1
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Deshchenya V, Kondratyuk N, Lankin A, Norman G. Molecular dynamics study of sucrose aqueous solutions: from solution structure to transport coefficients. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.120456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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2
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Comparison of Methods for Bulk Automated Simulation of Glycosidic Bond Conformations. Int J Mol Sci 2020; 21:ijms21207626. [PMID: 33076365 PMCID: PMC7589101 DOI: 10.3390/ijms21207626] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 10/10/2020] [Accepted: 10/10/2020] [Indexed: 02/08/2023] Open
Abstract
Six empirical force fields were tested for applicability to calculations for automated carbohydrate database filling. They were probed on eleven disaccharide molecules containing representative structural features from widespread classes of carbohydrates. The accuracy of each method was queried by predictions of nuclear Overhauser effects (NOEs) from conformational ensembles obtained from 50 to 100 ns molecular dynamics (MD) trajectories and their comparison to the published experimental data. Using various ranking schemes, it was concluded that explicit solvent MM3 MD yielded non-inferior NOE accuracy with newer GLYCAM-06, and ultimately PBE0-D3/def2-TZVP (Triple-Zeta Valence Polarized) Density Functional Theory (DFT) simulations. For seven of eleven molecules, at least one empirical force field with explicit solvent outperformed DFT in NOE prediction. The aggregate of characteristics (accuracy, speed, and compatibility) made MM3 dynamics with explicit solvent at 300 K the most favorable method for bulk generation of disaccharide conformation maps for massive database filling.
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3
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Affiliation(s)
- Darón I. Freedberg
- Center for Biologics Evaluation and ResearchFood and Drug Administration 10903 New Hampshire Ave. Silver Spring MD. 20993
| | - Jeahoo Kwon
- Center for Biologics Evaluation and ResearchFood and Drug Administration 10903 New Hampshire Ave. Silver Spring MD. 20993
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4
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Nester K, Gaweda K, Plazinski W. A GROMOS Force Field for Furanose-Based Carbohydrates. J Chem Theory Comput 2019; 15:1168-1186. [DOI: 10.1021/acs.jctc.8b00838] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Karina Nester
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Karolina Gaweda
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
| | - Wojciech Plazinski
- Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek Str., 8, 30-239 Cracow, Poland
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5
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Ndukwe IE, Wang X, Pelczer I, Reibarkh M, Williamson RT, Liu Y, Martin GE. PBLG as a versatile liquid crystalline medium for anisotropic NMR data acquisition. Chem Commun (Camb) 2019; 55:4327-4330. [DOI: 10.1039/c9cc01130g] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The chiral nematic phase of poly-γ-benzyl-l-glutamate (PBLG) formed in a chloroform–DMSO co-solvent system can be used as a versatile alignment medium for the acquisition of high quality anisotropic NMR data for molecules of varying polarities.
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Affiliation(s)
- Ikenna E. Ndukwe
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
| | - Xiao Wang
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
| | | | - Mikhail Reibarkh
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
| | | | - Yizhou Liu
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
| | - Gary E. Martin
- Analytical Research and Development (Rahway)
- Merck & Co. Inc
- Kenilworth
- USA
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6
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Aytenfisu AH, Yang M, MacKerell AD. CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses. J Chem Theory Comput 2018; 14:3132-3143. [PMID: 29694037 PMCID: PMC5997548 DOI: 10.1021/acs.jctc.8b00175] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We present an extension of the CHARMM Drude polarizable force field to enable modeling of polysaccharides containing pyranose and furanose monosaccharides. The new force field parameters encompass 1↔2, 1→3, 1→4, and 1→6 pyranose-furanose linkages, 2→1 and 2→6 furanose-furanose linkages, 2→2, 2→3, and 2→4 furanose-pyranose, and 1↔1, 1→2, 1→3, 1→4, and 1→6 pyranose-pyranose linkages. For the glycosidic linkages, both simple model compounds and the full disaccharides with methylation at the reducing end were used for parameter optimization. The model compounds were chosen to be monomers or glycosidic-linked dimers of tetrahydropyran (THP) and tetrahydrofuran (THF). Target data for optimization included one- and two-dimensional potential energy scans of ω and the Φ/Ψ glycosidic dihedral angles in the model compounds and full disaccharides computed by quantum mechanical (QM) RIMP2/cc-pVQZ single point energies on MP2/6-31G(d) optimized structures. Also included in the target data are extensive sets of QM gas phase monohydrate water-saccharide interactions, dipole moments, and molecular polarizabilities for both model compounds and full disaccharides. The resulting polarizable model is shown to be in good agreement with a range of QM data, offering a significant improvement over the additive CHARMM36 carbohydrate force field, as well as experimental data including crystal structures and conformational properties of disaccharides and a trisaccharide in aqueous solution.
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Affiliation(s)
- Asaminew H. Aytenfisu
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201, USA
| | - Mingjun Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201, USA
- XtalPi Inc., Shennan Road 6025, Futian District, Shenzhen, China
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, 20 Penn Street, Baltimore, MD 21201, USA
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7
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Wang P, Rong ZM, Ma CX, Zhao XF, Xiao CN, Zheng XH. Distribution of Metabolites in Root Barks of Seven Tree Peony Cultivars for Quality Assessment Using NMR-based Metabolomics. CHINESE HERBAL MEDICINES 2017. [DOI: 10.1016/s1674-6384(17)60073-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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8
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Neelamraju S, Johnston RL, Schön JC. A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide. J Chem Theory Comput 2016; 12:2471-9. [PMID: 27049524 DOI: 10.1021/acs.jctc.6b00118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a scheme, called the threshold-minimization method, for globally exploring the energy landscapes of small systems of biomolecular interest where typical exploration moves always require a certain degree of subsequent structural relaxation in order to be efficient, e.g., systems containing small or large circular carbon chains such as cyclic peptides or carbohydrates. We show that using this threshold-minimization method we can not only reproduce the global minimum and relevant local minima but also overcome energetic barriers associated with different types of isomerism for the example of a cyclic peptide, cyclo-(Gly)4. We then apply the new method to the disaccharide α-d-glucopyranose-1-2-β-d-fructofuranose, report energetically preferred configurations and barriers to boat-chair isomerization in the glucopyranosyl ring, and discuss the energy landscape.
