1
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Lutsyk V, Plazinski W. Exploring Ring Conformation in Uronate Monosaccharides: Insights from Ab Initio Calculations and Classical Molecular Dynamics Simulations. J Phys Chem B 2024; 128:472-491. [PMID: 38170925 DOI: 10.1021/acs.jpcb.3c06556] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The study focuses on the conformational properties of biologically relevant monosaccharides belonging to the group of uronates: α-l-iduronate, O2-sulfated-α-l-iduronate, and O2-sulfated-α-l-guluronate, either unfunctionalized or O1-methylated. We applied the previously proposed two-step methodology, combining classical MD simulations and subsequent ab initio (QM) calculations, performed on a rationally subsampled set of molecular configurations. We found that, regardless of the number of molecular configurations considered, the level of theory, and the weighting scheme applied, none of the QM approaches is capable of predicting the correct conformational equilibrium of sulfated iduronates as long as the tight counterion binding is not considered. Multicenter, ring-shape-specific binding of either Na+ or Ca2+ ions drastically shifts the conformational equilibrium of the pyranose ring in sulfated iduronates toward 1C4 but does not significantly affect the conformation of non-sulfated compounds. A similar shift is observed upon the protonation of carboxyl groups in all iduronates. In addition, we report a set of average J-coupling constant values related to vicinal protons bound to the pyranose ring of iduronates and corresponding to each of the three main groups of ring conformers, i.e., 4C1, B/S (boat/skew boat), and 1C4. In combination with the conformational energies or with the experimental data, these values allowed the relative proportions of the ring conformers to be estimated and the Karplus-type equations linking the 3JHH-coupling constants to the torsion angles within the pyranose ring to be refined.
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Affiliation(s)
- Valery Lutsyk
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Krakow, Poland
- Department of Biopharmacy, Medical University of Lublin, Chodzki 4a, 20-093 Lublin, Poland
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2
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Janke JJ, Yu Y, Pomin VH, Zhao J, Wang C, Linhardt RJ, García AE. Characterization of Heparin's Conformational Ensemble by Molecular Dynamics Simulations and Nuclear Magnetic Resonance Spectroscopy. J Chem Theory Comput 2022; 18:1894-1904. [PMID: 35108013 PMCID: PMC9027489 DOI: 10.1021/acs.jctc.1c00760] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Heparin is a highly charged, polysulfated polysaccharide and serves as an anticoagulant. Heparin binds to multiple proteins throughout the body, suggesting a large range of potential therapeutic applications. Although its function has been characterized in multiple physiological contexts, heparin's solution conformational dynamics and structure-function relationships are not fully understood. Molecular dynamics (MD) simulations facilitate the analysis of a molecule's underlying conformational ensemble, which then provides important information necessary for understanding structure-function relationships. However, for MD simulations to afford meaningful results, they must both provide adequate sampling and accurately represent the energy properties of a molecule. The aim of this study is to compare heparin's conformational ensemble using two well-developed force fields for carbohydrates, known as GLYCAM06 and CHARMM36, using replica exchange molecular dynamics (REMD) simulations, and to validate these results with NMR experiments. The anticoagulant sequence, an ultra-low-molecular-weight heparin, known as Arixtra (fondaparinux, sodium), was simulated with both parameter sets. The results suggest that GLYCAM06 matches experimental nuclear magnetic resonance three-bond J-coupling values measured for Arixtra better than CHARMM36. In addition, NOESY and ROESY experiments suggest that Arixtra is very flexible in the sub-millisecond time scale and does not adopt a unique structure at 25 C. Moreover, GLYCAM06 affords a much more dynamic conformational ensemble for Arixtra than CHARMM36.
