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Ruda A, Aytenfisu AH, Angles d’Ortoli T, MacKerell AD, Widmalm G. Glycosidic α-linked mannopyranose disaccharides: an NMR spectroscopy and molecular dynamics simulation study employing additive and Drude polarizable force fields. Phys Chem Chem Phys 2023; 25:3042-3060. [PMID: 36607620 PMCID: PMC9890503 DOI: 10.1039/d2cp05203b] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
D-Mannose is a structural component in N-linked glycoproteins from viruses and mammals as well as in polysaccharides from fungi and bacteria. Structural components often consist of D-Manp residues joined via α-(1→2)-, α-(1→3)-, α-(1→4)- or α-(1→6)-linkages. As models for these oligo- and polysaccharides, a series of mannose-containing disaccharides have been investigated with respect to conformation and dynamics. Translational diffusion NMR experiments were performed to deduce rotational correlation times for the molecules, 1D 1H,1H-NOESY and 1D 1H,1H-T-ROESY NMR experiments were carried out to obtain inter-residue proton-proton distances and one-dimensional long-range and 2D J-HMBC experiments were acquired to gain information about conformationally dependent heteronuclear coupling constants across glycosidic linkages. To attain further spectroscopic data, the doubly 13C-isotope labeled α-D-[1,2-13C2]Manp-(1→4)-α-D-Manp-OMe was synthesized thereby facilitating conformational analysis based on 13C,13C coupling constants as interpreted by Karplus-type relationships. Molecular dynamics simulations were carried out for the disaccharides with explicit water as solvent using the additive CHARMM36 and Drude polarizable force fields for carbohydrates, where the latter showed broader population distributions. Both simulations sampled conformational space in such a way that inter-glycosidic proton-proton distances were very well described whereas in some cases deviations were observed between calculated conformationally dependent NMR scalar coupling constants and those determined from experiment, with closely similar root-mean-square differences for the two force fields. However, analyses of dipole moments and radial distribution functions with water of the hydroxyl groups indicate differences in the underlying physical forces dictating the wider conformational sampling with the Drude polarizable versus additive C36 force field and indicate the improved utility of the Drude polarizable model in investigating complex carbohydrates.
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Affiliation(s)
- Alessandro Ruda
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
| | - Asaminew H. Aytenfisu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of MarylandBaltimoreMaryland 21201USA
| | - Thibault Angles d’Ortoli
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of MarylandBaltimoreMaryland 21201USA
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm UniversityS-106 91 StockholmSweden
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2
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Lalithamaheswari B, Anu Radha C. Structural and conformational dynamics of human milk oligosaccharides, lacto- N-fucopentaose I and II, through molecular dynamics simulation. J Carbohydr Chem 2022. [DOI: 10.1080/07328303.2022.2150203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- B. Lalithamaheswari
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C. Anu Radha
- Research Laboratory of Molecular Biophysics, Department of Physics, School of Advanced Sciences, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Jegatheeswaran S, Asnani A, Forman A, Hendel JL, Moore CJ, Nejatie A, Wang A, Wang JW, Auzanneau FI. Recognition of Dimeric Lewis X by Anti-Dimeric Le x Antibody SH2. Vaccines (Basel) 2020; 8:vaccines8030538. [PMID: 32957489 PMCID: PMC7563222 DOI: 10.3390/vaccines8030538] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/11/2020] [Accepted: 09/14/2020] [Indexed: 11/16/2022] Open
Abstract
