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Feng T, Li M, Zhou J, Zhuang H, Chen F, Ye R, Campanella O, Fang Z. Application of molecular dynamics simulation in food carbohydrate research—a review. INNOV FOOD SCI EMERG 2015. [DOI: 10.1016/j.ifset.2015.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Yan S, Yao L. DFT application in conformational determination of cellobiose. Carbohydr Res 2015; 404:117-23. [DOI: 10.1016/j.carres.2014.12.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 12/08/2014] [Accepted: 12/16/2014] [Indexed: 11/26/2022]
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3
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Bell NGA, Rigg G, Masters S, Bella J, Uhrín D. Detecting low-level flexibility using residual dipolar couplings: a study of the conformation of cellobiose. Phys Chem Chem Phys 2014; 15:18223-34. [PMID: 24064673 DOI: 10.1039/c3cp52987h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed novel NMR methods for the measurement of heteronuclear residual dipolar couplings (RDCs) in molecules with severely overlapping NMR resonances. These and other methods enabled us to obtain 31 RDCs for α-D-cellobiose and 24 RDCs for β-D-cellobiose. The interpretation of the data in the approximation of a rigid disaccharide structure, using RDCs and interglycosidic (3)J coupling constants, yielded conformation that is very close to that determined using X-ray crystallography. However, depending on which ring was used to calculate the order parameters, the dihedral angle ψH varied up to 30° or 40°, while the φH angle was always the same. This indicates residual flexibility of the glycosidic linkage between the two monosaccharide rings and was observed for both α- and β-D-cellobiose. The RDC analysis using rigid fragments rather than a complete molecule has thus shown that the glycosidic bond of cellobiose is not completely rigid and exhibits low-level flexibility. The sources of this flexibility are discussed and evidence presented to support a hypothesis that it is associated with the ψ more than the φ angle.
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Affiliation(s)
- Nicholle G A Bell
- EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh, EH9 3JJ, UK.
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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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French AD, Johnson GP, Cramer CJ, Csonka GI. Conformational analysis of cellobiose by electronic structure theories. Carbohydr Res 2012; 350:68-76. [PMID: 22265378 DOI: 10.1016/j.carres.2011.12.023] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 11/29/2022]
Abstract
Adiabatic Φ/ψ maps for cellobiose were prepared with B3LYP density functional theory. A mixed basis set was used for minimization, followed with 6-31+G(d) single-point calculations, with and without SMD continuum solvation. Different arrangements of the exocyclic groups (38 starting geometries) were considered for each Φ/ψ point. The vacuum calculations agreed with earlier computational and experimental results on the preferred gas phase conformation (anti-Φ(H), syn-ψ(H)), and the results from the solvated calculations were consistent with the (syn Φ(H)/ψ(H) conformations from condensed phases (crystals or solutions). Results from related studies were compared, and there is substantial dependence on the solvation model as well as arrangements of exocyclic groups. New stabilizing interactions were revealed by Atoms-In-Molecules theory.
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Affiliation(s)
- Alfred D French
- Southern Regional Research Center, U.S. Department of Agriculture, 1100 Robert E. Lee Blvd, New Orleans, LA 70124, USA.
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6
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Landström J, Widmalm G. Glycan flexibility: insights into nanosecond dynamics from a microsecond molecular dynamics simulation explaining an unusual nuclear Overhauser effect. Carbohydr Res 2010; 345:330-3. [DOI: 10.1016/j.carres.2009.11.003] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Revised: 11/02/2009] [Accepted: 11/03/2009] [Indexed: 11/24/2022]
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7
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Shen T, Langan P, French AD, Johnson GP, Gnanakaran S. Conformational Flexibility of Soluble Cellulose Oligomers: Chain Length and Temperature Dependence. J Am Chem Soc 2009; 131:14786-94. [DOI: 10.1021/ja9034158] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tongye Shen
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - Paul Langan
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - Alfred D. French
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - Glenn P. Johnson
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
| | - S. Gnanakaran