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Affiliation(s)
- J Joel Janke
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Yanlei Yu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Vitor H Pomin
- Department of BioMolecular Sciences, University of Mississippi, Oxford, Mississippi 38677, United States
| | - Jing Zhao
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Chunyu Wang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Robert J Linhardt
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Angel E García
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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3
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The conformation of the idopyranose ring revisited: How subtle O-substituent induced changes can be deduced from vicinal 1H-NMR coupling constants. Carbohydr Res 2020; 496:108052. [PMID: 32738719 DOI: 10.1016/j.carres.2020.108052] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/17/2020] [Accepted: 05/27/2020] [Indexed: 01/18/2023]
Abstract
The idopyranose ring plays a pivotal role in the conformational, dynamical, and intermolecular binding aspects of glycosaminoglycans like heparin and dermatan sulfate and it was early on assigned a role in the Sugar Code governing biological recognition processes. There is consensus that next to the two canonical 1C4 and 4C1 chair conformations, the conformational space accessible to the idopyranose ring entails a 2SO skew-boat conformation, but the equilibrium between these three ring puckers has evaded satisfactory quantification. In this study a meta-analysis of X-ray solid-state data and vicinal NMR coupling constants is presented, based on the Truncated Fourier Puckering (TFP) formalism and the generalized Karplus (CAGPLUS) equation. This approach yields a model-free, granular and consistent reckoning of 159 idopyranose solution puckering equilibria studied by NMR and allows us to reproduce the involved 636 NMR vicinal couplings with an overall residual RMS(Jobs-Jcalc) of 0.184 Hz. Our analyses show that for all ring systems examined, the idopyranosyl chair conformations take up the same ring pucker irrespective of the ring substituent pattern or a vast variety in experimental conditions. Instead, it is the (skew-)boat conformation that adapts to the substitution pattern of the idopyranose ring or a specific sulfation pattern of neighboring saccharides. All idopyranose rings are involved in conformational equilibria that subsume the aforementioned conformers which turn out to differ only a few kJ/mole in conformational energy. Thus, the plasticity and flexibility of idopyranose remains intact under practically all circumstances and, as the glycosidic linkages in heparin are considered to be relatively stiff, the iduronic moiety functions as the linchpin of heparin flexibility thereby being rather a "space(r)" than a "letter" in the alleged Sugar Code alphabet.
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4
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Alibay I, Bryce RA. Ring Puckering Landscapes of Glycosaminoglycan-Related Monosaccharides from Molecular Dynamics Simulations. J Chem Inf Model 2019; 59:4729-4741. [PMID: 31609614 DOI: 10.1021/acs.jcim.9b00529] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conformational flexibility of the glycosaminoglycans (GAGs) is known to be key in their binding and biological function, for example in regulating coagulation and cell growth. In this work, we employ enhanced sampling molecular dynamics simulations to probe the ring conformations of GAG-related monosaccharides, including a range of acetylated and sulfated GAG residues. We first perform unbiased MD simulations of glucose anomers and the epimers glucuronate and iduronate. These calculations indicate that in some cases, an excess of 15 μs is required for adequate sampling of ring pucker due to the high energy barriers between states. However, by applying our recently developed msesMD simulation method (multidimensional swarm-enhanced sampling molecular dynamics), we were able to quantitatively and rapidly reproduce these ring pucker landscapes. From msesMD simulations, the puckering free energy profiles were then compared for 15 further monosaccharides related to GAGs; this includes to our knowledge the first simulation study of sulfation effects on β-GalNAc ring puckering. For the force field employed, we find that in general the calculated pucker free energy profiles for sulfated sugars were similar to the corresponding unsulfated profiles. This accords with recent experimental studies suggesting that variation in ring pucker of sulfated GAG residues is primarily dictated by interactions with surrounding residues rather than by intrinsic conformational preference. As an exception to this, however, we predict that 4-O-sulfation of β-GalNAc leads to reduced ring rigidity, with a significant lowering in energy of the 1C4 ring conformation; this observation may have implications for understanding the structural basis of the biological function of β-GalNAc-containing glycosaminoglycans such as dermatan sulfate.