The carbohydrate antigen dimeric Lewis X (DimLex), which accumulates in colonic and liver adenocarcinomas, is a valuable target to develop anti-cancer therapeutics. Using the native DimLex antigen as a vaccine would elicit an autoimmune response against the Lex antigen found on normal, healthy cells. Thus, we aim to study the immunogenic potential of DimLex and search internal epitopes displayed by DimLex that remain to be recognized by anti-DimLex monoclonal antibodies (mAbs) but no longer possess epitopes recognized by anti-Lex mAbs. In this context, we attempted to map the epitope recognized by anti-DimLex mAb SH2 by titrations and competitive inhibition experiments using oligosaccharide fragments of DimLex as well as Lex analogues. We compare our results with that reported for anti-Lex mAb SH1 and anti-polymeric Lex mAbs 1G5F6 and 291-2G3-A. While SH1 recognizes an epitope localized to the non-reducing end Lex trisaccharide, SH2, 1G5F6, and 291-2G3-A have greater affinity for DimLex conjugates than for Lex conjugates. We show, however, that the Lex trisaccharide is still an important recognition element for SH2, which (like 1G5F6 and 291-2G3-A) makes contacts with all three sugar units of Lex. In contrast to mAb SH1, anti-polymeric Lex mAbs make contact with the GlcNAc acetamido group, suggesting that epitopes extend further from the non-reducing end Lex. Results with SH2 show that this epitope is only recognized when DimLex is presented by glycoconjugates. We have reported that DimLex adopts two conformations around the β-d-GlcNAc-(1→3)-d-Gal bond connecting the Lex trisaccharides. We propose that only one of these conformations is recognized by SH2 and that this conformation is favored when the hexasaccharide is presented as part of a glycoconjugate such as DimLex-bovine serum albumin (DimLex-BSA). Proper presentation of the oligosaccharide candidate via conjugation to a protein or lipid is essential for the design of an anti-cancer vaccine or immunotherapeutic based on DimLex.
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Affiliation(s)
- Sinthuja Jegatheeswaran
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Immunology Department, University of Toronto, 1 King’s College Circle, Toronto, ON M5S-1A8, Canada
| | - Ari Asnani
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Department of Chemistry, Universitas Jenderal Soedirman, Purwokerto, Jawa Tengah 53123, Indonesia
| | - Adam Forman
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON M5S-3H6, Canada
| | - Jenifer L. Hendel
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Research and Development, Ludger Ltd., Culham Science Centre, Abingdon, Oxfordshire OX14-3EB, UK
| | - Christopher J. Moore
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Quality Control, SteriMax Inc., 2770 Portland Dr, Oakville, ON L6H-6R4, Canada
| | - Ali Nejatie
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A1S6, Canada
| | - An Wang
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- SGS-CSTC Standards Technical Services Co., Ltd. 4/F, 4th Building, 889 Yishan Road, Xuhui District, Shanghai 200233, China
| | - Jo-Wen Wang
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- IQVIA, QuintilesIMS, Clinical Research, 10188 Telesis Ct #400, San Diego, CA 92121, USA
| | - France-Isabelle Auzanneau
- Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada; (S.J.); (A.A.); (A.F.); (J.L.H.); (C.J.M.); (A.N.); (A.W.); (J.-W.W.)
- Correspondence:
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4
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Grant OC, Montgomery D, Ito K, Woods RJ. Analysis of the SARS-CoV-2 spike protein glycan shield reveals implications for immune recognition. Sci Rep 2020; 10:14991. [PMID: 32929138 PMCID: PMC7490396 DOI: 10.1038/s41598-020-71748-7] [Citation(s) in RCA: 233] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/17/2020] [Indexed: 12/19/2022] Open
Abstract
Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses. These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the innate and adaptive immune response to the SARS-CoV-2 virus or to a related vaccine. The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the notable exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight of the S trimer (17% for the HEK293 glycoform) they shield approximately 40% of the protein surface.
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Affiliation(s)
- Oliver C Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - David Montgomery
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Keigo Ito
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA
| | - Robert J Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA, 30602, USA.