- Theoretical Biology & Biophysics Group, Center for Nonlinear Studies, and Biosciences, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, and Cotton Structure and Quality Research Unit, USDA, ARS, SRRC, New Orleans, Louisiana 70124
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Wakelyn P, Bertoniere N, French A, Thibodeaux D, Triplett B, Rousselle MA, Goynes W, Edwards J, Hunter L, McAlister D, Gamble G. Cotton Fibers. HANDBOOK OF FIBER CHEMISTRY, THIRD EDITION 2006. [DOI: 10.1201/9781420015270.ch9] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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9
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Stepwise hydration of cellobiose by DFT methods: 1. Conformational and structural changes brought about by the addition of one to four water molecules. ACTA ACUST UNITED AC 2006. [DOI: 10.1016/j.theochem.2006.07.024] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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10
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Bernabé M, Jiménez-Barbero J, Planas A. The Conformation of the Tri- and Tetrasaccharide Produced in the Hydrolysis of Barley Glucan with the Enzyme Endo-1,3-1,4-β-glucan 4-Glucanohydrolase fromBacillus Licheniformis. J Carbohydr Chem 2006. [DOI: 10.1080/07328309408011681] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- M. Bernabé
- a Grupo de Carbohidratos , Instituto de Química Orgánica General (CSIC) , Juan de la Cierva 3, 28006 , Madrid , Spain
| | - J. Jiménez-Barbero
- a Grupo de Carbohidratos , Instituto de Química Orgánica General (CSIC) , Juan de la Cierva 3, 28006 , Madrid , Spain
| | - A. Planas
- b CETS Institut Químic de Sarriá, Universitat Ramón Llull , 08017 , Barcelona , Spain
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11
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Landersjö C, Stevensson B, Eklund R, Ostervall J, Söderman P, Widmalm G, Maliniak A. Molecular conformations of a disaccharide investigated using NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2006; 35:89-101. [PMID: 16791735 DOI: 10.1007/s10858-006-9006-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2005] [Revised: 02/14/2006] [Accepted: 03/10/2006] [Indexed: 05/10/2023]
Abstract
The molecular structure of alpha-L-Rhap-(1--> 2)-alpha-L-Rhap-OMe has been investigated using conformation sensitive NMR parameters: cross-relaxation rates, scalar 3J(CH) couplings and residual dipolar couplings obtained in a dilute liquid crystalline phase. The order matrices of the two sugar residues are different, which indicates that the molecule cannot exist in a single conformation. The conformational distribution function, P(phi, psi) related to the two glycosidic linkage torsion angles phi and psi was constructed using the APME method, valid in the low orientational order limit. The APME approach is based on the additive potential (AP) and maximum entropy (ME) models. The analyses of the trajectories generated in molecular dynamics and Langevin dynamics (LD) computer simulations gave support to the distribution functions constructed from the experimental NMR parameters. It is shown that at least two conformational regions are populated on the Ramachandran map and that these regions exhibit very different molecular order.
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Affiliation(s)
- Clas Landersjö
- Arrhenius Laboratory, Department of Organic Chemistry, Stockholm University, S-106 91, Stockholm, Sweden
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12
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Engelsen SB, Pérez S, Braccini I, Du Penhoat CH. Internal motions of carbohydrates as probed by comparative molecular modeling and nuclear magnetic resonance of ethyl β-lactoside. J Comput Chem 2004. [DOI: 10.1002/jcc.540160905] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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13
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Keglević D, Kojić-Prodić B, Tomisić ZB. Synthesis and conformational analysis of the repeating units of bacterial spore peptidoglycan. Carbohydr Res 2003; 338:1299-308. [PMID: 12791283 DOI: 10.1016/s0008-6215(03)00067-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Deprotection of the fully blocked disacharide allyl O-(2-amino-4,6-O-benzylidene-3-O-[(R)-1-carboxyethyl]-2-deoxy-beta-D-glucopyranosyl-1',2-lactam)-(1-->4)-2-acetamido-3,6-di-O-benzyl-2-deoxy-beta-D-glucopyranoside by selective de-O-allylation and parallel removal of the benzylidene and O-benzyl groups is described. The resulting beta-muramyl lactam-(1-->4)-GlcNAc disaccharide is characterised as the per-O-acetylated derivative by 1H and 13C NMR spectroscopy and X-ray structure analysis. Conformational analysis about glycosidic bond of repeating units of bacterial spore cortex is based on experimental data and molecular modelling.