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Affiliation(s)
- Irfan Alibay
- Division of Pharmacy and Optometry, School of Health Sciences , University of Manchester , Oxford Road , Manchester M13 9PT , U.K.,Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry , University of Oxford , South Parks Road , Oxford OX1 3QU , U.K
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences , University of Manchester , Oxford Road , Manchester M13 9PT , U.K
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5
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He QQ, Trim PJ, Lau AA, King BM, Hopwood JJ, Hemsley KM, Snel MF, Ferro V. Synthetic Disaccharide Standards Enable Quantitative Analysis of Stored Heparan Sulfate in MPS IIIA Murine Brain Regions. ACS Chem Neurosci 2019; 10:3847-3858. [PMID: 31264853 DOI: 10.1021/acschemneuro.9b00328] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Heparan sulfate (HS) is a complex polysaccharide from the glycosaminoglycan (GAG) family that accumulates in tissues in several neurological lysosomal storage diseases known as mucopolysaccharidosis (MPS) disorders. The quantitation of HS in biological samples is important for studying MPS disorders but is very challenging because of its high molecular weight and heterogeneity. Recently, acid-catalyzed butanolysis followed by LC-MS/MS analysis has emerged as a promising method for the determination of HS. Butanolysis of HS produces fully desulfated disaccharide cleavage products which are detected by LC-MS/MS. Herein we describe the synthesis of butylated HS disaccharide standards and their use for determining the identity of major product peaks in LC-MS chromatograms from butanolysis of HS as well as the related GAGs heparin and heparosan. Furthermore, synthesis of a d9-labeled disaccharide internal standard enabled the development of a quantitative LC-MS/MS assay for HS. The assay was utilized for the analysis of MPS IIIA mouse brain tissues, revealing significant differences in abundance and in the regional accumulation of the various HS disaccharides in affected mice.
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Affiliation(s)
- Qi Qi He
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Paul J. Trim
- Mass Spectrometry Group, Hopwood Centre for Neurobiology, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5000, Australia
- Proteomics, Metabolomics and MS-Imaging Core Facility, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia
| | - Adeline A. Lau
- Childhood Dementia Research Group, Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Barbara M. King
- Childhood Dementia Research Group, Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia
| | - John J. Hopwood
- Hopwood Centre for Neurobiology, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia
| | - Kim M. Hemsley
- Childhood Dementia Research Group, Hopwood Centre for Neurobiology, Lifelong Health Theme, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5000, Australia
| | - Marten F. Snel
- Mass Spectrometry Group, Hopwood Centre for Neurobiology, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, South Australia 5000, Australia
- Proteomics, Metabolomics and MS-Imaging Core Facility, South Australian Health and Medical Research Institute, Adelaide, South Australia 5000, Australia
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
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He QQ, Trim PJ, Snel MF, Hopwood JJ, Ferro V. Synthesis and mass spectrometric analysis of disaccharides from methanolysis of heparan sulfate. Org Biomol Chem 2018; 16:8791-8803. [DOI: 10.1039/c8ob02225a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Heparan sulfate (HS) disaccharides were synthesized to identify HS methanolysis products by LC-MS/MS with applications for mucopolysaccharidosis disorders.