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Grant OC, Montgomery D, Ito K, Woods RJ. Analysis of the SARS-CoV-2 spike protein glycan shield: implications for immune recognition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.07.030445. [PMID: 32511307 PMCID: PMC7217288 DOI: 10.1101/2020.04.07.030445] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Here we have generated 3D structures of glycoforms of the spike (S) glycoprotein from SARS-CoV-2, based on reported 3D structures and glycomics data for the protein produced in HEK293 cells. We also analyze structures for glycoforms representing those present in the nascent glycoproteins (prior to enzymatic modifications in the Golgi), as well as those that are commonly observed on antigens present in other viruses. These models were subjected to molecular dynamics (MD) simulation to determine the extent to which glycan microheterogeneity impacts the antigenicity of the S glycoprotein. Lastly, we have identified peptides in the S glycoprotein that are likely to be presented in human leukocyte antigen (HLA) complexes, and discuss the role of S protein glycosylation in potentially modulating the adaptive immune response to the SARS-CoV-2 virus or to a related vaccine. The 3D structures show that the protein surface is extensively shielded from antibody recognition by glycans, with the exception of the ACE2 receptor binding domain, and also that the degree of shielding is largely insensitive to the specific glycoform. Despite the relatively modest contribution of the glycans to the total molecular weight (17% for the HEK293 glycoform) the level of surface shielding is disproportionately high at 42%.
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Affiliation(s)
- Oliver C. Grant
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| | - David Montgomery
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| | - Keigo Ito
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
| | - Robert J. Woods
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602
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6
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Abstract
Complex carbohydrates are ubiquitous in nature, and together with proteins and nucleic acids they comprise the building blocks of life. But unlike proteins and nucleic acids, carbohydrates form nonlinear polymers, and they are not characterized by robust secondary or tertiary structures but rather by distributions of well-defined conformational states. Their molecular flexibility means that oligosaccharides are often refractory to crystallization, and nuclear magnetic resonance (NMR) spectroscopy augmented by molecular dynamics (MD) simulation is the leading method for their characterization in solution. The biological importance of carbohydrate-protein interactions, in organismal development as well as in disease, places urgency on the creation of innovative experimental and theoretical methods that can predict the specificity of such interactions and quantify their strengths. Additionally, the emerging realization that protein glycosylation impacts protein function and immunogenicity places the ability to define the mechanisms by which glycosylation impacts these features at the forefront of carbohydrate modeling. This review will discuss the relevant theoretical approaches to studying the three-dimensional structures of this fascinating class of molecules and interactions, with reference to the relevant experimental data and techniques that are key for validation of the theoretical predictions.
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Affiliation(s)
- Robert J Woods
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology , University of Georgia , 315 Riverbend Road , Athens , Georgia 30602 , United States
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7
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Engström O, Mobarak H, Ståhle J, Widmalm G. Conformational Dynamics and Exchange Kinetics of N-Formyl and N-Acetyl Groups Substituting 3-Amino-3,6-dideoxy-α-d-galactopyranose, a Sugar Found in Bacterial O-Antigen Polysaccharides. J Phys Chem B 2017; 121:9487-9497. [PMID: 28933544 DOI: 10.1021/acs.jpcb.7b05611] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Three dimensional shape and conformation of carbohydrates are important factors in molecular recognition events and the N-acetyl group of a monosaccharide residue can function as a conformational gatekeeper whereby it influences the overall shape of the oligosaccharide. NMR spectroscopy and quantum mechanics (QM) calculations are used herein to investigate both the conformational preferences and the dynamic behavior of N-acetyl and N-formyl substituents of 3-amino-3,6-dideoxy-α-d-galactopyranose, a sugar and substitution pattern found in bacterial O-antigen polysaccharides. QM calculations suggest that the amide oxygen can be involved in hydrogen bonding with the axial OH4 group primarily but also with the equatorial OH2 group. However, an NMR J coupling analysis indicates that the θ1 torsion angle, adjacent to the sugar ring, prefers an ap conformation where conformations <180° also are accessible, but does not allow for intramolecular hydrogen bonding. In the formyl-substituted compound 4JHH coupling constants to the exo-cyclic group were detected and analyzed. A van't Hoff analysis revealed that the trans conformation at the amide bond is favored by ΔG° ≈ - 0.8 kcal·mol-1 in the formyl-containing compound and with ΔG° ≈ - 2.5 kcal·mol-1 when the N-acetyl group is the substituent. In both cases the enthalpic term dominates to the free energy, irrespective of water or DMSO as solvent, with only a small contribution from the entropic term. The cis-trans isomerization of the θ2 torsion angle, centered at the amide bond, was also investigated by employing 1H NMR line shape analysis and 13C NMR saturation transfer experiments. The extracted transition rate constants were utilized to calculate transition energy barriers that were found to be about 20 kcal·mol-1 in both DMSO-d6 and D2O. Enthalpy had a higher contribution to the energy barriers in DMSO-d6 compared to in D2O, where entropy compensated for the loss of enthalpy.
