Conformational analysis of two xylose-containing N-glycans in aqueous solution by using 1H NMR ROESY and NOESY spectroscopy in combination with MD simulations

Lommerse, Jos P. M.; Rooijen, Johannes J.M. van; Kroon-Batenburg, Loes M. J.; Kamerling, Johannis P.; Vliegenthart, Johannes F.G.

doi:10.1016/s0008-6215(02)00212-4

Cited by 10 publications

(8 citation statements)

References 36 publications

(46 reference statements)

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“…[44][45][46][47][48][49][50][51][52][53][54][55] Furthermore, the sign (again confirmed by the 1 H, 13 C HSQC-HECADE experiment) and the magnitude of…”

Section: Ja C H T U N G T R E N N U N G (H5c6mentioning

confidence: 67%

Conformational Flexibility and Dynamics of Two (1→6)‐Linked Disaccharides Related to an Oligosaccharide Epitope Expressed on Malignant Tumour Cells

Olsson

Säwén

Stenutz

et al. 2009

Chemistry A European J

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The conformational flexibility and dynamics of two (1-->6)-linked disaccharides that are related to the action of the glycosyl transferase GnT-V have been investigated. NMR NOE and T-ROE spectroscopy experiments, conformation-dependent coupling constants and molecular dynamics (MD) simulations were used in the analyses. To facilitate these studies, the compounds were synthesised as alpha-d-[6-(13)C]-Manp-OMe derivatives, which reduced the (1)H NMR spectral overlap and facilitated the determination of two- and three-bond (1)H,(1)H, (1)H,(13)C and (13)C,(13)C-coupling constants. The population distribution for the glycosidic omega torsion angle in alpha-d-Manp-(1-->6)-alpha-d-Manp-OMe for gt/gg/tg was equal to 45:50:5, whereas in alpha-d-Manp-OMe it was determined to be 56:36:8. The dynamic model that was generated for beta-d-GlcpNAc-(1-->6)-alpha-d-Manp-OMe by MD simulations employing the PARM22/SU01 CHARMM-based force field was in very good agreement with experimental observations. beta-d-GlcpNAc-(1-->6)-alpha-d-Manp-OMe is described by an equilibrium of populated states in which the phi torsion angle has the exo-anomeric conformation, the psi torsion angle an extended antiperiplanar conformation and the omega torsion angle a distribution of populations predominantly between the gauche-trans and the gauche-gauche conformational states (i.e., gt/gg/tg) is equal to 60:35:5, respectively. The use of site-specific (13)C labelling in these disaccharides leads to increased spectral dispersion, thereby making NMR spectroscopy based conformational analysis possible that otherwise might be difficult to attain.

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“…[44][45][46][47][48][49][50][51][52][53][54][55] Furthermore, the sign (again confirmed by the 1 H, 13 C HSQC-HECADE experiment) and the magnitude of…”

Section: Ja C H T U N G T R E N N U N G (H5c6mentioning

confidence: 67%

Conformational Flexibility and Dynamics of Two (1→6)‐Linked Disaccharides Related to an Oligosaccharide Epitope Expressed on Malignant Tumour Cells

Olsson

Säwén

Stenutz

et al. 2009

Chemistry A European J

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“…Brisson & Carver, 1983;Sabesan et al, 1991;Koles et al, 2004;Petersen et al, 2008), the latter often in combination with MD simulations (e.g. Hö ö g et al, 2001;Lommerse et al, 2002;Eklund et al, 2005;Siebert et al, 2005), have been used to resolve the threedimensional structures of carbohydrates, glycoproteins and protein-carbohydrate complexes. X-ray crystallography can also be combined with computational chemistry (Ali et al, 2008) or NMR (Viegas et al, 2008).…”

Section: Analysis Of Carbohydrate and Glycoprotein Three-dimensional mentioning

confidence: 99%

Analysis and validation of carbohydrate three-dimensional structures

Lütteke

2009

Acta Crystallogr D Biol Cryst

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Knowledge of the three-dimensional structures of the carbohydrate molecules is indispensable for a full understanding of the molecular processes in which carbohydrates are involved, such as protein glycosylation or protein-carbohydrate interactions. The Protein Data Bank (PDB) is a valuable resource for three-dimensional structural information on glycoproteins and protein-carbohydrate complexes. Unfortunately, many carbohydrate moieties in the PDB contain inconsistencies or errors. This article gives an overview of the information that can be obtained from individual PDB entries and from statistical analyses of sets of three-dimensional structures, of typical problems that arise during the analysis of carbohydrate three-dimensional structures and of the validation tools that are currently available to scientists to evaluate the quality of these structures.

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“…Apart from evaluating other structural parameters with different averaging behavior or distance dependence, one way to address these problems is employing more sophisticated molecular modeling that involves backcalculation of NOE and ROE intensities from molecular dynamics (MD) trajectories as has been recently demonstrated by Lommerse et al for two core N-glycans of snail ctD-hemocyanin ( Fig. 9 and Table 4) [65].…”

Section: Nuclear Overhauser Enhancementsmentioning

confidence: 99%

“…(12). (Reproduced with permission from [65]) Table 4 Stability of local minima at the glycosidic linkages, probed by short MD simulations for 11 and 12 from Fig. 9.…”

Section: Nuclear Overhauser Enhancementsmentioning

confidence: 99%

Conformation of Glycopeptides and Glycoproteins

Meyer¹,

Moeller²

2007

ChemInform

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Glycosylation is the most frequent post-translational modification found in proteins. Glycoproteins are involved in a highly diverse spectrum of biological functions, ranging from protein folding and molecular and cellular recognition to attack of pathogens and regulation of biological half-life. Consequently, understanding the structural role of glycosylation provides key insight into biological processes as well as ideas for medicinal applications. Here, we review the current methodology to arrive at highresolution structures of glycopeptides and glycoproteins. To achieve this, significant obstacles have to be overcome like preparation of sufficient amounts of sufficiently pure and homogeneous material, analyzing highly ambiguous spectroscopic data, and dealing with molecules that show local or global disorder. We will provide an overview of our knowledge of glycoprotein and glycopeptide structure, and illustrate with selected examples the performance and limitations of current methodology.

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Conformational analysis of two xylose-containing N-glycans in aqueous solution by using 1H NMR ROESY and NOESY spectroscopy in combination with MD simulations

Cited by 10 publications

References 36 publications

Conformational Flexibility and Dynamics of Two (1→6)‐Linked Disaccharides Related to an Oligosaccharide Epitope Expressed on Malignant Tumour Cells

Conformational Flexibility and Dynamics of Two (1→6)‐Linked Disaccharides Related to an Oligosaccharide Epitope Expressed on Malignant Tumour Cells

Analysis and validation of carbohydrate three-dimensional structures

Conformation of Glycopeptides and Glycoproteins

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