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Affiliation(s)
- Qi Qi He
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
| | - Paul J. Trim
- Hopwood Centre for Neurobiology
- South Australian Health and Medical Research Institute
- Adelaide
- Australia
| | - Marten F. Snel
- Hopwood Centre for Neurobiology
- South Australian Health and Medical Research Institute
- Adelaide
- Australia
| | - John J. Hopwood
- Hopwood Centre for Neurobiology
- South Australian Health and Medical Research Institute
- Adelaide
- Australia
| | - Vito Ferro
- School of Chemistry and Molecular Biosciences
- The University of Queensland
- Brisbane
- Australia
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7
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Huang TY, Irene D, Zulueta MML, Tai TJ, Lain SH, Cheng CP, Tsai PX, Lin SY, Chen ZG, Ku CC, Hsiao CD, Chyan CL, Hung SC. Structure of the Complex between a Heparan Sulfate Octasaccharide and Mycobacterial Heparin-Binding Hemagglutinin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201612518] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Teng-Yi Huang
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Deli Irene
- Department of Chemistry; National Dong Hwa University; No. 1, Section 2, Da Hsueh Road, Shoufeng Hualien 974 Taiwan
| | - Medel Manuel L. Zulueta
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Tzu-Jui Tai
- Department of Chemistry; National Dong Hwa University; No. 1, Section 2, Da Hsueh Road, Shoufeng Hualien 974 Taiwan
| | - Shih-Han Lain
- Department of Chemistry; National Dong Hwa University; No. 1, Section 2, Da Hsueh Road, Shoufeng Hualien 974 Taiwan
| | - Cheng-Po Cheng
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Ping-Xi Tsai
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Shu-Yi Lin
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Zhi-Geng Chen
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Chiao-Chu Ku
- Institute of Molecular Biology; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
| | - Chia-Lin Chyan
- Department of Chemistry; National Dong Hwa University; No. 1, Section 2, Da Hsueh Road, Shoufeng Hualien 974 Taiwan
| | - Shang-Cheng Hung
- Genomics Research Center; Academia Sinica; No. 128, Section 2, Academia Road Taipei 115 Taiwan
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8
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Huang TY, Irene D, Zulueta MML, Tai TJ, Lain SH, Cheng CP, Tsai PX, Lin SY, Chen ZG, Ku CC, Hsiao CD, Chyan CL, Hung SC. Structure of the Complex between a Heparan Sulfate Octasaccharide and Mycobacterial Heparin-Binding Hemagglutinin. Angew Chem Int Ed Engl 2017; 56:4192-4196. [PMID: 28294485 DOI: 10.1002/anie.201612518] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2016] [Revised: 02/11/2016] [Indexed: 11/06/2022]
Abstract
Heparin-binding hemagglutinin (HBHA) is a 199 amino acid virulence factor at the envelope of Mycobacterium tuberculosis that contributes to latent tuberculosis. The binding of HBHA to respiratory epithelial cells, which leads to extrapulmonary dissemination of the pathogen, is mediated by cell-surface heparan sulfate (HS). We report the structural characterization of the HBHA/HS complex by NMR spectroscopy. To develop a model for the molecular recognition, the first chemically synthesized uniformly 13 C- and 15 N-labeled HS octasaccharide and a uniformly 13 C- and 15 N-labeled form of HBHA were prepared. Residues 180-195 at the C-terminal region of HBHA show large chemical shift perturbation upon association with the octasaccharide. Molecular dynamics simulations conforming to the multidimensional NMR data revealed key electrostatic and even hydrophobic interactions between the binding partners that may aid in the development of agents targeting the binding event.
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Affiliation(s)
- Teng-Yi Huang
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Deli Irene
- Department of Chemistry, National Dong Hwa University, No. 1, Section 2, Da Hsueh Road, Shoufeng, Hualien, 974, Taiwan
| | - Medel Manuel L Zulueta
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Tzu-Jui Tai
- Department of Chemistry, National Dong Hwa University, No. 1, Section 2, Da Hsueh Road, Shoufeng, Hualien, 974, Taiwan
| | - Shih-Han Lain
- Department of Chemistry, National Dong Hwa University, No. 1, Section 2, Da Hsueh Road, Shoufeng, Hualien, 974, Taiwan
| | - Cheng-Po Cheng
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Ping-Xi Tsai
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Shu-Yi Lin
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Zhi-Geng Chen
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Chiao-Chu Ku
- Institute of Molecular Biology, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Chwan-Deng Hsiao
- Institute of Molecular Biology, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
| | - Chia-Lin Chyan
- Department of Chemistry, National Dong Hwa University, No. 1, Section 2, Da Hsueh Road, Shoufeng, Hualien, 974, Taiwan