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Affiliation(s)
- Olof Engström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Hani Mobarak
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Jonas Ståhle
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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8
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Baumgärtner F, Jurzitza L, Conrad J, Beifuss U, Sprenger GA, Albermann C. Synthesis of fucosylated lacto-N-tetraose using whole-cell biotransformation. Bioorg Med Chem 2015; 23:6799-806. [DOI: 10.1016/j.bmc.2015.10.005] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/01/2015] [Accepted: 10/05/2015] [Indexed: 02/06/2023]
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9
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Jackson TA, Robertson V, Auzanneau FI. Evidence for Two Populated Conformations for the Dimeric LeX and LeALeX Tumor-Associated Carbohydrate Antigens. J Med Chem 2014; 57:817-27. [DOI: 10.1021/jm401576x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Trudy A. Jackson
- Department of Chemistry, University of Guelph, Guelph, Ontario, N1G2W1, Canada
| | - Valerie Robertson
- Department of Chemistry, University of Guelph, Guelph, Ontario, N1G2W1, Canada
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10
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Abstract
Glycan structural information is a prerequisite for elucidation of carbohydrate function in biological systems. To this end we employ a tripod approach for investigation of carbohydrate 3D structure and dynamics based on organic synthesis; different experimental spectroscopy techniques, NMR being of prime importance; and molecular simulations using, in particular, molecular dynamics (MD) simulations. The synthesis of oligosaccharides in the form of glucosyl fluorides is described, and their use as substrates for the Lam16A E115S glucosyl synthase is exemplified as well as a conformational analysis of a cyclic β-(1→3)-heptaglucan based on molecular simulations. The flexibility of the N-acetyl group of aminosugars is by MD simulations indicated to function as a gatekeeper for transitions of glycosidic torsion angles to other regions of conformational space. A novel approach to visualize glycoprotein (GP) structures is presented in which the protein is shown by, for example, ribbons, but instead of stick or space-filling models for the carbohydrate portion it is visualized by the colored geometrical figures known as CFG representation in a 3D way, which we denote 3D-CFG, thereby effectively highlighting the sugar residues of the glycan part of the GP and the position(s) on the protein.