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Affiliation(s)
- Dina Keglević
- Rudjer Bosković Institute, P.O. Box 180, Bijenicka 54, HR-10002, Zagreb, Croatia
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Lommerse JPM, van Rooijen JJM, Kroon-Batenburg LMJ, Kamerling JP, Vliegenthart JFG. Conformational analysis of two xylose-containing N-glycans in aqueous solution by using 1H NMR ROESY and NOESY spectroscopy in combination with MD simulations. Carbohydr Res 2002; 337:2279-99. [PMID: 12433493 DOI: 10.1016/s0008-6215(02)00212-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The conformational behavior of the synthetic hexa- and heptasaccharide methyl beta-glycosides alpha-D-Manp-(1 --> 6)-[alpha-D-Manp-(1 --> 3)-][beta-D-Xylp-(1 --> 2)-]beta-D-Manp-(1 --> 4)-beta-D-GlcpNAc-(1 --> 4)-beta-D-GlcpNAc-(1 --> OMe and alpha-D-Manp-(1 --> 6)-[alpha-D-Manp-(1 --> 3)-][beta-D-Xylp-(1 --> 2)-]beta-D-Manp-(1 --> 4)-beta-D-GlcpNAc-(1 --> 4)-[alpha-L-Fucp-(1 --> 6)-]beta-D-GlcpNAc-(1 --> OMe, representing the xylosylated and the xylosylated alpha-(1 --> 6)-fucosylated core structures of N-glycans in alpha(D)-hemocyanin of the snail Helix pomatia, respectively, were investigated by 1H NMR spectroscopy in combination with molecular dynamics (MD) simulations in water. 1H and 13C chemical shifts of the oligosaccharides were assigned using 1H-(1)H COSY, TOCSY, and NOESY, and 1H-(13)C HMQC techniques. Experimental 2D 1H cross-peak intensities from one series of NOESY and one series of ROESY experiments of the two oligosaccharides were compared with calculated values derived from MD trajectories using the CROSREL program, yielding information about the conformation of each glycosidic linkage of the methyl glycosides. The flexibility of the linkages was described by generalized order parameters and internal rotation correlation times. Analysis of the data indicated that several conformations are likely to exist for the alpha-D-Man-(1 --> 6)-beta-D-Man, the alpha-L-Fuc-(1 --> 6)-beta-D-GlcNAc, and the alpha-D-Man-(1 --> 3)-beta-D-Man linkage, whereas the beta-D-Xyl-(1 --> 2)-beta-D-Man-(1 --> 4)-beta-D-GlcNAc-(1 --> 4)-beta-D-GlcNAc fragment occurs in one rigid conformation. No significant differences were found between the corresponding structural elements in both methyl glycosides. NOESY and ROESY experiments proved to be suitable for providing the experimental data required, however, due to more overlap within the ROESY spectra, reducing the accuracy of the analysis, NOESY spectral analysis is preferred.
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Affiliation(s)
- Jos P M Lommerse
- Bijvoet Center, Department of Bio-Organic Chemistry, Section of Glycoscience and Biocatalysis, Utrecht University, Padualaan 8, NL-3584 CH Utrecht, The Netherlands
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15
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Mackie ID, Röhrling J, Gould RO, Pauli J, Jäger C, Walkinshaw M, Potthast A, Rosenau T, Kosma P. Crystal and molecular structure of methyl 4-O-methyl-beta-D-glucopyranosyl-(1-->4)-beta-D-glucopyranoside. Carbohydr Res 2002; 337:161-6. [PMID: 11814448 DOI: 10.1016/s0008-6215(01)00299-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The cellulose model compound methyl 4-O-methyl-beta-D-glucopyranosyl-(1-->4)-beta-D-glucopyranoside (6) was synthesised in high overall yield from methyl beta-D-cellobioside. The compound was crystallised from methanol to give colourless prisms, and the crystal structure was determined. The monoclinic space group is P2(1) with Z=2 and unit cell parameters a=6.6060 (13), b=14.074 (3), c=9.3180 (19) A, beta=108.95(3) degrees. The structure was solved by direct methods and refined to R=0.0286 for 2528 reflections. Both glucopyranoses occur in the 4C(1) chair conformation with endocyclic bond angles in the range of standard values. The relative orientation of both units described by the interglycosidic torsional angles [phi (O-5' [bond] C-1' [bond] O-4 [bond] C-4) -89.1 degrees, Phi (C-1' [bond] O-4 [bond] C-4 [bond] C-5) -152.0 degrees] is responsible for the very flat shape of the molecule and is similar to those found in other cellodextrins. Different rotamers at the exocyclic hydroxymethyl group for both units are present. The hydroxymethyl group of the terminal glucose moiety displays a gauche-trans orientation, whereas the side chain of the reducing unit occurs in a gauche-gauche conformation. The solid state (13)C NMR spectrum of compound 6 exhibits all 14 carbon resonances. By using different cross polarisation times, the resonances of the two methyl groups and C-6 carbons can easily be distinguished. Distinct differences of the C-1 and C-4 chemical shifts in the solid and liquid states are found.
