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

Abstract

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, ...

Characterization of a Novel Branched Tetrasaccharide of 3-Deoxy-d-manno-oct-2-ulopyranosonic Acid

“…Conformational Analysis-Conformational analysis was performed using the hard sphere exoanomeric-based GEGOP program (27,28) at 800 and 1200 K with Metropolis Monte Carlo simulations with up to 3 ϫ 10 6 steps. The ␣-and ␤-D-Kdo coordinates were taken from a published x-ray structure (29).…”

“…4, Table III). In order to determine the structure and explain the NOE connectivities observed, a conformational analysis of the structural elements GlcpN␣134Kdo␣235(Kdo␣234)Kdo␣23 6GlcpN␤ (F-E-D-C-B) and GlcpN␣134(Kdo␣235 or ␣237)-Kdo␣235(Kdo␣234)Kdo␣236GlcpN␤ (F-(J-)E-D-C-B, GlcpN was set as residue instead of GlcpNA) was performed using Metropolis Monte Carlo simulations and the program GEGOP (27,28). The structure with residue J ␣237-linked to E showed distances between protons of these residues not in agreement with observations.…”

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

“…HSEA calculations.-HSEA energy calculations were performed using the GEGOP program 23 on a mVAX/ VMS computer. This force field only calculates the non-bonded interactions as expressed by the Kitaigorodsky energy function, 24 and accounts for the exoanomeric effect by an additional energy term.…”

Molecular structures of glycoprotein hormones and functions of their carbohydrate components

“…This perception is based on the observations that the al-6 bond of di-or tri-antennary oligosaccharides is flexible [240][241][242][243][244][245][246] and that analytical centrifugation of native and deglycosylated hormones revealed essentially no difference in sedimentation constant [247].…”

“…While refinement of force-field programmes for the calculation of energetically favoured conformations of glycopeptides [245] should lead to computer-generated structures of hormonal subunits in the foreseeable future, experimentally derived data related to the three-dimensional structures of the glycosylated and deglycosylated hormonal heterodimers are obligatory. Even then, heterogeneity of the attached oligosaccharides, particularly those that are N-linked, will remain problematic.…”