| | - Shang-Cheng Hung
- Genomics Research Center, Academia Sinica, No. 128, Section 2, Academia Road, Taipei, 115, Taiwan
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Abstract
High-resolution NMR and density functional theory (DFT) calculations have been applied to analysis of heparin pentasaccharide 3D structure in aqueous solution. The fully optimized molecular geometry of two pentasaccharide conformations (differing from each other in the form, one (1)C4 and the other (2)S0, of the sulfated iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as explicit water molecules. The presented approach enabled insight into variations of the bond lengths, bond angles, and torsion angles, formations of intra- and intermolecular hydrogen bonds, and ionic interactions in the two pentasaccharide conformations. A rather complex hydrogen bond network is formed, including inter-residue and intraresidue bonds between the NH group in the GlcN,3,6S with oxygens linked to C-2 at the IdoA2S residue and the glycosidic O-1 and the neighboring OSO3(-) group linked to C-3 in the same residue. On the other hand, because the first hydration shell is strongly influenced by strong ion-ion and ion-dipole interactions between sodium ions, sulfates, carboxylates, and -OH groups, ionic interactions play an important role in the stabilization of the 3D structure. The DFT-computed three-bond proton-proton coupling constants also showed that best agreement with experiment was obtained with a weighted average of 15:85 ((1)C4/(2)S0) of the sulfated iduronic acid forms indicating that the ratio is even more shifted toward the (2)S0 form than previously supposed. The DFT-computed pentasaccharide conformation differs from the previously published data, with the main changes at the glycosidic linkages, namely, the ψ1 torsion angles and the ϕ3 angle. The comparison of the glycosidic linkage torsion angle values in solution with the antithrombin-pentasaccharide complex also indicates that the pentasaccharide conformation changes upon binding to antithrombin III. The data supports the assumption that the protein selects the more populated (2)S0 conformer of heparin pentasaccharide and, consequently, the binding process of heparin pentasaccharide with antithrombin III is energetically more favorable than formerly expected.
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Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava, Slovakia
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Hricovíni M, Driguez PA, Malkina OL. NMR and DFT analysis of trisaccharide from heparin repeating sequence. J Phys Chem B 2014; 118:11931-42. [PMID: 25254635 DOI: 10.1021/jp508045n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
NMR and density functional theory (DFT) have afforded detailed information on the molecular geometry and spin-spin coupling constants of a trisaccharide from the heparin repeating-sequence. The fully optimized molecular structures of two trisaccharide conformations (differing from each other in the form of the central iduronic acid residue) were obtained using the B3LYP/6-311+G(d,p) level of theory in the presence of solvent, the latter included as either explicit water molecules or via a continuum solvent model. NMR spin-spin coupling constants were also computed using various basis sets and functionals and then compared with measured experimental values. Optimized structures for both conformers showed differences in geometry at the glycosidic linkages and in the formation of intramolecular hydrogen bonds. Three-bond proton-proton coupling constants ((3)JH-C-C-H), based on fully optimized geometry computed using the B3LYP/6-311+G(d,p)/UFF level of theory and hydrated with 57 water molecules, showed that the best agreement with experiment was obtained with the 6-311+G(d,p) basis set and a weighted average of 55:45 ((1)C4:(2)S0) of the IdoA2S forms. Other basis sets, DGDZVP and TZVP, also gave acceptable data for most coupling constants, with DGDZVP outperforming the TZVP. Detailed analysis of Fermi-contact contributions to (3)JH-C-C-H showed that important contributions arise from oxygen at both glycosidic linkages, as well as from oxygen atoms on the neighboring monosaccharide units. Their contribution to the Fermi term cannot be neglected and must be taken into account for a correct description of coupling constants. The analysis also showed that the magnitude of paramagnetic (PSO) and diamagnetic (DSO) spin-orbit contributions is comparable to the magnitude of the Fermi-contact contribution in some coupling constants in the IdoA2S residue. Calculations of the localized molecular orbital contributions to the DSO terms from separate conformational residues showed that the contribution from adjacent residues is not negligible and can be important for the spin-spin coupling constants between protons located close to the geometrical center of the molecule. These contributions should be taken into account when interpreting DSO terms in spin-spin coupling constants especially in large molecules.
