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Zerbetto M, Angles d'Ortoli T, Polimeno A, Widmalm G. Differential Dynamics at Glycosidic Linkages of an Oligosaccharide as Revealed by 13C NMR Spin Relaxation and Stochastic Modeling. J Phys Chem B 2018; 122:2287-2294. [PMID: 29385337 DOI: 10.1021/acs.jpcb.7b12478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Among biomolecules, carbohydrates are unique in that not only can linkages be formed through different positions, but the structures may also be branched. The trisaccharide β-d-Glcp-(1→3)[β-d-Glcp-(1→2)]-α-d-Manp-OMe represents a model of a branched vicinally disubstituted structure. A 13C site-specific isotopologue, with labeling in each of the two terminal glucosyl residues, enabled the acquisition of high-quality 13C NMR relaxation parameters, T1 and T2, and heteronuclear NOE, with standard deviations of ≤0.5%. For interpretation of the experimental NMR data, a diffusive chain model was used, in which the dynamics of the glycosidic linkages is coupled to the global reorientation motion of the trisaccharide. Brownian dynamics simulations relying on the potential of mean force at the glycosidic linkages were employed to evaluate spectral densities of the spin probes. Calculated NMR relaxation parameters showed a very good agreement with experimental data, deviating <3%. The resulting dynamics are described by correlation times of 196 and 174 ps for the β-(1→2)- and β-(1→3)-linked glucosyl residues, respectively, i.e., different and linkage dependent. Notably, the devised computational protocol was performed without any fitting of parameters.
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Affiliation(s)
- Mirco Zerbetto
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova , Padova 35131, Italy
| | - Thibault Angles d'Ortoli
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
| | - Antonino Polimeno
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova , Padova 35131, Italy
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , S-106 91 Stockholm, Sweden
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2
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Blasco P, Patel DS, Engström O, Im W, Widmalm G. Conformational Dynamics of the Lipopolysaccharide from Escherichia coli O91 Revealed by Nuclear Magnetic Resonance Spectroscopy and Molecular Simulations. Biochemistry 2017; 56:3826-3839. [DOI: 10.1021/acs.biochem.7b00106] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Pilar Blasco
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Dhilon S. Patel
- Department
of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Olof Engström
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
| | - Wonpil Im
- Department
of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Göran Widmalm
- Department
of Organic Chemistry, Arrhenius Laboratory, Stockholm University, SE-106
91 Stockholm, Sweden
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3
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Pendrill R, Engström O, Volpato A, Zerbetto M, Polimeno A, Widmalm G. Flexibility at a glycosidic linkage revealed by molecular dynamics, stochastic modeling, and (13)C NMR spin relaxation: conformational preferences of α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe in water and dimethyl sulfoxide solutions. Phys Chem Chem Phys 2016; 18:3086-96. [PMID: 26741055 DOI: 10.1039/c5cp06288h] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The monosaccharide L-rhamnose is common in bacterial polysaccharides and the disaccharide α-L-Rhap-α-(1 → 2)-α-L-Rhap-OMe represents a structural model for a part of Shigella flexneri O-antigen polysaccharides. Utilization of [1'-(13)C]-site-specific labeling in the anomeric position at the glycosidic linkage between the two sugar residues facilitated the determination of transglycosidic NMR (3)JCH and (3)JCC coupling constants. Based on these spin-spin couplings the major state and the conformational distribution could be determined with respect to the ψ torsion angle, which changed between water and dimethyl sulfoxide (DMSO) as solvents, a finding mirrored by molecular dynamics (MD) simulations with explicit solvent molecules. The (13)C NMR spin relaxation parameters T1, T2, and heteronuclear NOE of the probe were measured for the disaccharide in DMSO-d6 at two magnetic field strengths, with standard deviations ≤1%. The combination of MD simulation and a stochastic description based on the diffusive chain model resulted in excellent agreement between calculated and experimentally observed (13)C relaxation parameters, with an average error of <2%. The coupling between the global reorientation of the molecule and the local motion of the spin probe is deemed essential if reproduction of NMR relaxation parameters should succeed, since decoupling of the two modes of motion results in significantly worse agreement. Calculation of (13)C relaxation parameters based on the correlation functions obtained directly from the MD simulation of the solute molecule in DMSO as solvent showed satisfactory agreement with errors on the order of 10% or less.