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Affiliation(s)
- Sridhar Neelamraju
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - Roy L Johnston
- School of Chemistry, University of Birmingham , Edgbaston, Birmingham B15 2TT, United Kingdom
| | - J Christian Schön
- Max Planck Institute for Solid State Research , Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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9
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Pelletier G, Zwicker A, Allen CL, Schepartz A, Miller SJ. Aqueous Glycosylation of Unprotected Sucrose Employing Glycosyl Fluorides in the Presence of Calcium Ion and Trimethylamine. J Am Chem Soc 2016; 138:3175-82. [PMID: 26859619 PMCID: PMC4817112 DOI: 10.1021/jacs.5b13384] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report a synthetic glycosylation reaction between sucrosyl acceptors and glycosyl fluoride donors to yield the derived trisaccharides. This reaction proceeds at room temperature in an aqueous solvent mixture. Calcium salts and a tertiary amine base promote the reaction with high site-selectivity for either the 3'-position or 1'-position of the fructofuranoside unit. Because nonenzymatic aqueous oligosaccharide syntheses are underdeveloped, mechanistic studies were carried out in order to identify the origin of the selectivity, which we hypothesized was related to the structure of the hydroxyl group array in sucrose. The solution conformation of various monodeoxysucrose analogs revealed the co-operative nature of the hydroxyl groups in mediating both this aqueous glycosyl bond-forming reaction and the site-selectivity at the same time.
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Affiliation(s)
- Guillaume Pelletier
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107
| | - Aaron Zwicker
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107
| | - C. Liana Allen
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107
| | - Alanna Schepartz
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107
| | - Scott J. Miller
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520-8107
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10
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Rozada TDC, Pontes RM, Rittner R, Basso EA. Stereoelectronic effects of the glycosidic linkage on the conformational preference of d-sucrose. RSC Adv 2016. [DOI: 10.1039/c6ra24413k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
d-Sucrose conformational analysis at DFT theory level applying NBO and NCI methodology.
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Affiliation(s)
| | | | - Roberto Rittner
- Instituto de Química
- Universidade Estadual de Campinas
- 13083-970 Campinas
- Brazil
| | - Ernani Abicht Basso
- Departamento de Química
- Universidade Estadual de Maringá
- 87020-900 Maringá
- Brazil
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11
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Jawad R, Drake AF, Elleman C, Martin GP, Warren FJ, Perston BB, Ellis PR, Hassoun MA, Royall PG. Stability of Sugar Solutions: A Novel Study of the Epimerization Kinetics of Lactose in Water. Mol Pharm 2014; 11:2224-38. [DOI: 10.1021/mp400509t] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rim Jawad
- Institute
of Pharmaceutical Science, King’s College London, Franklin-Wilkins
Building, 150 Stamford Street, London SE1 9NH, U.K
| | - Alex F. Drake
- Institute
of Pharmaceutical Science, King’s College London, Franklin-Wilkins
Building, 150 Stamford Street, London SE1 9NH, U.K
| | - Carole Elleman
- The
Reading Science Centre, Reading Scientific Services, Ltd., Whiteknights
Campus, Pepper Lane, Reading RG6 6LA, U.K
| | - Gary P. Martin
- Institute
of Pharmaceutical Science, King’s College London, Franklin-Wilkins
Building, 150 Stamford Street, London SE1 9NH, U.K
| | - Frederick J. Warren
- Centre
for Nutrition and Food Sciences, Queensland Alliance for Agriculture
and Food Innovation, The University of Queensland, St. Lucia, Brisbane, Queensland 4072, Australia
| | | | - Peter R. Ellis
- Biopolymers
Group, Diabetes and Nutritional Sciences Division, King’s College London, Franklin-Wilkins Building, 150 Stamford Street, London SE1 9NH, U.K
| | - Mireille A. Hassoun
- Institute
of Pharmaceutical Science, King’s College London, Franklin-Wilkins
Building, 150 Stamford Street, London SE1 9NH, U.K
| | - Paul G. Royall
- Institute
of Pharmaceutical Science, King’s College London, Franklin-Wilkins
Building, 150 Stamford Street, London SE1 9NH, U.K
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12
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Battistel MD, Azurmendi HF, Yu B, Freedberg DI. NMR of glycans: shedding new light on old problems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2014; 79:48-68. [PMID: 24815364 DOI: 10.1016/j.pnmrs.2014.01.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 01/10/2014] [Indexed: 06/03/2023]
Abstract
The diversity in molecular arrangements and dynamics displayed by glycans renders traditional NMR strategies, employed for proteins and nucleic acids, insufficient. Because of the unique properties of glycans, structural studies often require the adoption of a different repertoire of tailor-made experiments and protocols. We present an account of recent developments in NMR techniques that will deepen our understanding of structure-function relations in glycans. We open with a survey and comparison of methods utilized to determine the structure of proteins, nucleic acids and carbohydrates. Next, we discuss the structural information obtained from traditional NMR techniques like chemical shifts, NOEs/ROEs, and coupling-constants, along with the limitations imposed by the unique intrinsic characteristics of glycan structure on these approaches: flexibility, range of conformers, signal overlap, and non-first-order scalar (strong) coupling. Novel experiments taking advantage of isotopic labeling are presented as an option for overcoming spectral overlap and raising sensitivity. Computational tools used to explore conformational averaging in conjunction with NMR parameters are described. In addition, recent developments in hydroxyl detection and hydrogen bond detection in protonated solvents, in contrast to traditional sample preparations in D2O for carbohydrates, further increase the tools available for both structure information and chemical shift assignments. We also include previously unpublished data in this context. Accurate determination of couplings in carbohydrates has been historically challenging due to the common presence of strong-couplings. We present new strategies proposed for dealing with their influence on NMR signals. We close with a discussion of residual dipolar couplings (RDCs) and the advantages of using (13)C isotope labeling that allows gathering one-bond (13)C-(13)C couplings with a recently improved constant-time COSY technique, in addition to the commonly measured (1)H-(13)C RDCs.