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Affiliation(s)
- Iain D Mackie
- Department of Chemistry, University of Edinburgh, Edinburgh EH9 3JJ, UK
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16
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Faber EJ, van Kuik JA, Kamerling JP, Vliegenthart JFG. Modeling of the structure in aqueous solution of the exopolysaccharide produced by Lactobacillus helveticus 766. Biopolymers 2002; 63:66-76. [PMID: 11754349 DOI: 10.1002/bip.1063] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A method is described for constructing a conformational model in water of a heteropolysaccharide built up from repeating units, and is applied to the exopolysaccharide produced by Lactobacillus helveticus 766. The molecular modeling method is based on energy minima, obtained from molecular mechanics calculations of each of the constituting disaccharide fragments of the repeating unit in vacuo, as starting points. Subsequently, adaptive umbrella sampling of the potential of mean force is applied to extract rotamer populations of glycosidic dihedral angles of oligosaccharide fragments in solution. From these analyses, the most probable conformations are constructed for the hexasaccharide-repeating unit of the polysaccharide. After exploring the conformational space of each of the individual structures by molecular dynamics simulations, the different repeating unit conformations are used as building blocks for the generation of oligo- and polysaccharide models, by using a polysaccharide building program. The created models of the exopolysaccharide produced by L. helveticus 766 exhibit a flexible twisted secondary structure and tend to adopt a random coil conformation as tertiary structure.
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Affiliation(s)
- Elisabeth J Faber
- Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, PO Box 80.075, NL-3508 TB Utrecht, The Netherlands
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17
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Engelsen SB, Monteiro C, Hervé de Penhoat C, Pérez S. The diluted aqueous solvation of carbohydrates as inferred from molecular dynamics simulations and NMR spectroscopy. Biophys Chem 2001; 93:103-27. [PMID: 11804720 DOI: 10.1016/s0301-4622(01)00215-0] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The purpose of this paper is to review our understanding of the dilute hydration (aqueous solvation) behaviour of disaccharide compounds. To this end we discuss and scrutinize the results that have been obtained for the three model disaccharides: maltose, sucrose and trehalose from experimental NMR studies and from theoretical molecular dynamics studies in explicit aqueous solutions. The focus is on the description of molecular hydration features that will influence macroscopic entities such as diffusion and relaxation: residence times of hydration waters, hydration numbers and hydration densities. The principles of molecular dynamics simulation are briefly outlined while a detailed presentation is given of the key features that characterise hydration: the solvation of the glycosidic linkage, the radial hydration of the solute, the water density anisotropy around the solute, the residential behaviour of water molecules in the periphery of the solute, and rotational and translational diffusion coefficients. With respect to the use of NMR in characterising the structure and dynamics of the hydration, the hydrodynamic theory of rotational and translational diffusion of biomolecules as well as the use of pulse field gradient spin echo experiments are briefly presented. The NMR-defined rotational diffusion coefficients (D(r)) and the experimentally determined translational diffusion (D(t)) coefficients are reported for 4% (w/w) solutions of sucrose, trehalose and maltose. These results are compared with theoretical data obtained from molecular dynamics simulations of sucrose, trehalose and maltose under identical conditions (concentration, temperature, etc.). With our present level of knowledge we can propose that although carbohydrates share a number of hydration characteristics, evidence is accumulating in support of the notion that it is not the amount or overall hydration but rather the detailed individual carbohydrate-water interaction that is likely to determine carbohydrate structure and functionality.
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Affiliation(s)
- S B Engelsen
- The Royal Veterinary and Agricultural University, Centre for Advanced food Studies, Rolighedsvej 30, DK-1958 Frederiksberg C, Denmark.
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Leeflang BR, Faber EJ, Erbel P, Vliegenthart JF. Structure elucidation of glycoprotein glycans and of polysaccharides by NMR spectroscopy. J Biotechnol 2000; 77:115-22. [PMID: 10674218 DOI: 10.1016/s0168-1656(99)00212-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The applicability of 1H-NMR spectroscopy for the determination of the primary and tertiary structure of carbohydrate-containing molecules is demonstrated. For classes of known compounds the characterization can be based on chemical shifts observed in 1D NMR spectra with or without the aid of a computer database. For more complex structure determinations 2D NMR techniques are required. Here the application of 2D NMR is demonstrated for the primary structure determination of two bacterial exopolysaccharides, for the spatial structure determination of a disaccharide and a glycoprotein hormone.
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Affiliation(s)
- B R Leeflang
- Bijvoet Center for Biomolecular Research, Utrecht University, The Netherlands.
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20
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Montero E, Vallmitjana M, Pérez-Pons JA, Querol E, Jiménez-Barbero J, Cañada FJ. NMR studies of the conformation of thiocellobiose bound to a beta-glucosidase from Streptomyces sp. FEBS Lett 1998; 421:243-8. [PMID: 9468315 DOI: 10.1016/s0014-5793(97)01571-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The conformation of 4-thiocellobiose bound to beta-glucosidase from Streptomyces sp. has been studied by 1H-NMR transferred nuclear Overhauser effect spectroscopy (TR-NOE). Thiocellobiose behaves as an inhibitor of this glucosidase when cellobiose is used as substrate. NOE measurements and molecular mechanics calculations have also been performed to estimate the probability distribution of conformers of thiocellobiose when free in solution. Experimental data show that, in contrast with the natural O-analogue, thiocellobiose presents three conformational families in the free state, namely syn, anti-psi and anti-phi, whilst only one of them (syn) is recognized by the enzyme.