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Affiliation(s)
- Robert Pendrill
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
| | - Olof Engström
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
| | - Andrea Volpato
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova 35131, Italy.
| | - Mirco Zerbetto
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova 35131, Italy.
| | - Antonino Polimeno
- Dipartimento di Scienze Chimiche, Università degli Studi di Padova, Padova 35131, Italy.
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden.
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4
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Yang M, Angles d’Ortoli T, Säwén E, Jana M, Widmalm G, MacKerell AD. Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations. Phys Chem Chem Phys 2016; 18:18776-94. [PMID: 27346493 PMCID: PMC4945446 DOI: 10.1039/c6cp02970a] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The conformation of saccharides in solution is challenging to characterize in the context of a single well-defined three-dimensional structure. Instead, they are better represented by an ensemble of conformations associated with their structural diversity and flexibility. In this study, we delineate the conformational heterogeneity of five trisaccharides via a combination of experimental and computational techniques. Experimental NMR measurements target conformationally sensitive parameters, including J couplings and effective distances around the glycosidic linkages, while the computational simulations apply the well-calibrated additive CHARMM carbohydrate force field in combination with efficient enhanced sampling molecular dynamics simulation methods. Analysis of conformational heterogeneity is performed based on sampling of discreet states as defined by dihedral angles, on root-mean-square differences of Cartesian coordinates and on the extent of volume sampled. Conformational clustering, based on the glycosidic linkage dihedral angles, shows that accounting for the full range of sampled conformations is required to reproduce the experimental data, emphasizing the utility of the molecular simulations in obtaining an atomic detailed description of the conformational properties of the saccharides. Results show the presence of differential conformational preferences as a function of primary sequence and glycosidic linkage types. Significant differences in conformational ensembles associated with the anomeric configuration of a single glycosidic linkage reinforce the impact of such changes on the conformational properties of carbohydrates. The present structural insights of the studied trisaccharides represent a foundation for understanding the range of conformations adopted in larger oligosaccharides and how these molecules encode their conformational heterogeneity into the monosaccharide sequence.
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Affiliation(s)
- Mingjun Yang
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
| | - Thibault Angles d’Ortoli
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Elin Säwén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Madhurima Jana
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
- Department of Chemistry, National Institute of Technology Rourkela, Odisha, India 769008
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Alexander D. MacKerell
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland, Baltimore, Maryland 21201
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5
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Säwén E, Massad T, Landersjö C, Damberg P, Widmalm G. Population distribution of flexible molecules from maximum entropy analysis using different priors as background information: application to the Φ, Ψ-conformational space of the α-(1-->2)-linked mannose disaccharide present in N- and O-linked glycoproteins. Org Biomol Chem 2010; 8:3684-95. [PMID: 20574564 DOI: 10.1039/c003958f] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The conformational space available to the flexible molecule α-D-Manp-(1-->2)-α-D-Manp-OMe, a model for the α-(1-->2)-linked mannose disaccharide in N- or O-linked glycoproteins, is determined using experimental data and molecular simulation combined with a maximum entropy approach that leads to a converged population distribution utilizing different input information. A database survey of the Protein Data Bank where structures having the constituent disaccharide were retrieved resulted in an ensemble with >200 structures. Subsequent filtering removed erroneous structures and gave the database (DB) ensemble having three classes of mannose-containing compounds, viz., N- and O-linked structures, and ligands to proteins. A molecular dynamics (MD) simulation of the disaccharide revealed a two-state equilibrium with a major and a minor conformational state, i.e., the MD ensemble. These two different conformation ensembles of the disaccharide were compared to measured experimental spectroscopic data for the molecule in water solution. However, neither of the two populations were compatible with experimental data from optical rotation, NMR (1)H,(1)H cross-relaxation rates as well as homo- and heteronuclear (3)J couplings. The conformational distributions were subsequently used as background information to generate priors that were used in a maximum entropy analysis. The resulting posteriors, i.e., the population distributions after the application of the maximum entropy analysis, still showed notable deviations that were not anticipated based on the prior information. Therefore, reparameterization of homo- and heteronuclear Karplus relationships for the glycosidic torsion angles Φ and Ψ were carried out in which the importance of electronegative substituents on the coupling pathway was deemed essential resulting in four derived equations, two (3)J(COCC) and two (3)J(COCH) being different for the Φ and Ψ torsions, respectively. These Karplus relationships are denoted JCX/SU09. Reapplication of the maximum entropy analysis gave excellent agreement between the MD- and DB-posteriors. The information entropies show that the current reparametrization of the Karplus relationships constitutes a significant improvement. The Φ(H) torsion angle of the disaccharide is governed by the exo-anomeric effect and for the dominating conformation Φ(H) = -40 degrees and Ψ(H) = 33 degrees. The minor conformational state has a negative Ψ(H) torsion angle; the relative populations of the major and the minor states are approximately 3 : 1. It is anticipated that application of the methodology will be useful to flexible molecules ranging from small organic molecules to large biomolecules.