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Jo S, Lee HS, Skolnick J, Im W. Restricted N-glycan conformational space in the PDB and its implication in glycan structure modeling. PLoS Comput Biol 2013; 9:e1002946. [PMID: 23516343 PMCID: PMC3597548 DOI: 10.1371/journal.pcbi.1002946] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2012] [Accepted: 01/10/2013] [Indexed: 11/29/2022] Open
Abstract
Understanding glycan structure and dynamics is central to understanding protein-carbohydrate recognition and its role in protein-protein interactions. Given the difficulties in obtaining the glycan's crystal structure in glycoconjugates due to its flexibility and heterogeneity, computational modeling could play an important role in providing glycosylated protein structure models. To address if glycan structures available in the PDB can be used as templates or fragments for glycan modeling, we present a survey of the N-glycan structures of 35 different sequences in the PDB. Our statistical analysis shows that the N-glycan structures found on homologous glycoproteins are significantly conserved compared to the random background, suggesting that N-glycan chains can be confidently modeled with template glycan structures whose parent glycoproteins share sequence similarity. On the other hand, N-glycan structures found on non-homologous glycoproteins do not show significant global structural similarity. Nonetheless, the internal substructures of these N-glycans, particularly, the substructures that are closer to the protein, show significantly similar structures, suggesting that such substructures can be used as fragments in glycan modeling. Increased interactions with protein might be responsible for the restricted conformational space of N-glycan chains. Our results suggest that structure prediction/modeling of N-glycans of glycoconjugates using structure database could be effective and different modeling approaches would be needed depending on the availability of template structures. An N-glycan is a carbohydrate chain covalently linked to the side chain of asparagine. Due to the flexibility of carbohydrate chains, it is believed that the N-glycan chains would not have a well-defined structure. However, our survey of N-glycan structures in the PDB shows that the N-glycan structures found on the surfaces of homologous glycoproteins are significantly conserved. This suggests that the interaction between the carbohydrate and the protein structure around the glycan chain plays an important role in determining the N-glycan structure. While the global N-glycan structures found on the surfaces of non-homologous glycoproteins are not conserved, the conformations of the carbohydrate residues that are closer to the protein appear to be more conserved. Our analysis highlights the applicability of template-based approaches used in protein structure prediction to structure prediction and modeling of N-glycans of glycoproteins.
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Affiliation(s)
- Sunhwan Jo
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, United States of America
| | - Hui Sun Lee
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, United States of America
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, Georgia, United States of America
| | - Wonpil Im
- Department of Molecular Biosciences and Center for Bioinformatics, The University of Kansas, Lawrence, Kansas, United States of America
- * E-mail:
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Kotsyubynskyy D, Zerbetto M, Soltesova M, Engström O, Pendrill R, Kowalewski J, Widmalm G, Polimeno A. Stochastic modeling of flexible biomolecules applied to NMR relaxation. 2. Interpretation of complex dynamics in linear oligosaccharides. J Phys Chem B 2012. [PMID: 23185964 DOI: 10.1021/jp306627q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A computational stochastic approach is applied to the description of flexible molecules. By combining (i) molecular dynamics simulations, (ii) hydrodynamics approaches, and (iii) a multidimensional diffusive description for internal and global dynamics, it is possible to build an efficient integrated approach to the interpretation of relaxation processes in flexible systems. In particular, the model is applied to the interpretation of nuclear magnetic relaxation measurements of linear oligosaccharides, namely a mannose-containing trisaccharide and the pentasaccharide LNF-1. Experimental data are reproduced with sufficient accuracy without free model parameters.
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Affiliation(s)
- Dmytro Kotsyubynskyy
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova 35131, Italy
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Canales A, Jiménez-Barbero J, Martín-Pastor M. Review: Use of residual dipolar couplings to determine the structure of carbohydrates. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2012; 50 Suppl 1:S80-S85. [PMID: 23280664 DOI: 10.1002/mrc.3888] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 09/08/2012] [Accepted: 09/20/2012] [Indexed: 05/28/2023]
Abstract
Solution nuclear magnetic resonance spectroscopy is especially useful in the carbohydrate field. The measurement of residual dipolar couplings provides long-range structural information, a valuable complement for the structural study of carbohydrates either in its free form or in the bound state to proteins. They permit to deduce the geometry and the flexibility of the glycosidic linkages, which have a major influence on the conformation of carbohydrates and their overall shape. This article reviews the current application of the residual dipolar couplings methodology to carbohydrates.