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Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences , 845 38 Bratislava, Slovakia
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11
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Künze G, Gehrcke JP, Pisabarro MT, Huster D. NMR characterization of the binding properties and conformation of glycosaminoglycans interacting with interleukin-10. Glycobiology 2014; 24:1036-49. [DOI: 10.1093/glycob/cwu069] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
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12
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Solution NMR conformation of glycosaminoglycans. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 114:61-8. [DOI: 10.1016/j.pbiomolbio.2014.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2013] [Revised: 01/10/2014] [Accepted: 01/17/2014] [Indexed: 11/18/2022]
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13
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Abstract
Dynamical behaviors of glycosaminoglycans, as here illustrated with a hyaluronan oligosaccharide, are key regulators of biological functions.
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Affiliation(s)
- Vitor H. Pomin
- Program of Glycobiology
- Institute of Medical Biochemistry Leopoldo de Meis, and University Hospital Clementino Fraga Filho
- Federal University of Rio de Janeiro
- Rio de Janeiro, Brazil
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14
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Sattelle BM, Shakeri J, Almond A. Does Microsecond Sugar Ring Flexing Encode 3D-Shape and Bioactivity in the Heparanome? Biomacromolecules 2013; 14:1149-59. [DOI: 10.1021/bm400067g] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Benedict M. Sattelle
- Faculty of Life Sciences, University of Manchester, Manchester
Institute of Biotechnology,
131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Javad Shakeri
- Faculty of Life Sciences, University of Manchester, Manchester
Institute of Biotechnology,
131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Andrew Almond
- Faculty of Life Sciences, University of Manchester, Manchester
Institute of Biotechnology,
131 Princess Street, Manchester, M1 7DN, United Kingdom
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15
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Oborský P, Tvaroška I, Králová B, Spiwok V. Toward an accurate conformational modeling of iduronic acid. J Phys Chem B 2013; 117:1003-9. [PMID: 23286518 DOI: 10.1021/jp3100552] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Iduronic acid (IdoA), unlike most other monosaccharides, can adopt different ring conformations, depending on the context of the molecular structure. Accurate modeling of this building block is essential for understanding the role of glycosaminoglycans and other glycoconjugates. Here, we use metadynamics to predict equilibria of (1)C(4), (4)C(1) and (2)S(O) conformations of α-L-IdoA-OMe and α-L-IdoA2S-OMe. Different schemes of scaling of atoms separated by three bonds (1-4 interaction) were tested. It was found that scaling (reduction) of 1-4 electrostatic interactions significantly changes conformational preferences toward the (4)C(1) conformation. More interestingly, scaling of 1-4 van der Waals interaction favors skew-boat conformations. This shows that a minor modification of noncovalent 1-4 interactions parameters can provide a good agreement between populations of conformers of iduronic acid in water from simulations and experiments.
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Affiliation(s)
- Pavel Oborský
- Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague, Technická 3, Prague 6 166 28, Czech Republic
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16
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Toukach FV, Ananikov VP. Recent advances in computational predictions of NMR parameters for the structure elucidation of carbohydrates: methods and limitations. Chem Soc Rev 2013; 42:8376-415. [DOI: 10.1039/c3cs60073d] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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Sattelle BM, Almond A. Is N-acetyl-D-glucosamine a rigid 4C1 chair? Glycobiology 2011; 21:1651-62. [PMID: 21807769 PMCID: PMC3219419 DOI: 10.1093/glycob/cwr101] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2011] [Revised: 06/28/2011] [Accepted: 07/19/2011] [Indexed: 12/17/2022] Open
Abstract
Understanding microsecond-timescale dynamics is crucial to establish three-dimensional (3D) structure-activity relationships in sugars but has been intractable to experiments and simulations. As a consequence, whether arguably the most important chemical scaffold in glycobiology, N-acetyl-d-glucosamine (GlcNAc), deviates from a rigid (4)C(1) chair is unknown. Here, conformer populations and exchange kinetics were quantified from the longest aqueous carbohydrate simulations to date (0.2 ms total) of GlcNAc, four derivatives from heparan sulfate and their methylglycosides. Unmodified GlcNAc took 3-5 μs to reach a conformational equilibrium, which comprised a metastable (4)C(1) chair that underwent (4)C(1) ↔ (1)C(4) transitions at a predicted forward rate of 0.8 μs(-1) with an average (1)C(4)-chair lifetime of 3 ns. These predictions agree with high-resolution crystallography and nuclear magnetic resonance but not with the hypothesis that GlcNAc is a rigid (4)C(1) chair, concluded from previous experimental analyses and non-aqueous modeling. The methylglycoside was calculated to have a slower forward rate (0.3 μs(-1)) and a more stable (4)C(1) conformer (0.2 kcal mol(-1)), suggesting that pivotal 3D intermediates (particularly (2)S(O), (1)S(5) and B(2,5)) increased in energy, and water was implicated as a major cause. Sulfonation (N-, 3-O and 6-O) significantly augmented this effect by blocking pseudorotation, but did not alter the rotational preferences of hydroyxl or hydroxymethyl groups. We therefore propose that GlcNAc undergoes puckering exchange that is dependent on polymerization and sulfo substituents. Our analyses, and 3D model of the equilibrium GlcNAc conformer in water, can be used as dictionary data and present new opportunities to rationally modify puckering and carbohydrate bioactivity, with diverse applications from improving crop yields to disease amelioration.
