ChemInform Abstract: CONFORMATIONAL ANALYSIS, XXV. CONFORMATIONS OF OCTASACCHARIDE AND PENTASACCHARIDE SEQUENCES IN N‐GLYCOPROTEINS OF THE LACTOSAMINE TYPE

Paulsen, Hans; Peters, T.; Sinnwell, Volker; Lebuhn, Rolf; Meyer, Benjamin

doi:10.1002/chin.198526059

Cited by 4 publications

(10 citation statements)

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“…The oligosaccharide adopts a conformation in l e that is very similar to conformation 2a which is preferred in solution. However, the orientation of the glycosyl residues of the 6-branch 6-5'-4' trisaccharide relative to each other is different compared to 2a [22]. The peptide part remains in the extended j-strand without exhibiting any significant changes when compared to Id.…”

Section: Resultsmentioning

confidence: 94%

“…The starting conformations of 1 have the decasaccharide part of conformation 2a (Fig. 1A) preferred in solution [22] or in conformation 2c (Fig. 1C) found in the crystal structure of the whole Fc fragment [32].…”

Section: Resultsmentioning

confidence: 99%

“…The X-ray-crystal-structure analysis of the Fc fragment of human IgG, revealed not only the protein at atomic resolution but also showed the carbohydrate moiety at atomic resolution. The solution conformation of the free decasaccharide was elucidated by a combination of NMR spectroscopy and forcefield calculations [22]. Comparison of the results of these two studies revealed that the conformation of the decasaccharide bound to the protein part of IgGl differs from the solution structure of the free reducing decasaccharide [38].…”

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confidence: 99%

“…The solution conformation of 5 was determined by NMR spectroscopy and forcefield calculations (HSEA, GESA) [22]. According to these calculations, the octasaccharide 5 and the decasaccharide 2 adopt very similar conformations in solution.…”

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confidence: 99%

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A new force‐field program for the calculation of glycopeptides and its application to a heptacosapeptide‐decasaccharide of immunoglobulin G₁

Stuike-Prill¹,

Meyer²

1990

European Journal of Biochemistry

109

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Energetically favored conformations of glycopeptide 1 were calculated using the newly developed force-field program, GEGOP (geometry of glycopeptides). The three-dimensional structure of glycopeptide 1, which is part of the Fc fragment of IgG1, has been calculated. 1 contains 27 amino acid residues from Pro291 to Lys317 and a biantennary decasaccharide N-linked to Asn297. The conformations of the peptide and the carbohydrate parts are shown to be mutually dependent. Single glycosyl residues of 1 exhibit interaction energies of up to -31.8 kJ/ mol with the peptide portion. Generally, only a few of the glycosyl residues of the oligosaccharide moiety express significant interaction energies with the peptide part. No easy prediction is possible of glycosyl residues which exhibit favorable interaction energies. However, in all of the calculated structures, the glycosyl residues of the 1 -6-linked branches show strong attractive forces for the peptide part. 1 -6-glycosidically linked branches can adopt a larger number of conformations than other linkages due to their high flexibility which allows more favorable interactions with proteins.We developed the GEGOP program in order to be able to study the preferred conformations of large glycopeptides. The program is based on the GESA (geometry of saccharides) program and utilizes the HSEA (hard sphere exo anomeric) force field for the carbohydrate part and the ECEPP/2 (empirical conformation energy program for peptides) force field [Nkmethy, G., Pottle, M. S. & Scheraga, H. A. (1983) J . Phys. Chem. 87,1883-18871 for the peptide part. The GEGOP program allows the simultaneous relaxation of all rotational degrees of freedom of these glycoconjugates during the energy optimization process. Thus, mutual interactions between glycosyl and amino acid residues can be studied in detail.The biological activity of glycoproteins is often expressed by the oligosaccharide part [I, 21, e.g. the binding of the 120-kDa envelope glycoprotein from the human immunodeficiency virus to the cell-differentiation-marker-4 receptor (CD4) is dependent on the oligosaccharide chains of the 120-kDa envelope glycoprotein [3, 41. In glycoprotein/receptor interaction, the overall shape of the glycoprotein as well as specific functional groups are usually recognized [5 -91. This raises the need for acquiring knowledge of the three-dimensional structure of glycoproteins.There is little experimental data in the literature that describes the three-dimensional structure of glycoproteins. Most published work has focused on either the protein or the carbohydrate structures. The three-dimensional structure of. proCorrespondence to B. Meyer, Complex Carbohydrate Research Center, University of Georgia, 220 Riverbend Road, Athens, Georgia 30602, USA Abbreviations. Fuc, fucose; HSEA, hard sphere exo anomeric; GESA, geometry of saccharides; ECEPP, empirical conformation energy program for peptides; GEGOP, geometry of glycopeptides; HGEN, hydrogen generation; PLATO, plot atoms; RMS, root mean square; sug, sugar; pep, ...