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Affiliation(s)
- Elin Säwén
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91, Stockholm, Sweden
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6
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Eklund R, Lycknert K, Söderman P, Widmalm G. A conformational dynamics study of alpha-l-Rhap-(1-->2)[alpha-l-Rhap-(1-->3)]-alpha-l-Rhap-OMe in solution by NMR experiments and molecular simulations. J Phys Chem B 2007; 109:19936-45. [PMID: 16853578 DOI: 10.1021/jp053198o] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational preference of alpha-l-Rhap-(1-->2)[alpha-l-Rhap-(1-->3)]-alpha-l-Rhap-OMe in solution has been studied by NMR spectroscopy using one-dimensional (1)H,(1)H T-ROESY experiments and measurement of trans-glycosidic (3)J(C,H) coupling constants. Molecular dynamics (MD) simulations with a CHARMM22 type of force field modified for carbohydrates were performed with water as the explicit solvent. The homonuclear cross-relaxation rates, interpreted as effective proton-proton distances, were compared to those obtained from simulation. Via a Karplus torsional relationship, (3)J(C,H) values were calculated from simulation and compared to experimental data. Good agreement was observed between experimental data and the MD simulation, except for one inter-residue T-ROE between protons in the terminal sugar residues. The results show that the trisaccharide exhibits substantial conformational flexibility, in particular along the psi glycosidic torsion angles. Notably, for these torsions, a high degree of correlation (77%) was observed in the MD simulation revealing either psi(2)(+) psi(3)(+) or psi(2)(-)psi(3)(-) states. The simulations also showed that non-exoanomeric conformations were present at the phi torsion angles, but to a limited extent, with the phi(3) state populated to a larger extent than the phi(2) state. Further NMR analysis of the trisaccharide by translational diffusion measurements and (13)C T(1) relaxation experiments quantified global reorientation using an anisotropic model together with interpretation of the internal dynamics via the "model-free" approach. Fitting of the dynamically averaged states to experimental data showed that the psi(2)(+)psi(3)(+) state is present to approximately 49%, psi(2)(-) psi(3)(-) to approximately 39%, and phi(3) (non-exo) to approximately 12%. Finally, using a dynamic and population-averaged model, (1)H,(1)H T-ROE buildup curves were calculated using a full relaxation matrix approach and were found to be in excellent agreement with experimental data, in particular for the above inter-residue proton-proton interaction between the terminal residues.
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Affiliation(s)
- Robert Eklund
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-10691 Stockholm, Sweden
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7
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Andersson A, Ahl A, Eklund R, Widmalm G, Mäler L. Dynamics in the cyclic Enterobacterial common antigen as studied by 13C NMR relaxation. JOURNAL OF BIOMOLECULAR NMR 2005; 31:311-20. [PMID: 15928997 DOI: 10.1007/s10858-005-1605-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2004] [Accepted: 01/21/2005] [Indexed: 05/02/2023]
Abstract
The motional properties of the cyclic enterobacterial common antigen (cECA), consisting of four trisaccharide repeat units, have been investigated by carbon-13 spin relaxation. R(1), R(2) and NOE relaxation parameters have been determined at three magnetic field strengths. The data were interpreted within the model-free framework to include the possibility of motional anisotropy, and overall as well as local dynamical parameters were fitted separately for each ring carbon. The motional anisotropy was addressed by assuming an axially symmetric diffusion tensor, which was fitted from the overall correlation times for each site in the sugar residues using the previously determined crystal structure. The data were found to be in agreement with an oblate shape of the molecule, and the values for D(iso) and D(||)/D(perpendicular sign) were in good agreement with translational diffusion data and an estimate based on calculation of the moment of inertia tensor, respectively. The local dynamics in cECA were found to be residue-dependent. Somewhat lower values for the order parameters, as well as longer local correlation times, were observed for the beta-linked ManNAcA residue compared to the two alpha-linked residues in the trisaccharide repeat unit.