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Affiliation(s)
- Marcos D Battistel
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States
| | - Hugo F Azurmendi
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States
| | - Bingwu Yu
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States
| | - Darón I Freedberg
- Laboratory of Bacterial Polysaccharides, Center for Biologics Evaluation and Research, Food and Drug Administration, 1401 Rockville Pike, Rockville, MD 20852-1448, United States.
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13
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Taha HA, Richards MR, Lowary TL. Conformational Analysis of Furanoside-Containing Mono- and Oligosaccharides. Chem Rev 2012; 113:1851-76. [DOI: 10.1021/cr300249c] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Hashem A. Taha
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Michele R. Richards
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
| | - Todd L. Lowary
- Alberta Glycomics Centre and Department of Chemistry, Gunning−Lemieux Chemistry Centre, University of Alberta, Edmonton, AB, Canada T6G 2G2
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14
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Xia J, Case DA. Sucrose in aqueous solution revisited, Part 1: molecular dynamics simulations and direct and indirect dipolar coupling analysis. Biopolymers 2012; 97:276-88. [PMID: 22189655 PMCID: PMC3290335 DOI: 10.1002/bip.22017] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 11/29/2011] [Accepted: 12/01/2011] [Indexed: 11/10/2022]
Abstract
Although the crystal structure of the disaccharide sucrose was solved more than 30 years ago, its conformational distribution in aqueous solution is still a matter of debate. We report here a variety of molecular dynamics simulations (mostly of 100 ns) using the GLYCAM06 force field and various water models, paying particular attention to comparisons to NMR measurements of residual dipolar couplings and electron-mediated spin-spin couplings. We focus on the glycosidic linkage conformation, the puckering phase angle of the fructose ring, and intramolecular hydrogen bonds between the two sugars. Our results show that sucrose is indeed a dynamic molecule, but the crystal conformation is qualitatively the dominant one in dilute solution. A second conformational basin, populated in many force fields, is probably overstabilized in the calculations.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854, USA
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15
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Xia J, Case DA. Sucrose in aqueous solution revisited, Part 2: adaptively biased molecular dynamics simulations and computational analysis of NMR relaxation. Biopolymers 2011; 97:289-302. [PMID: 22058066 DOI: 10.1002/bip.22004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2011] [Revised: 10/21/2011] [Accepted: 10/26/2011] [Indexed: 11/07/2022]
Abstract
We report 100 ns molecular dynamics simulations, at various temperatures, of sucrose in water (with concentrations of sucrose ranging from 0.02 to 4M), and in a 7:3 water-DMSO mixture. Convergence of the resulting conformational ensembles was checked using adaptive-biased simulations along the glycosidic Φ and ψ torsion angles. NMR relaxation parameters, including longitudinal (R₁) and transverse (R₂) relaxation rates, nuclear Overhauser enhancements (NOE), and generalized order parameter (S²) were computed from the resulting time-correlation functions. The amplitude and time scales of molecular motions change with temperature and concentration in ways that track closely with experimental results, and are consistent with a model in which sucrose conformational fluctuations are limited (with 80-90% of the conformations having ϕ-ψ values within 20° of an average conformation), but with some important differences in conformation between pure water and DMSO-water mixtures.
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Affiliation(s)
- Junchao Xia
- Department of Chemistry and Chemical Biology, BioMaPS Institute for Quantitative Biology, Rutgers University, 610 Taylor Rd., Piscataway, NJ 08854, USA
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16
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Raman EP, Guvench O, MacKerell AD. CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses. J Phys Chem B 2011; 114:12981-94. [PMID: 20845956 DOI: 10.1021/jp105758h] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Presented is an extension of the CHARMM additive carbohydrate all-atom force field to enable modeling of polysaccharides containing furanose sugars. The new force field parameters encompass 1 ↔ 2, 1 → 3, 1 → 4, and 1 → 6 pyranose-furanose linkages and 2 → 1 and 2 → 6 furanose-furanose linkages, building on existing hexopyranose and furanose monosaccharide parameters. The model compounds were chosen to be monomers or glycosidic-linked dimers of tetrahydropyran (THP) and tetrahydrofuran (THF) as to contain the key atoms in full carbohydrates. Target data for optimization included two-dimensional quantum mechanical (QM) potential energy scans of the Φ/Ψ glycosidic dihedral angles, with geometry optimization at the MP2/6-31G(d) level followed by MP2/cc-pVTZ single-point energies. All possible chiralities of the model compounds at the linkage carbons were considered, and for each geometry, the THF ring was constrained to the favorable south or north conformations. Target data also included QM vibrational frequencies and pair interaction energies and distances with water molecules. Force field validation included comparison of computed crystal properties, aqueous solution densities, and NMR J-coupling constants to experimental reference values. Simulations of infinite crystals showed good agreement with experimental values for intramolecular geometries as well as for crystal unit cell parameters. Additionally, aqueous solution densities and available NMR data were reproduced to a high degree of accuracy, thus validating the hierarchically optimized parameters in both crystalline and aqueous condensed phases. The newly developed parameters allow for the modeling of linear, branched, and cyclic pyranose/furanose polysaccharides both alone and in heterogeneous systems including proteins, nucleic acids, and/or lipids when combined with existing additive CHARMM biomolecular force fields.
