Carbohydrates and Glycoconjugates

Halbeek, Herman van

doi:10.1002/9780470034590.emrstm0052

Cited by 2 publications

(3 citation statements)

References 212 publications

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“…Ring puckering distributions were readily obtained from the long MD simulations and the combined umbrella sampling simulation trajectories. Note that it has been previously found by both experiment and computational study that the ring puckering occurs on a much faster time scale than the exocyclic torsion. , To study the correlation of rotamers and ring puckering, a joint probability distribution was also constructed from analysis of umbrella sampling simulations. For each window trajectory, values of P were obtained.…”

Section: Methodsmentioning

confidence: 99%

Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment

Islam

Roy

2012

J. Chem. Theory Comput.

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The solution conformations of biologically important mono- and di-α-d-arabinofuranosides were investigated using the dispersion-corrected self-consistent charge density functional tight binding (SCC-DFTB) and the AMBER/GLYCAM models. Simulations were performed using both long dynamics and umbrella sampling simulations. Angular distributions about the exocyclic C-C bonds and puckering distributions of the rings obtained from the SCC-DFTB model were quite different from those obtained with the AMBER/GLYCAM approach. The joint probability distribution of rotamer and ring puckering parameters reveals further discrepancies, while both methods predict weak correlation between exocyclic torsions and ring puckering. To assess the reliability of the simulations, ensemble-averaged vicinal proton-proton coupling constants ((3)JH,H) were calculated and compared directly to experimental NMR coupling constants. It is found that the (3)JH,H values obtained from the AMBER/GLYCAM simulations agree with experiment, while those obtained from the SCC-DFTB method, in most cases, differ from experimental (3)JH,H values. Potential energy surfaces (PES) along the exocyclic torsion obtained from ab initio and DFT calculations differ significantly from those obtained with the SCC-DFTB method. This study establishes that a high-quality all-atom force field would be more suitable than one of the superior semiempirical methods, SCC-DFTB, for investigation of rotamer populations and ring puckering in floppy ring systems such as furanosides.

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Section: Methodsmentioning

confidence: 99%

Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment

Islam

Roy

2012

J. Chem. Theory Comput.

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“…Because the structural-reporter-group region of the ' H spectrum of IV has been interpreted [12], the assignment of C1 and C2 of Man-4' could be confirmed by selective decoupling experiments, as could the C1 and C2 resonances of Man-3 and the CI resonances of GlcNAc-l and GlcNAc-2 in this compound.…”

Section: Resultsmentioning

confidence: 91%

“…"C-NMR of proton-bearing carbon atoms is particularly well suited for thc study of dynamics because the relaxation is dominated by the fluctuating dipolar interactions between I3C nuclei and directly bonded protons. (Man)z(GlcNAc)zAsn (compound IV) was obtaincd from the urinc of a patient with Caucher's disease [12]. The complete structures of these compounds are shown in Fig.…”

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confidence: 99%

Natural‐Abundance ¹³C‐NMR Spectroscopy of Two Glyco‐asparagines Derived from the Core of N‐Glycosidic Carbohydrate Chains

Dijkstra¹,

Vliegenthart²,

Strecker³

et al. 1983

European Journal of Biochemistry

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"C-NMR spectroscopic studies were carried out on Manx(l+6)ManP( 1 +4)GlcNAcb( 1 -+4)GlcNAcli( 1 +N)-Asn and Mancc(1 -r6)Man/j( 1 -+4)GlcNAc/l(I -.4) [Fucu.( 1 +6)]GlcNAc/j( I+N)Asn, which are part of the invariant corc of N-glycosidically linked carbohydrates of glycoproteins. All resonances of' proton-bearing carbon atoms were unambiguously assigned. Where possible, the assignmcnts were confirmed by selective proton-decoupling experimcntsThe discovery that glycoconjugates are involved in cellcell recognition, the immune response, hormone-receptor functions and internalization of various macromolecular materials, has widely stimulated research ef'orts to characterize these molecules and, especially, their glycan parts. Recent revicws by Sharon and Lis [I] and Montreuil [3] summarize our current understanding of the importance of glycoproteins for the living organism. Although the elucidation of the primary structure of oligosaccharides has become a rather straightforward procedure, at least when sufficient material is available, little is known of the spatial conformation of the glycan chains. Knowledge of the three-dimensional structure is a prerequisitc to explain their mode of interaction with ligands. A number of models have been proposed for their spatial conformation, mostly based on model building [3] or theoretical approachcs [4], but thc experimental evidcnce for these models is scarce. N o crystallographic data exist on major parts of the N-glycosidically linked carbohydrates of glycoprotcins. One of the largest partial structures crystallized so Far is Mancx(l-+3)Manfl(I +4)GlcNAc 151. In the fcw crystallked glycoproteins [6,7] the glycan part was found to be disordered for the greater part. I t is not clear whether this disorder is static, i.e. due to irregular packing of the glycan chains in the crystals. or dynamic, i.e. reflecting mobility of the glycan chains in the crystals.Wc decided to initiate an investigation into the dynamic aspects of glycan structures by means of nuclear magnetic resonance (NMR) spectroscopy. N M R relaxation measureinents provide an important probe of the dynamics of' molccules, since the spin-lattice (TI) rclaxation time, the spinspin (T,) relaxation time and the nuclear Overhauser enhancemcnt (NOE) factor are parameters which reflect thermal motions. "C-NMR of proton-bearing carbon atoms is particularly well suited for thc study of dynamics because the relaxation is dominated by the fluctuating dipolar interactions between I3C nuclei and directly bonded protons.-~.

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Carbohydrates and Glycoconjugates

Cited by 2 publications

References 212 publications

Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment

Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment

Natural‐Abundance ¹³C‐NMR Spectroscopy of Two Glyco‐asparagines Derived from the Core of N‐Glycosidic Carbohydrate Chains

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Carbohydrates and Glycoconjugates

Cited by 2 publications

References 212 publications

Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment

Performance of the SCC-DFTB Model for Description of Five-Membered Ring Carbohydrate Conformations: Comparison to Force Fields, High-Level Electronic Structure Methods, and Experiment

Natural‐Abundance 13C‐NMR Spectroscopy of Two Glyco‐asparagines Derived from the Core of N‐Glycosidic Carbohydrate Chains

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Natural‐Abundance ¹³C‐NMR Spectroscopy of Two Glyco‐asparagines Derived from the Core of N‐Glycosidic Carbohydrate Chains