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Affiliation(s)
- August Andersson
- Department of Biochemistry and Biophysics, Arrhenius Laboratory, Stockholm University, Sweden
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8
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Almond A, DeAngelis PL, Blundell CD. Dynamics of Hyaluronan Oligosaccharides Revealed by 15N Relaxation. J Am Chem Soc 2005; 127:1086-7. [PMID: 15669832 DOI: 10.1021/ja043526i] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Complex carbohydrates are considered to be flexible biomolecules, yet few experimental techniques are available to characterize their dynamics. In this study, we investigate the potential of 15N relaxation to probe the dynamics of hyaluronan oligosaccharides by adapting approaches previously applied to proteins. Unlike the 13C nucleus, 15N provides considerably enhanced spectral resolution, allowing position-specific information to be measured even in the middle of oligomers as large as decasaccharides. Moreover, isotopic incorporation maintains the 1H-15N group as an isolated spin-pair, allowing relaxation experiments to be performed and interpreted at low concentrations. A methodology is described for calculating the Lipari and Szabo model-free parameters at specific positions in hyaluronan oligomers and is used to produce a dynamic representation for the hexasaccharide. In this model, the glycosidic linkages and acetamido rotamer were determined to deviate by 18 degrees and 24 degrees from their mean positions, respectively. This approach allows the dynamic structural characterization of hyaluronan and other nitrogen-containing carbohydrates. The resultant models provide crucial insights into the physical properties and biology of these flexible molecules, which are at present poorly understood.
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Affiliation(s)
- Andrew Almond
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
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9
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Potrzebowski MJ, Kaźmierski S, Olejniczak S, Heliński J, Ciesielski W, Dőlle A. Comparative analysis of NMR spectral parameters and molecular dynamics of 1:6-anhydro-3:4-thia-2-O-tosyl-β-D-allopyranose and 1,6:3,4-dianhydro-2-O-tosyl-β-D-galactopyranose in the solid phase. J PHYS ORG CHEM 2005. [DOI: 10.1002/poc.906] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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10
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Kowalewski J, Effemey M, Jokisaari J. Dipole-dipole coupling constant for a directly bonded CH pair--a carbon-13 relaxation study. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2002; 157:171-177. [PMID: 12323134 DOI: 10.1006/jmre.2002.2590] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Multiple-field (4.7, 9.4, 14.1 T) carbon-13 relaxation data are reported for hexamethylenetetramine (HMTA) in the cryosolvent D(2)O/DMSO at 243 K. Under these conditions, the reorientational motion of HMTA is outside of the extreme narrowing range and the relaxation data can be subjected to a quantitative interpretation. Because of the high symmetry of the HMTA molecule, the reorientation must be isotropic. Treating the reorientation as a small-step rotational diffusion of a rigid body, we obtain a rotational correlation time of 1.0 ns and a carbon-proton dipole-dipole coupling constant corresponding to an effective internuclear distance of 114. 2 pm. The harmonic vibrational correction to the dipole-dipole coupling constant, based on a known force field, yields an NMR estimate of the r(alpha) distance of 110.8 +/- 0.3 pm.