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Affiliation(s)
- E Prabhu Raman
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street HSF II, Baltimore, Maryland 21201, USA
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17
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Jäger W, Mayer M, Reznicek G, Buchbauer G. Percutaneous absorption of the montoterpene carvone: implication of stereoselective metabolism on blood levels. J Pharm Pharmacol 2010; 53:637-42. [PMID: 11370703 DOI: 10.1211/0022357011775965] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
Abstract
The purpose of this study was to determine whether an enantioselective difference in the metabolism of topically applied R-(—)- and S-(+)-carvone could be observed in man. In a previous investigation we found that R-(—)- and S-(+)-carvone are stereoselectively biotransformed by human liver microsomes to 4R,6S-(—)- and 4S,6S-(+)-carveol, respectively, and 4R,6S-(—)-carveol is further glucuronidated. We therefore investigated the metabolism and pharmacokinetics of R-(—)- and S-(+)-carvone in four healthy subjects using chiral gas chromatography as the analytical method. Following separate topical applications at a dose of 300 mg, R-(—)- and S-(+)-carvone were rapidly absorbed, resulting in significantly higher Cmax levels for S-(+)-carvone (88.0 vs 23.9 ng mL−1) and longer distribution half-lives (t2α1) (19.4 vs 7.8 min), resulting in 3.4-fold higher areas under the blood concentration-time curves (5420 vs 1611 ng min mL−1). The biotransformation products for both enantiomers in plasma were below detection limit. Analysis of control- and β-glucuronidase pretreated urine samples, however, revealed a stereoselective metabolism of R-(—)-carvone to 4R,6S-(—)-carveol and 4R,6S-(—)-carveol glucuronide. No metabolites could be found in urine samples after S-(+)-carvone application. These data indicate that stereoselectivity in phase-I and phase-II metabolism has significant effects on R-(—)- and S-(+)-carvone pharmacokinetics. This might serve to explain the increased blood levels of S-(+)-carvone.
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Affiliation(s)
- W Jäger
- Institute of Pharmaceutical Chemistry, University of Vienna, Austria.
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18
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Synthesis and complexation properties towards the ammonium cation of aza-coronand analogues containing sucrose. Carbohydr Res 2008; 343:965-9. [DOI: 10.1016/j.carres.2008.01.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2007] [Revised: 01/09/2008] [Accepted: 01/14/2008] [Indexed: 10/22/2022]
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19
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López-Méndez B, Jia C, Zhang Y, Zhang LH, Sinaÿ P, Jiménez-Barbero J, Sollogoub M. Hemicarbasucrose: Turning off the Exoanomeric Effect Induces Less Flexibility. Chem Asian J 2008; 3:51-8. [DOI: 10.1002/asia.200700281] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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20
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Tafazzoli M, Ghiasi M. Conformational study of anomeric center in some carbohydrate derivatives. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.03.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Queneau Y, Jarosz S, Lewandowski B, Fitremann J. Sucrose Chemistry and Applications of Sucrochemicals. Adv Carbohydr Chem Biochem 2007; 61:217-92. [DOI: 10.1016/s0065-2318(07)61005-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Molinier V, Fenet B, Fitremann J, Bouchu A, Queneau Y. PFGSE-NMR study of the self-diffusion of sucrose fatty acid monoesters in water. J Colloid Interface Sci 2006; 286:360-8. [PMID: 15848439 DOI: 10.1016/j.jcis.2004.12.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2004] [Accepted: 12/08/2004] [Indexed: 10/25/2022]
Abstract
The micellization of pure monosubstituted sucrose fatty acid esters in water, namely sucrose octanoate, sucrose decanoate, sucrose laurate, sucrose dodec-5-cis-enoate, sucrose myristate, and sucrose palmitate, has been investigated by means of two NMR methods, pulsed field gradient spin-echo NMR (PFGSE-NMR), giving access to the self-diffusion coefficients of free molecules and micelles in solution, and the ERETIC method (electronic reference to access in vivo concentrations) for the measurement of concentrations by external calibration of a synthetic NMR signal. The early micellar regions and, when possible, the premicellar regions were investigated. By this method, we obtained the hydrodynamic radii of micelles, displaying a linear progression in relation to the chain length and an accurate determination of critical micellar concentration (CMC) for each sucrose ester. The effect of the regiochemistry of fatty chain grafting has been investigated, showing special behavior for 1'-O-sucrose palmitate.