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Section: Resultsmentioning

confidence: 94%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

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confidence: 99%

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A new force‐field program for the calculation of glycopeptides and its application to a heptacosapeptide‐decasaccharide of immunoglobulin G₁

Stuike-Prill¹,

Meyer²

1990

European Journal of Biochemistry

109

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“…Potential energy calculations were performed using the GESA (Paulsen et al 1985) aleorithm. The atomic coordinates for t h e constituent monosaciharides of the polysaccharide repeating unit were taken from X-ray data for 2-acetamido-2-deoxy-P-D-galactopyranose (Winter et al 1978) and P-D-glucopyranose (Arene et al 1979), and neutron diffraction data for a-D-glucopyranose (Jeffrey et al 1977), a-L-rhamnopyranose (Takagi and Jeffrey 1978), and a-D-galactopyranose (Takagi and Jeffrey 1979).…”

Section: Potential Energy Calculationsmentioning

confidence: 99%

Structural studies of the O-chain of the phenol-phase soluble lipopolysaccharide from Haemophilus pleuropneumoniae serotype 2

Altman

Brisson²,

Bundle³

et al. 1987

Biochem. Cell Biol.

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The phenol-phase soluble cellular lipopolysaccharide that was isolated by the phenol-water extraction from Haemophilus pleuropneumoniae serotype 2 was shown to be of the S type by sodium dodecyl sulfate--polyacrylamide gel electrophoresis, hydrolysis, methylation, specific degradations, and both one- and two-dimensional 1H and 13C nuclear magnetic resonance studies. It could be cleaved to yield a lipid A and an O-chain polysaccharide. This O-polysaccharide was identified as a high molecular weight unbranched linear polymer of a pentasaccharide repeating unit having the structure: (Formula: see text).

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N.m.r. and conformational studies of some 3-O-, 4-O-, and 3,4-di-O-glycopyranosyl-substituted methyl α-D-galactopyranosides

Baumann¹,

Erbing²,

Jansson³

et al. 1989

J. Chem. Soc., Perkin Trans. 1

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Both 'H and 13C n.m.r. studies and conformational analyses have been performed o n methyl a-Dgalactopyranosides substituted in the 3-, 4-, and 3,4-positions with different anomeric forms of either L-fucopyranosyl or o-glucopyranosyl groups. Conformational analysis using the HSEA and G ESA approaches indicated restricted rotational freedom around the glycosidic bonds of the trisaccharides compared to those of the disaccharides. It also indicated a number of proton-oxygen and proton-proton interactions which could be correlated to downfield and upfield glycosylation shifts, respectively, of the proton signals in both the di-and the tri-saccharides. Similar inter-residue atomic interactions could also be correlated t o the 13C n.m.r. glycosylation shifts observed for the disaccharides and to some extent for the trisaccharides. Comparison was made between the observed glycosylation shifts of the trisaccharides and those calculated by using the glycosylation shifts for each disaccharide element. Large deviations, in most cases upfield shifts, were found for the signals for many linkage carbons.

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ChemInform Abstract: CONFORMATIONAL ANALYSIS, XXV. CONFORMATIONS OF OCTASACCHARIDE AND PENTASACCHARIDE SEQUENCES IN N‐GLYCOPROTEINS OF THE LACTOSAMINE TYPE

Cited by 4 publications

References 1 publication

A new force‐field program for the calculation of glycopeptides and its application to a heptacosapeptide‐decasaccharide of immunoglobulin G₁

A new force‐field program for the calculation of glycopeptides and its application to a heptacosapeptide‐decasaccharide of immunoglobulin G₁

Structural studies of the O-chain of the phenol-phase soluble lipopolysaccharide from Haemophilus pleuropneumoniae serotype 2

N.m.r. and conformational studies of some 3-O-, 4-O-, and 3,4-di-O-glycopyranosyl-substituted methyl α-D-galactopyranosides

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ChemInform Abstract: CONFORMATIONAL ANALYSIS, XXV. CONFORMATIONS OF OCTASACCHARIDE AND PENTASACCHARIDE SEQUENCES IN N‐GLYCOPROTEINS OF THE LACTOSAMINE TYPE

Cited by 4 publications

References 1 publication

A new force‐field program for the calculation of glycopeptides and its application to a heptacosapeptide‐decasaccharide of immunoglobulin G1

A new force‐field program for the calculation of glycopeptides and its application to a heptacosapeptide‐decasaccharide of immunoglobulin G1

Structural studies of the O-chain of the phenol-phase soluble lipopolysaccharide from Haemophilus pleuropneumoniae serotype 2

N.m.r. and conformational studies of some 3-O-, 4-O-, and 3,4-di-O-glycopyranosyl-substituted methyl α-D-galactopyranosides

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A new force‐field program for the calculation of glycopeptides and its application to a heptacosapeptide‐decasaccharide of immunoglobulin G₁

A new force‐field program for the calculation of glycopeptides and its application to a heptacosapeptide‐decasaccharide of immunoglobulin G₁