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Affiliation(s)
- E Montero
- Instituto de Química Orgánica, CSIC, Madrid, Spain
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21
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Spronk BA, Rademaker GJ, Haverkamp J, Thomas-Oates JE, Vincken JP, Voragen AG, Kamerling JP, Vliegenthart JF. Dimers of a GFG hexasaccharide occur in apple fruit xyloglucan. Carbohydr Res 1997; 305:233-42. [PMID: 9581277 DOI: 10.1016/s0008-6215(97)10027-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Apple fruit xyloglucan is predominantly built up from XXXG, XXFG, and XLFG units (G = beta-D-Glcp-, X = alpha-D-Xylp-(1-->6)-beta-D-Glcp-, L = beta-D-Galp-(1-->2)-alpha-D-Xylp-(1-->6)-beta-D-Glcp-, F = alpha-L-Fucp-(1-->2)-beta-D-Galp-(1-->2)-alpha-D-Xyl p-(1-->6)-beta-D-Glcp-). However, small amounts of oligosaccharides with a less heavily branched glucan backbone also occur. Structural analysis of two such oligosaccharides, isolated from a xyloglucan preparation digested with endoglucanase i.v., using a combination of FAB mass spectrometry and 1H NMR spectroscopy, afforded the identification of GFG and a dimer of GFG. The finding of the dodecasaccharide GFGGFG as a structural element of apple fruit xyloglucan is most unusual.
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Affiliation(s)
- B A Spronk
- Department of Bio-Organic Chemistry, Utrecht University, Netherlands
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22
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Mikhailov D, Linhardt RJ, Mayo KH. NMR solution conformation of heparin-derived hexasaccharide. Biochem J 1997; 328 ( Pt 1):51-61. [PMID: 9359833 PMCID: PMC1218886 DOI: 10.1042/bj3280051] [Citation(s) in RCA: 77] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The solution conformation of homogeneous, heparin-derived hexasaccharide (residues A, B, C, D, E, F) has been investigated by using 1H-NMR spectroscopy. Intra-ring conformations have been defined by J-coupling constants and inter-proton nuclear Overhauser effects (NOEs), and the orientation of one ring with respect to the other has been defined by inter-ring NOEs. NOE-based conformational modelling has been done by using the iterative relaxation matrix approach (IRMA), restrained energy minimization to refine structures and to distinguish between minor structural differences and equilibria between various intra-ring forms. All glucosamine residues B, D and F are in the 4C1 chair conformation. The uronate (A) residue is mostly represented by the 1H2 form, whereas internal iduronates (C and E) exist in equilibrium between the chair and skewed boat forms. Deviations in some NOEs indicate a minor contribution of the 2H1 form to the A ring. Glycosidic dihedral angles, which define the overall oligosaccharide conformation, were further refined by combining in vacuo energy map calculations and restrained energy minimization in explicit solvent water. Conformational stability was further assessed by subjecting NOE and IRMA-derived structures to 600 ps of unrestrained molecular dynamics in explicit solvent.
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Affiliation(s)
- D Mikhailov
- Department of Biochemistry, University of Minnesota Health Science Center, 435 Delaware Street, S.E., Minneapolis, MN 55455, USA
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23
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Hricovíni M, Guerrini M, Torri G, Casu B. Motional properties of E. coli polysaccharide K5 in aqueous solution analyzed by NMR relaxation measurements. Carbohydr Res 1997; 300:69-76. [PMID: 9203334 DOI: 10.1016/s0008-6215(97)00036-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
13C NMR relaxation measurements at three different magnetic field strengths have been used to analyse the motional properties of a low molecular weight K5 polysaccharide (delta UA-[-->4)-beta-D-GlcNAc(1-->4)-beta-D-GlcA(1-->]n-GlcNAcred) from E. coli. Two-dimensional double INEPT spectra with suppression of cross-correlation effects between dipolar and chemical shift anisotropy relaxation mechanisms were collected in order to determine carbon longitudinal and transverse relaxation times. The values of the overall correlation time and the rate of internal motions were obtained using the model free spectral densities. The data indicate that the overall motion of the molecule is non-isotropic and can be approximated with the symmetric top model with an axial ratio of approximately 22. The magnitude of the generalized order parameters (S2 approximately 0.8) and the internal motion correlation time (tau e approximately 30 ps) differ from those found for iduronic acid-containing glycosaminoglycans and suggest that the internal motions in K5 polysaccharide are more limited.