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Affiliation(s)
- Jozef Kowalewski
- Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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11
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Lycknert K, Rundlöf T, Widmalm G. Solution Structure of a Type 1 H Antigen Trisaccharide at a Micellar Surface: NMR Relaxation and Molecular Dynamics Simulation Studies. J Phys Chem B 2002. [DOI: 10.1021/jp0136462] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kristina Lycknert
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Torgny Rundlöf
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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12
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Best RB, Jackson GE, Naidoo KJ. Modeling the α(1→6) Branch Point of Amylopectin in Solution. J Phys Chem B 2002. [DOI: 10.1021/jp013753w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Robert B. Best
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Graham E. Jackson
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
| | - Kevin J. Naidoo
- Department of Chemistry, University of Cape Town, Rondebosch 7701, South Africa
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13
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Potrzebowski M, Kaźmierski S, Michalska M, Olejniczak S, Ciesielski W, Latanowicz L. Investigation of structure and motional behavior of 1,6:3,4-dianhydro-2-O-tosyl-β-d-galactopyranose in solution by means of multiple-field NMR spectroscopy. J Mol Struct 2001. [DOI: 10.1016/s0022-2860(01)00571-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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14
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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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15
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Rundlöf T, Eriksson L, Widmalm G. A Conformational Study of the Trisaccharideβ-D-Glcp-(1→2)[β-D-Glcp-(1→3)]α-D-Glcp-OMe by NMR NOESY and TROESY Experiments, Computer Simulations, and X-Ray Crystal Structure Analysis. Chemistry 2001; 7:1750-8. [PMID: 11349917 DOI: 10.1002/1521-3765(20010417)7:8<1750::aid-chem17500>3.0.co;2-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Proton-proton cross-relaxation rates have been measured for the trisaccharide beta-D-Glcp-(l --> 2)[beta-D-Glcp-(1 --> 3)]alpha-D-Glcp-OMe in D2O as well as in D2O/[D6]DMSO 7:3 solution at 30 degrees C by means of one-dimensional NMR pulsed field gradient 1H,1H NOESY and TROESY experiments. Interatomic distances for the trisaccharide in D2O were calculated from the cross-relaxation rates for two intraresidue and three interglycosidic proton pairs, using the isolated spin-pair approximation. In the solvent mixture one intraresidue and three interglycosidic distances were derived without the use of a specific molecular model. In this case the distances were calculated from the cross-relaxation rates in combination with "model-free" motional parameters previously derived from 13C relaxation measurements. The proton-proton distances for interglycosidic pairs were compared with those averaged from Metropolis Monte Carlo and Langevin Dynamics simulations with the HSEA, PARM22, and CHEAT95 force fields. The crystal structure of the trisaccharide was solved by analysis of X-ray data. Interresidue proton pairs from the crystal structure and those observed by NMR experiments were similar. However, the corresponding proton-proton distances generated by computer simulations were longer. For the (1 --> 2) linkage the glycosidic torsion angles of the crystal structure were found in a region of conformational space populated by all three force fields, whereas for the (1 --> 3) linkage they occupied a region of low population density, as seen from the simulations.
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Affiliation(s)
- T Rundlöf
- Department of Organic Chemistry, Stockholm University, Sweden
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16
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Martin-Pastor M, Bush CA. Comparison of the conformation and dynamics of a polysaccharide and of its isolated heptasaccharide repeating unit on the basis of nuclear Overhauser effect, long-range C-C and C-H coupling constants, and NMR relaxation data. Biopolymers 2000; 54:235-48. [PMID: 10867632 DOI: 10.1002/1097-0282(20001005)54:4<235::aid-bip10>3.0.co;2-v] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A comparison of the conformation and dynamics of the cell wall polysaccharide of S. mitis J22 and the heptasaccharide repeating unit made from this polysaccharide was performed on the basis on nmr data. We have previously reported a model for this highly flexible polysaccharide in which four residues of the antigenic epitope adopt a defined conformation as do the two residues of the lectin-binding epitope. These domains are connected by a 6-substituted galactofuranoside residue that acts as a flexible hinge and the repeating subunits are joined by phosphodiester linkages that provide further flexibility. Homonuclear nuclear Overhauser effect (NOE) and long-range C-C and C-H scalar coupling constants measured in uniform (13)C-labeled samples of the polysaccharide and heptasaccharide were very similar, indicating a similar conformational average in solution. Significant differences in the solution dynamics were found from the heteronuclear relaxation data, T(1), T(1 rho), and NOE, which reflect the faster molecular tumbling of the heptasaccharide. Internal motions occurring on a picosecond time scale are relatively uniform along the polymer while dynamics on the time scale longer than a few nanoseconds is characteristic of hinge motion.