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Affiliation(s)
- Valérie Molinier
- Laboratoire de Chimie Organique, UMR CNRS 5181, INSA, Bât. J. Verne, 20 av. A. Einstein, F-69621 Villeurbanne cedex, France
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23
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Navia JL, Roberts RA, Wingard RE. Study on the Selectivity of Benzoylation of Metal Chelates of Sucrose1. J Carbohydr Chem 2006. [DOI: 10.1080/07328309508005351] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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24
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Venable RM, Delaglio F, Norris SE, Freedberg DI. The utility of residual dipolar couplings in detecting motion in carbohydrates: application to sucrose. Carbohydr Res 2005; 340:863-74. [PMID: 15780252 DOI: 10.1016/j.carres.2005.01.025] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2004] [Accepted: 01/18/2005] [Indexed: 11/17/2022]
Abstract
The solution structure and dynamics of sucrose are examined using a combination of NMR residual dipolar coupling and molecular mechanics force fields. It is found that the alignment tensors of the individual rings are different, and that fitting 35 measured residual dipolar couplings to structures with specific phi, psi values indicates the presence of three major conformations: phi, psi=(120 degrees ,270 degrees), (45 degrees, 300 degrees) and (90 degrees ,180 degrees). Furthermore, fitting two structures simultaneously to the 35 residual dipolar couplings results in a substantial improvement in the fits. The existence of multiple conformations having similar stabilities is a strong indication of motion, due to the interconversion among these states. Results from four molecular mechanics force fields are in general agreement with the experimental results. However, there are major disagreements between force fields. Because fits of residual dipolar couplings to structures are dependent on the force field used to calculate the structures, multiple force fields were used to interpret NMR data. It is demonstrated that the pucker of the fructofuranosyl ring affects the calculated potential energy surface, and the fit to the residual dipolar couplings data. Previously published 13C nuclear relaxation results suggesting that sucrose is rigid are not inconsistent with the present results when motional timescales are considered.
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Affiliation(s)
- Richard M Venable
- Laboratory of Biophysics, Center for Biologics Evaluation and Research, FDA, 1401 Rockville Pike, HFM-419, MD 20852, USA
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25
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Loris R, Imberty A, Beeckmans S, Van Driessche E, Read JS, Bouckaert J, De Greve H, Buts L, Wyns L. Crystal structure of Pterocarpus angolensis lectin in complex with glucose, sucrose, and turanose. J Biol Chem 2003; 278:16297-303. [PMID: 12595543 DOI: 10.1074/jbc.m211148200] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The crystal structure of the Man/Glc-specific seed lectin from Pterocarpus angolensis was determined in complex with methyl-alpha-d-glucose, sucrose, and turanose. The carbohydrate binding site contains a classic Man/Glc type specificity loop. Its metal binding loop on the other hand is of the long type, different from what is observed in other Man/Glc-specific legume lectins. Glucose binding in the primary binding site is reminiscent of the glucose complexes of concanavalin A and lentil lectin. Sucrose is found to be bound in a conformation similar as seen in the binding site of lentil lectin. A direct hydrogen bond between Ser-137(OG) to Fru(O2) in Pterocarpus angolensis lectin replaces a water-mediated interaction in the equivalent complex of lentil lectin. In the turanose complex, the binding site of the first molecule in the asymmetric unit contains the alphaGlc1-3betaFruf form of furanose while the second molecule contains the alphaGlc1-3betaFrup form in its binding site.
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Affiliation(s)
- Remy Loris
- Laboratorium voor Ultrastructuur, Instituut voor Moleculaire Biologie, Vrije Universiteit Brussel, Pleinlaan 2, B-1050 Brussels, Belgium.
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26
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Parada J, Bunel S, Ibarra C, Larrazabal G, Gillitt ND, Bunton CA. Sucrose bis(1,10-phenanthroline)cobalt (III). Predicted distortion at the octahedral center. Polyhedron 2002. [DOI: 10.1016/s0277-5387(02)01167-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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27
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Baraguey C, Mertens D, Dölle A. Anisotropic Reorientation and Intermolecular Interactions of Sucrose Molecules in Aqueous Solution. A Temperature and Concentration-Dependent 13C NMR Relaxation Study. J Phys Chem B 2002. [DOI: 10.1021/jp014654l] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carine Baraguey
- Institut für Physikalische Chemie, Rheinisch-Westfälische Technische Hochschule Aachen, 52056 Aachen, Germany
| | - Dirk Mertens
- Institut für Physikalische Chemie, Rheinisch-Westfälische Technische Hochschule Aachen, 52056 Aachen, Germany
| | - Andreas Dölle
- Institut für Physikalische Chemie, Rheinisch-Westfälische Technische Hochschule Aachen, 52056 Aachen, Germany
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28
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Houseknecht JB, McCarren PR, Lowary TL, Hadad CM. Conformational studies of methyl 3-O-methyl-alpha-D-arabinofuranoside: an approach for studying the conformation of furanose rings. J Am Chem Soc 2001; 123:8811-24. [PMID: 11535088 DOI: 10.1021/ja003768s] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A computational method for probing furanose conformation has been developed using a methylated monosaccharide derivative 1. First, a large library of conformers was generated by a systematic pseudo Monte Carlo search followed by optimization with the AMBER molecular mechanics force field. A subset of these conformers was then subjected to ab initio and density functional theory calculations in both the gas and aqueous phases. These calculations indicate that entropic contributions to the Gibbs free energy are important determinants of the Boltzmann distribution for the conformational preferences of 1 in the gas phase. The results obtained at each level of theory are discussed and compared with the experimentally determined conformer distribution from NMR studies in aqueous solution. In addition, the ability of each level of theory to reproduce the experimentally measured 1H-1H coupling constants in 1 is discussed. Empirical Karplus equations and density functional theory methods were used to determine average 3J(H1,H2), 3J(H2,H3), and 3J(H3,H4) for each level of theory. On the basis of this comparison, consideration of solvation with the MN-GSM model provided good agreement with the experimental data.