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Affiliation(s)
| | - Andrew Almond
- Manchester Interdisciplinary Biocentre, 131 Princess Street, Manchester M1 7DN, UK
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18
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Sattelle BM, Hansen SU, Gardiner J, Almond A. Free energy landscapes of iduronic acid and related monosaccharides. J Am Chem Soc 2010; 132:13132-4. [PMID: 20809637 DOI: 10.1021/ja1054143] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The pyranose ring of L-iduronic acid (IdoA), a major constituent of the anticoagulant heparin, is an equilibrium of multiple ring puckers that have evaded quantification by experiment or computation. In order to resolve this enigma, we have calculated the free energy landscape of IdoA and two related monosaccharides from extensive microsecond simulations. After establishing that the simulated puckers had reached equilibrium, hypotheses were confirmed that (a) IdoA (1)C(4)- and (4)C(1)-chair conformations exchange on the microsecond time scale, (b) C5 epimerization leads to a (4)C(1)-chair, and (c) IdoA 2-O-sulfation (IdoA2S) stabilizes the (1)C(4) conformer. The IdoA and IdoA2S (1)C(4) conformers were isoenergetic and computed to be 0.9 and 2.6 kcal mol(-1) lower in free energy than their respective (4)C(1)-chair conformations. The simulations also predicted that the IdoA (2)S(O)-skew-boat was less populated than previously thought. Novel chemical synthesis and ultra-high-field NMR supported these observations, but slight discrepancies in observed and predicted NMR vicinal couplings implied that the simulation overestimated the population of the IdoA (4)C(1)-chair with respect to (1)C(4)-chair due to small force field inaccuracies that only manifest in long simulations. These free-energy calculations drive improvements in computational methods and provide a novel route to carbohydrate mimetic biomaterials and pharmaceuticals.
