GLYCOSYLATION OF IgG-Fc

P. Kolenko^1,2, J. Dohnálek¹, J. Dušková¹, T. Skálová¹, J. Hašek¹

¹Institute of Macromolecular Chemistry AS CR, v.v.i., Heyrovského nám.2, 162 00, Prague 6

²Dept.of Solid State Physics, FJFI, CTU, Trojanova 13, 120 00, Prague 2

kolenko@imc.cas.cz

Keywords: Fc, crystal, X-ray diffraction, structure, saccharides

Introduction

The crystallisable fragment (Fc) of antibody (Ig) mediates the response of the adaptive part of immune system. Ten structures of IgG-Fc in non-liganded form were deposited in the Protein Data Bank [1] up to now. Although chemical properties and the structure of Fc were assessed by many physical and chemical techniques, some new details of the oligosaccharide structure were known after evaluation of the most recently deposited structure [2] and our non-deposited structure [3].

Localization of fucose

Interpretation of saccharides in electron density maps is difficult. Inspection of structures and electron density maps showed doubtful structure refinement of fucose. All structures of Fc deposited by December 2006 contained beta-L-fucose. Low-resolution structural data did not allow distinguishing the proper glycoform, e.g. two of the structures with electron density maps are shown in Fig. 1.

Figure 1. Electron density map in surroundings of fucose for structures: a) 1I1C, b) 1H3U. The figures were prepared with Pymol [4].

In May 2007, the structure of non-liganded IgG1-Fc with the highest resolution of 2 Å [2] was deposited in the PDB. Our structure solution of IgG2b-Fc was described two years ago [3]. The structure contains alpha-L-fucose. The experimental data (high resolution limit lower than 2.2 Å) allowed localization of fucose with good agreement with electron density (Fig.2).

Figure 2. Electron density map in surroundings of fucose for structures: a) 2DTQ, b) our structure. The electron density observed in the lower left corner belongs to the continuation of the oligosaccharide chains in both cases.

About 30 % of all PDB entries containing saccharides have at least one error in glycan interpretation [5]. The glycosylation and quality of structures deposited in the PDB will be discussed.

References

1. H.M. Berman, J. Westbrook, Z. Feng, G. Gililand, T.N. Bhat, H. Weissing, I.N. Shindyalov, P.E. Bourne, Nucleic Acids Research, 28, 2000, 235-242.

2. S. Matsumiya, Y. Yamaguchi, J. Saito, M. Nagano, H. Sasakawa, S. Otaki, M. Satoh, K. Shitara, K. Kato, Journal of Molecular Biology, 368, 2007, 767.

3. P. Kolenko, J. Dohnálek, R. Šťouračová, T. Skálová, G. Tiščenko, J. Dušková, J. Hašek, Materials Structure, 12, 2005, 146.

4. W.L. DeLano, The PYMOL User’s Manual, DeLano Scientific, San Carlos, CA, USA, 2002.

5. T. Lütteke, M. Frank, C-W. von der Lieth, Carbohydrate Research, 339, 2004.

Acknowledgements

The project is supported by the Ministry of Education, Youth and Sports of the Czech Republic (project no. 1K05008) and by the project “Spine 2 – Complexes” of the European Commission (LSHG-CT-2006-031220).