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Affiliation(s)
- J B Houseknecht
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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29
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Höög C, Landersjö C, Widmalm G. Oligosaccharides display both rigidity and high flexibility in water as determined by 13C NMR relaxation and 1H,1H NOE spectroscopy: evidence of anti-phi and anti-psi torsions in the same glycosidic linkage. Chemistry 2001; 7:3069-77. [PMID: 11495434 DOI: 10.1002/1521-3765(20010716)7:14<3069::aid-chem3069>3.0.co;2-a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The trisaccharide beta-D-Glcp-(1-->2)-beta-D-Glcp-(1-->3)-alpha-D-Glcp-OMe has been investigated by molecular dynamics (MD) simulations and NMR experiments in water. 13C spin-lattice (T1) and spin-spin (T2) relaxation times, together with 1H,13C NOE data were measured at two magnetic field strengths (9.4 and 14.1 T) in a 277 K D2O solution. Relaxation data interpreted by means of the model-free formalism revealed a rigid (S2 approximately 0.9) oligosaccharide tumbling in solution. 1H,1H Cross-relaxation rates were determined at 600 MHz by 1D DPFGSE NOESY and T-ROESY experiments, which provided high quality data and subsequently proton-proton distances within the trisaccharide. The presence of anti conformers at both torsions of a glycosidic linkage is demonstrated for the first time. MD simulations were carried out to facilitate analysis of the NOE data. In total, 15 simulations-starting from five different conformational states--were performed, with production runs of up to 10 ns, resulting in 83 ns of oligosaccharide dynamics in water. anti Conformers were populated to different degrees in the simulations, especially at the phi2 torsion angle. By combining the results from the NOE experiments and the MD simulations, the anti conformers at the (1-->2)-linkage were quantified as 7% anti-phi2 and 2% anti-psi2, revealing a highly flexible trisaccharide in which large conformational changes occur. From the MD simulations, interresidue hydrogen bonding, from HO2" to O2 or O3, was significantly populated (approximately 40%) in both of the anti conformational states. The contentious issue over rigidity versus flexibility in oligosaccharides has thus been thoroughly examined, showing that the dynamics should be taken into account for a relevant description of the molecular system.
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Affiliation(s)
- C Höög
- Department of Organic Chemistry, Arrhenius Laboratory Stockholm University, Sweden
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30
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Parada J, Bunel S, Ibarra C, Larrazabal G, Moraga E, Gillitt ND, Bunton CA. Formation and structure of a complex of sucrose with cobalt(III)bis(phenanthroline). Carbohydr Res 2001; 333:185-95. [PMID: 11448682 DOI: 10.1016/s0008-6215(01)00147-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Sucrose forms a dicationic complex with cobalt(III)bis(phenanthroline) which can be isolated as the sparingly water-soluble triiodide salt or the water-soluble chloride. The circular dichroism (CD) spectrum demonstrates the Delta configuration at Co(III) and the presence of two phenanthroline and one sucrose residues in the complex. The O-2(g)--O-1(f) distance in crystalline sucrose permits strain-free coordination of these centers with Co(III) and in the complex the H-1,1'(f) singlet of sucrose separates into a pair of doublets. The 1H NMR spectrum in DMSO-d(6) shows that OH-2(g) is deprotonated and the signal of OH-1(f) is shifted strongly downfield by complexation with Co(III). Coordination involving glucose and fructose residues is consistent with neither alpha-methyl glucoside nor fructofuranose forming mixed complexes with phenanthroline. Structure simulation with the semi-empirical PM3(tm) basis set indicates that complexation by O-2(g) and OH-1(f) can give a Delta-complex with little structural distortion, whereas in hypothetical Lambda-complexes there is distortion of the sucrose residue. Observation of an NOE involving the sucrose and phenanthroline residues supports the postulated structure of the Delta-complex.
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Affiliation(s)
- J Parada
- Departamento de Química Inorgánica y Analitica, Facultad de Ciencias Químicacs y Farmaceuticas, Universidad de Chile, Santiago, Chile
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31
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Jiménez-Barbero J, Espinosa JF, Asensio JL, Cañada FJ, Poveda A. The conformation of C-glycosyl compounds. Adv Carbohydr Chem Biochem 2001; 56:235-84. [PMID: 11039113 DOI: 10.1016/s0065-2318(01)56006-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Parfenyuk EV, Davydova OI. Calorimetric study of the interactions of disaccharides with crown ethers in water. MENDELEEV COMMUNICATIONS 2001. [DOI: 10.1070/mc2001v011n05abeh001455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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33
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Dixon AM, Widmalm G, Bull TE. Modified GOESY in the analysis of disaccharide conformation. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2000; 147:266-272. [PMID: 11097818 DOI: 10.1006/jmre.2000.2211] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
One-dimensional nuclear magnetic resonance techniques were applied to the conformational investigation of a disaccharide. More specifically, nuclear Overhauser enhancements (NOEs) of protons on either side of the glycosidic bond have been used to determine the conformation of the disaccharide alpha-l-Rhap-(1 --> 2)-alpha-l-Rhap-OMe. A modified GOESY sequence, incorporating selective excitation and pulsed field gradient enhancement, was developed and used to accurately measure small NOE signals of interest. These experiments were named M-GOESY, for modified GOESY, and the data they provided were used to calculate internuclear distances in the disaccharide molecule. The accuracy of the M-GOESY measurements was enhanced by elimination of indirect effects, or spin diffusion, by selective inversion(s) of either the intermediate magnetization or the source and target magnetization during the mixing time. Results of this study indicate that the alpha-l-Rhap-(1 --> 2)-alpha-l-Rhap-OMe disaccharide molecule exists primarily in one conformation, with the glycosidic torsion angle psi approximately -30 degrees based on past molecular dynamics simulations.
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Affiliation(s)
- A M Dixon
- Laboratory of Biophysics, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20893, USA
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34
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Parada J, Bunel S, Ibarra C, Larrazabal G, Moraga E, Gillitt ND, Bunton CA. Complexation of sucrose with cobalt(III)bis(phenanthroline). Carbohydr Res 2000; 329:195-7. [PMID: 11086699 DOI: 10.1016/s0008-6215(00)00164-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The delta-[Co(III)bis(phenanthroline)(sucrose)]3+ complex forms with little perturbation of the sucrose conformation, and complexation by HO-2(g) and HO-1(f).