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Affiliation(s)
- Benedict M Sattelle
- Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK
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19
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Rudd TR, Skidmore MA, Guerrini M, Hricovini M, Powell AK, Siligardi G, Yates EA. The conformation and structure of GAGs: recent progress and perspectives. Curr Opin Struct Biol 2010; 20:567-74. [DOI: 10.1016/j.sbi.2010.08.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2010] [Revised: 07/23/2010] [Accepted: 08/11/2010] [Indexed: 10/19/2022]
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20
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Molecular structure of basic oligomeric building units of heparan-sulfate glycosaminoglycans. Struct Chem 2010. [DOI: 10.1007/s11224-010-9633-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Synthesis and conformational analysis of carbasugar bioisosteres of α-l-iduronic acid and its methyl glycoside. Carbohydr Res 2010; 345:984-93. [DOI: 10.1016/j.carres.2010.03.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 02/15/2010] [Accepted: 03/01/2010] [Indexed: 11/18/2022]
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22
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Gandhi NS, Mancera RL. Can current force fields reproduce ring puckering in 2-O-sulfo-α-l-iduronic acid? A molecular dynamics simulation study. Carbohydr Res 2010; 345:689-95. [DOI: 10.1016/j.carres.2009.12.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2009] [Revised: 11/30/2009] [Accepted: 12/20/2009] [Indexed: 10/20/2022]
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23
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Jin L, Hricovíni M, Deakin JA, Lyon M, Uhrín D. Residual dipolar coupling investigation of a heparin tetrasaccharide confirms the limited effect of flexibility of the iduronic acid on the molecular shape of heparin. Glycobiology 2009; 19:1185-96. [PMID: 19648354 PMCID: PMC2757574 DOI: 10.1093/glycob/cwp105] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The solution conformation of a fully sulfated heparin-derived tetrasaccharide, I, was studied in the presence of a 4-fold excess of Ca2+. Proton–proton and proton–carbon residual dipolar couplings (RDCs) were measured in a neutral aligning medium. The order parameters of two rigid hexosamine rings of I were determined separately using singular value decomposition and ab initio structures of disaccharide fragments of I. The order parameters were very similar implying that a common order tensor can be used to analyze the structure of I. Using one order tensor, RDCs of both hexosamine rings were used as restraints in molecular dynamics simulations. RDCs of the inner iduronic acid were calculated for every point of the molecular dynamics trajectory. The fitting of the calculated RDCs of the two forms of the iduronic acid to the experimental values yielded a population of 1C4 and 2So conformers of iduronic acid that agreed well with the analysis based on proton–proton scalar coupling constants. The glycosidic linkage torsion angles in RDC-restrained molecular dynamics (MD) structures of I are consistent with the interglycosidic three-bond proton–carbon coupling constants. These structures also show that the shape of heparin is not affected dramatically by the conformational flexibility of the iduronic acid ring. This is in line with conclusions of previous studies based on MD simulations and the analysis of 1H-1H NOEs. Our work therefore demonstrates the effectiveness of RDCs in the conformational analysis of glycosaminoglycans.
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Affiliation(s)
- Lan Jin
- School of Chemistry, University of Edinburgh, Edinburgh, Scotland
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24
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Guglieri S, Hricovíni M, Raman R, Polito L, Torri G, Casu B, Sasisekharan R, Guerrini M. Minimum FGF2 Binding Structural Requirements of Heparin and Heparan Sulfate Oligosaccharides As Determined by NMR Spectroscopy. Biochemistry 2008; 47:13862-9. [DOI: 10.1021/bi801007p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sara Guglieri
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Miloš Hricovíni
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Rahul Raman
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Laura Polito
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Giangiacomo Torri
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Benito Casu
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Ram Sasisekharan
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
| | - Marco Guerrini
- G. Ronzoni Institute for Chemical and Biochemical Research, Milan, Italy, Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia, Department of Biological Engineering, Harvard-MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, and Department of Organic and Industrial Chemistry, University of Milan, Milan, Italy
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25
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B3LYP/6-311++G* * study of structure and spin-spin coupling constant in heparin disaccharide. Carbohydr Res 2007; 342:1350-6. [PMID: 17445784 DOI: 10.1016/j.carres.2007.03.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 03/16/2007] [Accepted: 03/19/2007] [Indexed: 10/23/2022]
Abstract
Structures of heparin disaccharide have been analyzed by DFT using the B3LYP/6-311++G( * *) method. The optimized geometries of two forms of this disaccharide, differing in the conformation ((1)C(4) and (2)S(0)) of the IdoA2S residue, confirmed considerable influences of the sulfate and the carboxylate groups upon the pyranose ring geometries. The computed energies showed that disaccharide having the (1)C(4) form of the IdoA2S residue is more stable than that with the (2)S(0) form. Interatomic distances, bond and torsion angles showed that interconversion of the IdoA2S residue results in geometry changes in the GlcN,6S residue as well. Three-bond proton-proton and proton-carbon spin-spin coupling constants computed for both forms agree with the experimental data and indicate that only two chair forms contribute to the conformational equilibrium in disaccharide. Influences of the charged groups upon the magnitudes of spin-spin coupling constants are also discussed.
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