev NE. NMR and conformational studies of linear and cyclic oligo-(1→6)-β-D-glucosamines. Carbohydr Res 2011; 346:2499-510. [PMID: 21945383 PMCID: PMC3201778 DOI: 10.1016/j.carres.2011.08.031] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2011] [Accepted: 08/30/2011] [Indexed: 11/18/2022]
Abstract
The conformational behavior of a series of linear and cyclic oligo-(1→6)-β-D-glucosamines and their N-acetylated derivatives, which are related to fragments of natural poly-N-acetylglucosamine, was studied by theoretical molecular modeling and experimental determination of transglycosidic vicinal coupling constants (3)J(C,H) and (3)J(H,H). Molecular dynamics simulations were performed under several types of conditions varying in the consideration of ionization of amino groups, solvent effect, and temperature. Neural network clustering and asphericity calculations were performed on the basis of molecular dynamics data. It was shown that disaccharide fragments in the studied linear oligosaccharides were not rigid, and tended to have several conformers, thus determining the overall twisted shape with helical elements. In addition, it was found that the behavior of C5-C6 bond depended significantly upon the simulation conditions. The cyclic di-, tri-, and tetrasaccharides mostly had symmetrical ring-shaped conformations. The larger cycles tended to adopt more complicated shapes, and the conformational behavior of their disaccharide fragments was close to that in the linear oligosaccharides.
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Affiliation(s)
- Alexey A. Grachev
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow (Russia)
| | - Alexey G. Gerbst
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow (Russia)
| | - Marina L. Gening
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow (Russia)
| | - Denis V. Titov
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow (Russia)
| | - Olga N. Yudina
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow (Russia)
| | - Yury E. Tsvetkov
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow (Russia)
| | - Alexander S. Shashkov
- NMR spectroscopy, N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow (Russia)
| | - Gerald B. Pier
- Channing Laboratory, Brigham and Women’s Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA (USA)
| | - Nikolay E. Nifantiev
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry Russian Academy of Sciences, Leninsky prospect 47, 119991 Moscow (Russia)
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Rosen J, Miguet L, Pérez S. Shape: automatic conformation prediction of carbohydrates using a genetic algorithm. J Cheminform 2009; 1:16. [PMID: 20298520 PMCID: PMC2820494 DOI: 10.1186/1758-2946-1-16] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2009] [Accepted: 09/21/2009] [Indexed: 11/25/2022] Open
Abstract
Background Detailed experimental three dimensional structures of carbohydrates are often difficult to acquire. Molecular modelling and computational conformation prediction are therefore commonly used tools for three dimensional structure studies. Modelling procedures generally require significant training and computing resources, which is often impractical for most experimental chemists and biologists. Shape has been developed to improve the availability of modelling in this field. Results The Shape software package has been developed for simplicity of use and conformation prediction performance. A trivial user interface coupled to an efficient genetic algorithm conformation search makes it a powerful tool for automated modelling. Carbohydrates up to a few hundred atoms in size can be investigated on common computer hardware. It has been shown to perform well for the prediction of over four hundred bioactive oligosaccharides, as well as compare favourably with previously published studies on carbohydrate conformation prediction. Conclusion The Shape fully automated conformation prediction can be used by scientists who lack significant modelling training, and performs well on computing hardware such as laptops and desktops. It can also be deployed on computer clusters for increased capacity. The prediction accuracy under the default settings is good, as it agrees well with experimental data and previously published conformation prediction studies. This software is available both as open source and under commercial licenses.
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Affiliation(s)
- Jimmy Rosen
- Bio Organic Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, Netherlands.
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Gerbst AG, Grachev AA, Shashkov AS, Nifantiev NE. Computation techniques in the conformational analysis of carbohydrates. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2007. [DOI: 10.1134/s1068162007010037] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Siebert HC, Rosen J, Seyrek K, Kaltner H, André S, Bovin NV, Nyholm PG, Sinowatz F, Gabius HJ. α2,3/α2,6-Sialylation of N-glycans: non-synonymous signals with marked developmental regulation in bovine reproductive tracts. Biochimie 2006; 88:399-410. [PMID: 16360259 DOI: 10.1016/j.biochi.2005.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2005] [Accepted: 09/23/2005] [Indexed: 10/25/2022]
Abstract
The glycan part endows cellular glycoconjugates with significant potential for biological recognition. N-Glycan branches often end with alpha2,3/alpha2,6-sialylation, posing the question whether and how placement of the sialic acid at 3 - or 6 -acceptor positions of galactose has cell biological relevance. As attractive model to study developmental regulation we monitored the expression of alpha2,3/alpha2,6-sialylated determinants in fetal and adult bovine testes and ovaries by lectin histochemistry. Distinct expression patterns were detected in both organ types. Oocyte staining, as a prominent example, was restricted to the presence of alpha2,6-sialylated glycans. Treatment with sialidase abolished binding and thus excluded sulfate esters as lectin targets. We added computer simulations to rationalize the observed evidence for non-random expression of the two closely related sialylgalactose isomers. Extensive molecular mechanics and molecular dynamics calculations reveal that the seemingly minor shift of the glycosidic bond from the alpha2,3 position to the alpha2,6 configuration causes significant shape and flexibility changes. They give each disaccharide its own characteristic meaning as signal in the sugar code.