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Affiliation(s)
- M Hricovíni
- Institute of Chemistry and Biochemistry, G. Ronzoni, Milan, Italy
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Robijn GW, Imberty A, van den Berg DJ, Ledeboer AM, Kamerling JP, Vliegenthart JF, Pérez S. Predicting helical structures of the exopolysaccharide produced by Lactobacillus sake 0- 1. Carbohydr Res 1996; 288:57-74. [PMID: 8765727 DOI: 10.1016/s0008-6215(96)90777-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The viscous exopolysaccharide (EPS) produced by Lactobacillus sake 0- 1 is a high molecular mass polymer (Mm 6 x 10(6) Da) consisting of pentasaccharide repeating units with a composition of D-glucose, L-rhamnose, and sn-glycerol 3-phosphate in molar ratios of 3:2:1. One of the rhamnose residues in the repeating unit is partially 2-O-acetylated. The O-deacetylated, deglycerophosphorylated EPS has been investigated by molecular mechanics calculations. A complete conformational analysis of each of the constituent disaccharide fragments has been performed using the flexible residue approach with the MM3(92) force field. Furthermore, using the same force field, CICADA analyses were accomplished on hexa- and octasaccharide substructure of the polysaccharide. Based on these analyses, insight was obtained into nine conformational minima for the polysaccharide. The low energy conformations found by CICADA were extrapolated to regular polysaccharide structures using a polysaccharide builder program. The generated helices exhibit either 2-fold or 3- or 4-fold right-handed chiralities, and in each case the helices are highly extended.
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Affiliation(s)
- G W Robijn
- Bijvoet Center, Department of Bio-Organic Chemistry, Utrecht University, The Netherlands
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25
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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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26
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Brant DA, Liu HS, Zhu ZS. The dependence of glucan conformational dynamics on linkage position and stereochemistry. Carbohydr Res 1995; 278:11-26. [PMID: 8536263 DOI: 10.1016/0008-6215(95)00242-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The 13C NMR T1 relaxation times for the (1-->4)-linked maltooligomers (Mi) and the (1-->6)-linked isomaltooligomers (IMi) with i = 2, 4, 6, and 8 were measured in aqueous solution at 22 and 65 degrees C at a concentration (3%) low enough to have removed concentration-dependent effects on the measured T1 values. Separate T1 values were measured for each carbon in the residue at the reducing end of the oligosaccharide, in the residue at the non-reducing end, and in the interior, i.e., non-terminal, residue(s). Analogous data for the corresponding high polymers show that at 22 degrees C the relaxation times for the carbons of the interior residues of the oligomers have converged to their high chain length asymptotes at about i = 10. This observation suggests that at room temperature polymeric motions in the frequency domain effective for 13C NMR relaxation at a magnetic field strength of 11.7 T have a "wavelength" of the order of 10 residues. The relaxation times characterizing the two ends of the chain are different, with longer T1 values for the carbons of the reducing end than for those of the non-reducing end. Carbons of alpha-anomeric residues at the reducing end have shorter relaxation times than those of the corresponding beta-anomeric reducing sugars. Carbons of the interior residues have T1 values shorter than the carbons of either type of terminal residue. For oligomers of a given dp there is no T1 difference between oligomers of the Mi and IMi series at room temperature. This observation is seemingly at odds with the great differences in the inherent conformational freedom of the (1-->4)- and (1-->6)-linkages. At elevated temperatures the orientational relaxation behavior of the two series of oligomers measured by 13C T1 values show interesting differences, and in the case of the Mi series, structure develops in the chain length dependence of the T1 values.