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Affiliation(s)
- J Parada
- Departamento de Quimica Inorganica y Analitica, Facultad de Ciencias Quimicas y Farmaceuticas, Universidad de Chile, Santiago
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35
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Probing furanose ring conformation by gas-phase computational methods: energy profile and structural parameters in methyl beta-D-arabinofuranoside as a function of ring conformation. J Org Chem 2000; 65:4954-63. [PMID: 10956478 DOI: 10.1021/jo000426w] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The potential energy surface of methyl beta-D-arabinofuranoside (3) has been studied by ab initio molecular orbital (HF/6-31G) and density functional theory (B3LYP/6-31G) calculations via minimization of the 10 possible envelope conformers. The partial potential energy surface identified that the global minimum and lowest energy northern conformer was E(2). In the HF calculations, (2)E was the most stable southern conformer, while the density functional theory methods identified (4)E as the local minimum in this hemisphere. Additional calculations at higher levels of theory showed that the B3LYP-derived energies of many of the envelope conformers of 3 are dependent upon the basis set used. It has also been demonstrated that B3LYP/6-31+G//B3LYP/6-31G single point energies are essentially the same as those obtained from full geometry optimizations at the B3LYP/6-31+G level. The northern and southern minima of the B3LYP/6-31+G surface are, respectively, the E(2) and (2)E conformers. The B3LYP/6-31G geometries were used to study the relationship between ring conformation and various structural parameters including bond angles, dihedral angles, bond lengths, and interatomic distances.
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36
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D'Souza FW, Ayers JD, McCarren PR, Lowary TL. Arabinofuranosyl Oligosaccharides from Mycobacteria: Synthesis and Effect of Glycosylation on Ring Conformation and Hydroxymethyl Group Rotamer Populations. J Am Chem Soc 2000. [DOI: 10.1021/ja993543l] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Francis W. D'Souza
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Joseph D. Ayers
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Patrick R. McCarren
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
| | - Todd L. Lowary
- Contribution from the Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
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37
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Jäger W, Mayer M, Platzer P, Reznicek G, Dietrich H, Buchbauer G. Stereoselective metabolism of the monoterpene carvone by rat and human liver microsomes. J Pharm Pharmacol 2000; 52:191-7. [PMID: 10714949 DOI: 10.1211/0022357001773841] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
The large amounts of carvone enantiomers consumed as food additives and in dental formulations justifies the evaluation of their biotransformation pathway. The in-vitro metabolism of R-(-)- and S-(+)-carvone was studied in rat and human liver microsomes using chiral gas chromatography. Stereoselective biotransformation was observed when each enantiomer was incubated separately with liver microsomes. 4R, 6S-(-)-Carveol was NADPH-dependently formed from R-(-)-carvone, whereas 4S, 6S-(+)-carveol was produced from S-(+)-carvone. Metabolite formation followed Michaelis-Menten kinetics exhibiting a significant lower apparent Km (Michaelis-Menten Constant) for 4R, 6S-(-)-carveol compared with 4S, 6S-(+)-carveol in rat and human liver microsomes (28.4+/-10.6 microM and 69.4+/-10.3 microM vs 33.6+/-8-55 microM and 98.3+/-22.4 microM). The maximal formation rate (Vmax) determined in the same microsomal preparations yielded 30.2+/-5.0 and 32.3+/-3.9 pmol (mg protein)(-1) min(-1) in rat liver and 55.3+/-5.7 and 65.2+/-4.3 pmol (mg protein)(-1) min(-1) in human liver microsomes. Phase II conjugation of the carveol isomers by rat and human liver microsomes in the presence of UDPGA (uridine S'-diphosphogluaronic acid) only revealed glucuronidation of 4R, 6S-(-)-carveol. Vmax for glucuronide formation was more than 4-fold higher in the rat liver compared with human liver preparations (185.9+/-34.5 and 42.6+/-7.1 pmol (mg protein)(-1) min(-1), respectively). Km values, however, showed no species-related difference (13.9+/-4.1 microM and 10.2+/-2.2 microM). This study demonstrated stereoselectivity in phase-I and phase-II metabolism for R-(-)- and S-(+)-carvone and might be predictive for carvone biotransformation in man.
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Affiliation(s)
- W Jäger
- Institute of Pharmaceutical Chemistry, University of Vienna, Austria.