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Affiliation(s)
- Hans-Christian Siebert
- Institute of Physiological Chemistry, Faculty of Veterinary Medicine, Ludwig-Maximilians-University, Veterinärstr. 13, 80539 München, Germany
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Nahmany A, Strino F, Rosen J, Kemp GJL, Nyholm PG. The use of a genetic algorithm search for molecular mechanics (MM3)-based conformational analysis of oligosaccharides. Carbohydr Res 2005; 340:1059-64. [PMID: 15780270 DOI: 10.1016/j.carres.2004.12.037] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2004] [Accepted: 12/27/2004] [Indexed: 10/25/2022]
Abstract
We have implemented a system called glygal that can perform conformational searches on oligosaccharides using several different genetic algorithm (GA) search methods. The searches are performed in the torsion angle conformational space, considering both the primary glycosidic linkages as well as the pendant groups (C-5-C-6 and hydroxyl groups) where energy calculations are performed using the MM3(96) force field. The system includes a graphical user interface for setting calculation parameters and incorporates a 3D molecular viewer. The system was tested using dozens of structures and we present two case studies for two previously investigated O-specific oligosaccharides of the Shigella dysenteriae type 2 and 4. The results obtained using glygal show a significant reduction in the number of structures that need to be sampled in order to find the best conformation, as compared to filtered systematic search.
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Affiliation(s)
- Abraham Nahmany
- Department of Medical Biochemistry, Göteborg University, Medicinaregatan 7B, Box 440, SE-405 30 Göteborg, Sweden
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Rosen J, Robobi A, Nyholm PG. The conformations of the O-specific polysaccharides of Shigella dysenteriae type 4 and Escherichia coli O159 studied with molecular mechanics (MM3) filtered systematic search. Carbohydr Res 2004; 339:961-6. [PMID: 15010303 DOI: 10.1016/j.carres.2003.11.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2003] [Accepted: 11/19/2003] [Indexed: 11/18/2022]
Abstract
The branched O-antigens of Escherichia coli O159 and Shigella dysenteriae type 4 are structurally related and are known to show cross-reactivity with antibodies. In the present study, conformational analyses were performed on these two O-antigens using molecular mechanics MM3(96) with filtered systematic search. The results show very strong steric restrictions for the trisaccharide at the branch point of the E. coli O159 antigen, especially for the beta-d-GlcNAc-(1-->3)-beta-d-GlcNAc linkage of the main chain. For the type 4 O-antigen the calculations show essentially a single conformation with respect to the alpha-d-GlcNAc-(1-->3)-alpha-d-GlcNAc linkage of the main chain and three different favoured conformations for the fucose branch. Consecutive repeating units of the S. dysenteriae type 4 and E. coli O159 O-antigens form linear extended chains with significant flexibility between the branches. Comparative calculations carried out with the SWEET server indicate that our method of filtered systematic search is a superior method in the case of branched, constrained oligosaccharides. Based on the results of the MM3 calculations, we propose that the common epitope explaining the cross-reactivity comprises the fucose branch, the downstream GlcNAc and part of the uronic acid.
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Affiliation(s)
- Jimmy Rosen
- Department of Medical Biochemistry/Centre for Structural Biology, Göteborg University, Medicinaregatan 7B, S405 30 Göteborg, Sweden
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Lycknert K, Widmalm G. Dynamics of the Escherichia coli O91 O-Antigen Polysaccharide in Solution as Studied by Carbon-13 NMR Relaxation. Biomacromolecules 2004; 5:1015-20. [PMID: 15132695 DOI: 10.1021/bm0345108] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of the O-antigen part of the lipopolysaccharide from the enterohemorrhagic Escherichia coli O91 has been determined in solution using (13)C NMR relaxation measurements at two magnetic field strengths, 9.4 and 14.1 T, thereby facilitating the testing of several dynamical models. The biological repeating unit, consisting of five sugar residues and substituents, could be determined by spectral analysis of different (1)H,(13)C correlations and corroborated by the relaxation data. The site specifically (13)C-labeled material was shown to have approximately 10 repeating units with a narrow distribution. A model-free analysis of the relaxation data revealed a complex dynamical behavior where the sugar residues could be described by a global correlation time (tau(m) = 5.4 ns), generalized order parameters (S(2) approximately 0.63), and different correlation times for internal motions related to their position in the repeating unit along the polymer (tau(e) approximately 360-520 ps). One of the sugar residues showed, in addition, a chemical exchange contribution. Furthermore, a substituent on another sugar residue was described by two order parameters (S(f)(2) = 0.51 and S(s)(2) = 0.21). The solution dynamics of the polysaccharide are thus described by highly intricate motions, both in amplitude and time scales. These results are of significance in the general description of polysaccharides surrounding bacterial cell surfaces and in the presentation of antigenic epitopes to the immune system of an invaded host.
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Affiliation(s)
- Kristina Lycknert
- Department of Organic Chemistry, Stockholm University, S-106 91 Stockholm, Sweden
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