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Affiliation(s)
- D A Brant
- Department of Chemistry, University of California, Irvine 92717-2025, USA
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27
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Asensio JL, Cañada FJ, Jimenez-Barbero J. Studies of the bound conformations of methyl alpha-lactoside and methyl beta-allolactoside to ricin B chain using transferred NOE experiments in the laboratory and rotating frames, assisted by molecular mechanics and dynamics calculations. EUROPEAN JOURNAL OF BIOCHEMISTRY 1995; 233:618-30. [PMID: 7588809 DOI: 10.1111/j.1432-1033.1995.618_2.x] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The conformation in solution of methyl beta-galactopyranosyl-(1-->4)-alpha-glucopyranoside (methyl alpha-lactoside) and methyl beta-galactopyranosyl-(1-->6)-beta-glucopyranoside (methyl beta-allolactoside) has been studied through NMR spectroscopy and molecular mechanics calculations. NOE measurements both in the laboratory and rotating frames, have been interpreted in terms of an ensemble average distribution of conformers. Molecular mechanics calculations have been performed to estimate the probability distribution of conformers from the steric energy maps. The experimental results indicate that methyl alpha-lactoside spends about 90% of its time in a broad low-energy region close to the global minimum, while methyl beta-allolactoside presents much higher flexibility. The conformational changes that occur when both disaccharides are bound to the ricin B chain in aqueous solution have been studied using transferred NOE experiments at several protein/ligand ratios. The observed data indicate that the protein causes a conformational variation in the torsion angles of methyl alpha-lactoside changing towards smaller angle values (phi/psi approximately -20/-20), although the recognized conformer is still within the lowest energy region. In particular, the torsional changes separate Gal H1 from Glc H3 and Glc H6 protons, with a noticeable decrease in the intensities of the corresponding NOE cross-peaks, which were clearly observed for the free disaccharide. On the other hand, different conformations around the phi, psi, and omega glycosidic bonds of methyl beta-allolactoside are recognized by the lectin. In fact, for the methyl-beta-allolactoside-ricin-B complex, only the NOESY cross-peaks corresponding to the protons of the galactose residue are negative, as expected for a molecule in the slow motion regime. In contrast, the corresponding cross peaks for the glucose residue were about zero, as expected for a molecule whose motion is practically independent of the protein. However, for the methyl-alpha-lactoside-ricin-B complex, all the NOESY cross-peaks for both the galactose and glucose moieties were clearly negative. From the NMR experimental point of view, it is demonstrated that the comparison of longitudinal and transversal transferred NOEs allows one to clearly differentiate direct enhancements from spin diffusion effects, which are of major concern when analysing NOE spectra of macromolecules.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- J L Asensio
- Departamento de Química Orgánica Biológica, Instituto de Química Orgánica, Madrid, Spain
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28
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Spronk BA, Rivera-Sagredo A, Kamerling JP, Vliegenthart JF. A reinvestigation towards the conformation of methyl alpha-D-mannopyranosyl-(1-->6)-alpha-D-mannopyranoside by a combined ROE and molecular dynamics analysis. Carbohydr Res 1995; 273:11-26. [PMID: 7553667 DOI: 10.1016/0008-6215(95)00061-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Conformational analysis of alpha-D-Man p-(1-->6)-alpha-D-Man p1-OMe, by a combination of extensive molecular dynamics calculations in water and ROE buildup series, afforded two main minima, namely, phi/psi = 95/-178 and phi/psi = 140/-185. Transitions between these minima are observed, which have not previously been demonstrated using other approaches. In contrast to literature data for the glycosidic linkage, describing equal populations of both the gg and the gt rotamers, it was found that the gg conformer is present to ca. 96%. The non-reducing mannosyl unit showed approximately a 1:1 ratio for the gg:gt equilibrium, in accordance with earlier reports.
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Affiliation(s)
- B A Spronk
- Department of Bio-Organic Chemistry, Utrecht University, The Netherlands
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29
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Lommerse JP, Kroon-Batenburg LM, Kroon J, Kamerling JP, Vliegenthart JF. Conformations and internal mobility of a glycopeptide derived from bromelain using molecular dynamics simulations and NOESY analysis. JOURNAL OF BIOMOLECULAR NMR 1995; 6:79-94. [PMID: 7663144 DOI: 10.1007/bf00417494] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The conformation and internal flexibility of a glycopeptide Manalpha1-6 (Xylbeta1-2)Manbeta1-4GlcNAcbeta1-4(Fucalpha1-3) GlcNAcbeta1-N(Asn-Glu-Ser-Ser), prepared from pineapple stem bromelain, have been analyzed using a combination of molecular dynamics (MD) simulations in water with NOESY 1H NMR spectroscopy. Theoretical NOESY cross-peak intensities were calculated by the CROSREL program on the basis of models, obtained from MD simulations, using a full relaxation matrix approach. Special attention was paid to the description of internal flexibility of the hexasaccharide moiety by the use of generalized order parameters, in combination with the application of an individual rotation correlation tme for each monosaccharide residue. The tetrapeptide moiety appeared to be very mobile during the MD simulations, which was confirmed by the absence of NOE cross peaks. For the oligosaccharide part a model was developed to estimate characteristic times for large reorientational motions around the glycosidic linkages, associated with conformational transitions. For the Manalpha1-6Man and the Fucalpha1-3GlcNAc linkages such a flexibility was found with a characteristic time of 2 ns. In contrast, the Xylbeta1-2Manbeta1-4GlcNAcbeta1-4GlcNAc part of the glycan appears to be relatively rigid.