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38
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Rundlöf T, Venable RM, Pastor RW, Kowalewski J, Widmalm G. Distinguishing Anisotropy and Flexibility of the Pentasaccharide LNF-1 in Solution by Carbon-13 NMR Relaxation and Hydrodynamic Modeling. J Am Chem Soc 1999. [DOI: 10.1021/ja992675b] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Torgny Rundlöf
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Richard M. Venable
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Richard W. Pastor
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Jozef Kowalewski
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
| | - Göran Widmalm
- Contribution from the Department of Organic Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden, and Biophysics Laboratory, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland 20892
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39
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Gordon MT, Lowary TL, Hadad CM. A Computational Study of Methyl α-D-Arabinofuranoside: Effect of Ring Conformation on Structural Parameters and Energy Profile. J Am Chem Soc 1999. [DOI: 10.1021/ja9915091] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Matthew T. Gordon
- Contribution from the Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Todd L. Lowary
- Contribution from the Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
| | - Christopher M. Hadad
- Contribution from the Department of Chemistry, The Ohio State University, Columbus, Ohio 43210
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40
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Thévenet S, Wernicke A, Belniak S, Descotes G, Bouchu A, Queneau Y. Esterification of unprotected sucrose with acid chlorides in aqueous medium: kinetic reactivity versus acyl- or alkyloxycarbonyl-group migrations. Carbohydr Res 1999. [DOI: 10.1016/s0008-6215(99)00079-8] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Cros S, Petitou M, Sizun P, Pérez S, Imberty A. Combined NMR and molecular modeling study of an iduronic acid-containing trisaccharide related to antithrombotic heparin fragments. Bioorg Med Chem 1997; 5:1301-9. [PMID: 9377090 DOI: 10.1016/s0968-0896(97)00087-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An iduronic acid-containing trisaccharide, methyl-O-(4-O-methyl-2,3,6-tri-O-sulfo-alpha-D-glucopyranosyl-(1-->4)-O- (2-O-sulfo-alpha-L-idopyranosyluronic acid)-(1-->4)-O-2,6-di-O-sulfo-alpha-D-glucopyranoside, related to antithrombotic heparin fragments has been subjected to a combined NMR and molecular modeling investigation. The conformational behavior of the two constituting disaccharide segments was investigated using a systematic grid search approach with the MM3 force field along with the proper parameters for the sulfate ester group. The exploration of the potential energy surfaces of the trisaccharide was performed through the use of the CICADA methods interfaced with the MM3 force field. In all cases, the 2-O-sulfo-alpha-L-iduronate moiety was given the three favored ring conformations (1)C4, (4)C1, and (2)S0. Conformations were clustered into families, four of which are likely to exhibit significant occupancy in solution. The different low-energy conformational families display different orientations at the glycosidic linkages and/or different ring shapes for the iduronate ring. The (2)S0 conformation is the major one for the 2-O-sulfo-alpha-L-iduronate but is still in equilibrium with the (1)C4 ring shape. The occurrence of such a conformational equilibrium in solution was probed via high-resolution NMR spectroscopy through measurements of coupling constants and NOE build-up. These results are in keeping with the observation that 2-O-sulfated pentasaccharides display a similar affinity for antithrombin III as their 2-N-sulfated counterparts.
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Affiliation(s)
- S Cros
- Ingénierie Moleculaire, INRA, BP 1627, Nantes, France
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42
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43
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Casset F, Imberty A, du Penhoat CH, Koca J, Pérez S. Validation of two conformational searching methods applied to sucrose: simulation of NMR and chiro-optical data. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0166-1280(96)04540-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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44
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Engelsen SB, Pérez S. Internal motions and hydration of sucrose in a diluted water solution. J Mol Graph Model 1997; 15:122-31, 107. [PMID: 9385559 DOI: 10.1016/s1093-3263(97)00002-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
This paper represents a synthesis of our most recent work on the hydration, internal and overall dynamics of sucrose in a diluted water solution. The studies were carried out as a total ensemble of 1.2 nanosecond condensed phase molecular dynamics trajectories. In this study the focus is on a 500 ps trajectory starting with the solute in the crystalline conformation. The presence of water was found to significantly alter the accessible conformational space of the solute. All potential intra-molecular hydrogen bonds were found to be exchanged to surrounding water molecules and the simulations suggest that the sucrose conformation is stabilized by the dynamic presence of two interring bridging water molecules: O-2g...Ow...O-3f and O-2g...Ow...O-lf. The overall shift in conformation of the solute induced by the presence of water was found to improve the theoretical models of experimental traits. It is demonstrated that the hydration structure and the internal and overall motions of sucrose compare extremely well with NMR data such as glycosidic heteronuclear coupling constants and the molecular tumbling time, with X-ray data of two partially hydrated sucrose structures in a protein complex and with translational diffusion coefficients and hydration numbers established from experimental studies.
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Affiliation(s)
- S B Engelsen
- Department of Dairy and Food Science, Royal Veterinary and Agricultural University, Frederiksberg, Denmark
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45
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Blériotc Y, Genre-Grandpierre A, Imberty A, Tellier C. Structure and Conformation of Mannoamidines by Nmr and Molecular Modeling: are They Good Transition State Mimics? J Carbohydr Chem 1996. [DOI: 10.1080/07328309608005704] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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46
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47
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Hardy BJ, Gutierrez A, Lesiak K, Seidl E, Widmalm G. Structural Analysis of the Solution Conformation of Methyl 4-O-β-d-Glucopyranosyl-α-d-Glucopyranoside by Molecular Mechanics and ab Initio Calculation, Stochastic Dynamics Simulation, and NMR Spectroscopy. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp953139i] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Barry J. Hardy
- Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford University, Oxford, OX1 3QZ, U.K
| | - Alberto Gutierrez
- FDA Biophysics Laboratory, Center for Biologics Evaluation and Research, 8800 Rockville Pike, Bethesda, Maryland 20892
| | - Krystyna Lesiak
- FDA Biophysics Laboratory, Center for Biologics Evaluation and Research, 8800 Rockville Pike, Bethesda, Maryland 20892
| | - Ed Seidl
- Division of Computer Research & Technology, National Institutes of Health, Bethesda, Maryland 20892
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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Highly regio- and stereoselective reductions of carbonyl compounds in aqueous glycosidic media. Tetrahedron Lett 1996. [DOI: 10.1016/0040-4039(95)02094-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Immel S, Lichtenthaler FW. Molecular modeling of saccharides, 7. The conformation of sucrose in water: A molecular dynamics approach. ACTA ACUST UNITED AC 1995. [DOI: 10.1002/jlac.1995199511272] [Citation(s) in RCA: 72] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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Houdier S, Pérez S. Assessing Sucrose Hydroxyl Acidities Through Semiempirical Calculations. J Carbohydr Chem 1995. [DOI: 10.1080/07328309508005399] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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