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Affiliation(s)
- A Canales
- Department Organic Chemistry, Universidad Complutense de Madrid, Madrid, Spain
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14
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Zaccheus M, Pendrill R, Jackson TA, Wang A, Auzanneau FI, Widmalm G. Conformational Dynamics of a Central Trisaccharide Fragment of the LeaLex Tumor Associated Antigen Studied by NMR Spectroscopy and Molecular Dynamics Simulations. European J Org Chem 2012. [DOI: 10.1002/ejoc.201200569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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15
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Lütteke T. The use of glycoinformatics in glycochemistry. Beilstein J Org Chem 2012; 8:915-29. [PMID: 23015842 PMCID: PMC3388882 DOI: 10.3762/bjoc.8.104] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 05/29/2012] [Indexed: 01/10/2023] Open
Abstract
Glycoinformatics is a small but growing branch of bioinformatics and chemoinformatics. Various resources are now available that can be of use to glycobiologists, but also to chemists who work on the synthesis or analysis of carbohydrates. This article gives an overview of existing glyco-specific databases and tools, with a focus on their application to glycochemistry: Databases can provide information on candidate glycan structures for synthesis, or on glyco-enzymes that can be used to synthesize carbohydrates. Statistical analyses of glycan databases help to plan glycan synthesis experiments. 3D-Structural data of protein-carbohydrate complexes are used in targeted drug design, and tools to support glycan structure analysis aid with quality control. Specific problems of glycoinformatics compared to bioinformatics for genomics or proteomics, especially concerning integration and long-term maintenance of the existing glycan databases, are also discussed.
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Affiliation(s)
- Thomas Lütteke
- Justus-Liebig-University Gießen, Institute of Veterinary Physiology and Biochemistry, Frankfurter Str. 100, 35392 Gießen, Germany
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16
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Säwén E, Hinterholzinger F, Landersjö C, Widmalm G. Conformational flexibility of the pentasaccharide LNF-2 deduced from NMR spectroscopy and molecular dynamics simulations. Org Biomol Chem 2012; 10:4577-85. [PMID: 22572908 DOI: 10.1039/c2ob25189b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human milk oligosaccharides (HMOs) are important as prebiotics since they stimulate the growth of beneficial bacteria in the intestine and act as receptor analogues that can inhibit the binding of pathogens. The conformation and dynamics of the HMO Lacto-N-fucopentaose 2 (LNF-2), α-L-Fucp-(1 → 4)[β-D-Galp-(1 → 3)]-β-D-GlcpNAc-(1 → 3)-β-D-Galp-(1 → 4)-D-Glcp, having a Lewis A epitope, has been investigated employing NMR spectroscopy and molecular dynamics (MD) computer simulations. 1D (1)H,(1)H-NOESY experiments were used to obtain proton-proton cross-relaxation rates from which effective distances were deduced and 2D J-HMBC and 1D long-range experiments were utilized to measure trans-glycosidic (3)J(CH) coupling constants. The MD simulations using the PARM22/SU01 force field for carbohydrates were carried out for 600 ns with explicit water as solvent which resulted in excellent sampling for flexible glycosidic torsion angles. In addition, in vacuo MD simulations were performed using an MM3-2000 force field, but the agreement was less satisfactory based on an analysis of heteronuclear trans-glycosidic coupling constants. LNF-2 has a conformationally well-defined region consisting of the terminal branched part of the pentasaccharide, i.e., the Lewis A epitope, and a flexible β-D-GlcpNAc-(1 → 3)-β-D-Galp-linkage towards the lactose unit, which is situated at the reducing end. For this β-(1 → 3)-linkage a negative ψ torsion angle is favored, when experimental NMR data is combined with the MD simulation in the analysis. In addition, flexibility on a similar time scale, i.e., on the order of the global overall molecular reorientation, may also be present for the ϕ torsion angle of the β-D-Galp-(1 → 4)-D-Glcp-linkage as suggested by the simulation. It was further observed from a temperature variation study that some (1)H NMR chemical shifts of LNF-2 were highly sensitive and this study indicates that Δδ/ΔT may be an additional tool for revealing conformational dynamics of oligosaccharides.
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Affiliation(s)
- Elin Säwén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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