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Affiliation(s)
- J P Lommerse
- Department of Bio-Organic Chemistry, Utrecht University, The Netherlands
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30
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Miertus S, Bertocchi C, Krempaska R, Paoletti S. Conformational analysis of segments of oxidized cellulose. Part I: Molecular modelling of glucuronic acid dimers considering the effect of counter-ions and a polar environment. Int J Biol Macromol 1995; 17:183-8. [PMID: 7577816 DOI: 10.1016/0141-8130(95)92684-i] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Conformational analysis of various forms of glucuronic acid dimers as the model structures of oxidized cellulose has been performed using molecular mechanics with a CVFF force field. The effects of ionization of carboxyl groups, ion pairing with explicit consideration of counter-ions (Na+, Mg2+) and the implicit inclusion of a solvent effect via the dielectric constant, epsilon, have been simulated. The non-ionized glucuronic acid dimer shows conformational behaviour similar to that of unoxidized cellobiose. The ionization of COOH groups leads to strong destabilization of C and D conformers (with both COO- groups on the same side of the molecule), while complexation with counter-ions leads to strong stabilization of these forms which yield highly wound low-pitch helices. An increase in the solvent polarity has an attenuating effect on the behaviour described above.
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31
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André I, Mazeau K, Taravel FR, Tvaroska I. Conformation and dynamics of a cyclic (1-->2)-beta-D-glucan. Int J Biol Macromol 1995; 17:189-98. [PMID: 7577817 DOI: 10.1016/0141-8130(95)92685-j] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A molecular modelling and nuclear magnetic resonance spectroscopic study was performed in order to gain insight into the conformational preferences of cyclosophoroheptadecaose. MM3 molecular mechanics calculations predicted a non-symmetric conformer with a small cavity of 3.7 A diameter as the lowest energy form. Molecular dynamics simulations gave insight into the dynamics of the free cyclosophoroheptadecaose and also supported the results of molecular mechanics calculations. A fair agreement was found between experimental data and corresponding average values predicted by molecular modelling.
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Affiliation(s)
- I André
- Centre de Recherches sur les Macromolécules Végétales, CNRS, Grenoble, France
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32
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Hricovíni M, Torri G. Dynamics in aqueous solutions of the pentasaccharide corresponding to the binding site of heparin for antithrombin III studied by NMR relaxation measurements. Carbohydr Res 1995; 268:159-75. [PMID: 7736468 DOI: 10.1016/0008-6215(94)00334-c] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
1H NMR and 13C NMR relaxation measurements at different magnetic field strengths were used to study the nature of overall and internal motions, in aqueous solution, of the synthetic pentasaccharide (A-G-A*-I-AM) corresponding to the binding site of heparin for antithrombin III. Two-dimensional double INEPT spectra were recorded at 11.7 T with and without suppression of cross-correlation effects between dipolar and chemical shift anisotropy relaxation mechanisms in measurements of spin-lattice and spin-spin relaxation times. Moreover, longitudinal relaxation times were collected at 7 T with the inversion recovery method. One dimensional NOESY spectra were recorded at 11.7 T and 9.4 T with various mixing times when spins of the A1* and A4* protons were inverted in the central residue of the pentasaccharide. Differences in the T1 relaxation times, as well as in the cross-relaxation rates between protons relaxing through fixed distances in the A* residue, indicated that the molecule tumbles anisotropically in solution. However, in order to achieve agreement between the spectral and the model data, the presence of internal motions had to be also considered, in addition to the assumption of a symmetric top model for the description of overall tumbling. The changes in the longitudinal and transversal relaxation times, collected with and without suppression of interference effects, supported the assumption that the cross-correlation between dipolar and chemical shift anisotropy relaxation mechanisms cannot be neglected in this medium-sized molecule. In fact, the influence of these effects was 10-15% in T1 and 20-25% in T2 relaxation times. The experimental data were analyzed using model free formalism and the computed order parameters indicate a decrease in spatial restriction from the central residue (S2 approximately 0.9) towards both ends of the pentasaccharide (S2 approximately 0.7). The anisotropy ratio found was approximately 3.3 with correlation times tau parallel = 450 ps and tau perpendicular = 1480 ps. The values of effective correlation time were within the range of tens of picoseconds. Thus, for a more precise interpretation of the experimental data for the pentasaccharide, in addition to internal motions and anisotropic tumbling, the effect of cross-correlation must be taken into account as well.
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Affiliation(s)
- M Hricovíni
- Istituto di Chimica e Biochimica G. Ronzoni, Milano, Italy
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33
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Van Halbeek H. NMR developments in structural studies of carbohydrates and their complexes. Curr Opin Struct Biol 1994. [DOI: 10.1016/s0959-440x(94)90168-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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