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Affiliation(s)
- M Martin-Pastor
- Department of Chemistry and Biochemistry, University of Maryland-Baltimore County, Baltimore, MD 21250, USA
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17
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Stevensson B, Höög C, Ulfstedt-Jäkel K, Huang Z, Widmalm G, Maliniak A. Solid-State Deuterium NMR and Molecular Modeling Studies of Conformational Dynamics in Carbohydrates. J Phys Chem B 2000. [DOI: 10.1021/jp0002805] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Baltzar Stevensson
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Christer Höög
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Kai Ulfstedt-Jäkel
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Zhi Huang
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Göran Widmalm
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
| | - Arnold Maliniak
- Division of Physical Chemistry and Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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18
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Kaźmierski S, Olejniczak S, Potrzebowski MJ. 13C high-resolution solid state NMR studies of the structure and dynamics of 1,6:3,4-dianhydro-2-O-tosyl-beta-D-galactopyranose. SOLID STATE NUCLEAR MAGNETIC RESONANCE 2000; 16:131-139. [PMID: 10868564 DOI: 10.1016/s0926-2040(00)00062-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
13C CP/MAS, dipolar dephasing MAS and theoretical GIAO calculations were employed to assign 13C resonances to the molecular structure of 1,6:3,4-dianhydro-2-O-tosyl-beta-D-galactopyranose 1. From spinning sideband intensities, employing the graphical method of Herzfeld and Berger the 13C delta(ii) parameters for aromatic residue were calculated. The experimental data were compared with computed results obtained by means of the B3PW91 hybrid method and 6-311G (df, p) basis set. The X-ray geometry of 1 with the correlated position of hydrogen atoms was taken as input data for theoretical calculations. As concluded from Cambridge Crystallographic Database (CSD) search, there are two reports describing the X-ray studies of 1 that show the slightly different geometry of the compound under investigation. This work shows that such discrepancies in geometry can generate differences between computed 13C delta(ii) parameters up to 6 ppm. 13C T1 and 1H T1rho relaxation times reveal that 1 is very rigid in crystal lattice. This structure is characterized by extremely long 1H T1rho, found to be in range ca. 200 ms.
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Affiliation(s)
- S Kaźmierski
- NMR Laboratory, Center of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lódz
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19
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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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20
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Kjellberg A, Widmalm G. A conformational study of the vicinally branched trisaccharide beta-D-glcp-(1 --> 2)[beta-D-glcp-(1 --> 3)]alpha-D-Manp-OMe by nuclear Overhauser effect spectroscopy (NOESY) and transverse rotating-frame Overhauser effect spectroscopy (TROESY) experiments: comparison to Monte Carlo and Langevin dynamics simulations. Biopolymers 1999; 50:391-9. [PMID: 10423548 DOI: 10.1002/(sici)1097-0282(19991005)50:4<391::aid-bip5>3.0.co;2-s] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The trisaccharide beta-D-Glcp-(1 --> 2)[beta-D-Glcp-(1 --> 3)]alpha-D-Manp-OMe, a model for branching regions in oligosaccharides, has been investigated by one-dimensional DPFGSE (1)H, (1)H nuclear Overhauser effect spectroscopy (NOESY) and transverse rotating-frame Overhauser effect spectroscopy (TROESY) experiments at 30 degrees C in water and in the solvent mixture water : dimethyl sulfoxide (7 : 3). Cross-relaxation rates were obtained from the nmr experiments and interpreted as proton-proton distances. From Metropolis Monte Carlo and Langevin dynamics simulations, distances were calculated and compared to those obtained from experiment. Using the previously determined dynamics from carbon-13 nmr relaxation measurements of the trisaccharide in the solvent mixture, intraresidue proton distances could be obtained that were in excellent to reasonable agreement with those calculated from simulations. In water, the isolated spin-pair approximation was used for comparison of interproton distances. The experimentally derived distances in both solvents showed that the trans-glycosidic distances were shorter between the anomeric proton of the glucosyl group and the proton at the linkage position, respectively, than to the proton on the adjacent carbon on the mannosyl residue. The interresidue distances calculated from the computer simulations, performed with three different force fields, namely HSEA, PARM22, and CHEAT95, resulted in the reverse order in all cases but one.
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Affiliation(s)
- A Kjellberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, S-106 91 Stockholm, Sweden
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