Knowledge-based model building of the tertiary structures for lectin domains of the selectin family
- 24 Downloads
A combination of a knowledge-based approach and energy minimization was used to predict the three-dimensional structures of the lectin domains of P-selectin, E-selectin, and L-selectin, respectively. Each of these domains contains 118 amino acids. The starting points for energy minimization were generated based on a framework that consists of a number of separated segments derived from the structure-known carbohydrate-recognition domain of the mannose-binding protein (MBP), which belongs to the same C-type lectin family as the selectin molecules do. The structures thus found for P-, L-, and E-selectin lectin domains share a common feature, i.e., they all contain twoα-helices, and two antiparallelΒ-sheets of which one is formed by two strands (strands 1 and 5) and the other by three (strands 2, 3, and 4). Besides, they all possess two intact disulfide bonds formed by the pair of Cys-19 and Cys-117, and the pair of Cys-90 and Cys-109. The root-meansquare deviations calculated over the set of backbone atoms between P- and L-selectin lectin domains is 3.10 å, that between P- and E-selectin lectin domains 2.48 å, and that between L- and E-selectin lectin domains 3.07 å. A notable feature is the convergencedivergence duality of the 77–107 polypeptide in the three domains; i.e., part of the peptide is folded into a closely similar conformation, and part of it into a highly different one.
Key wordsP-selectin E-selectin L-selectin convergence-divergence duality energy minimization ECEPP
Unable to display preview. Download preview PDF.
- Chou, K. C., Némethy, G., and Scheraga, H. A. (1984). Energy approach to the packing ofα-helices,J. Am. Chem. Soc. 106, 3161–3170.Google Scholar
- Drickamer, K., Dordal, M. S., and Reynolds, L. (1986). Mannose-binding proteins isolated from rat liver contain carbohydrate-recognition domains linked to collagenous tails—Complete primary structures and homology with pulmonary surfactant apoprotein,J. Biol. Chem. 261, 6878–6887.PubMedGoogle Scholar
- Erbe, D. V., Wolitzky, B. A., Presta, L. G., Norton, C. R., Ramos, R. J., Burns, D. K., Rumberger, J. M., Rao, B. N. N., Foxall, C., Brandly, B. K., and Lasky, L. A. (1992). Identification of an E-selectin region critical for carbohydrate recognition and cell adhesion,J. Cell. Biol. 119, 215–227.PubMedGoogle Scholar
- Gay, D. M. (1983). Subroutines for unconstrained minimization using a model/trust-region approach,Assoc. Comput. Mach. Trans. Math. Software 9, 503–524.Google Scholar
- Graves, B. J., Crowther, R. L., Chandran, C., Rumberger, J. M., Li, S., Huang, K. S., Presky, D. H., Familletti, P. C., Wolitzky, B. A., and Burns, D. K. (1994). Insight into E-selectin/ligand interaction from the crystal structure and mutagenesis of the lec/EGF domains.Nature 367, 532–538.PubMedGoogle Scholar
- IUPAC-IUB Commission on Biochemical Nomenclature (1970). Abbreviations and symbols for the description of the conformation of polypeptide chains,Biochemistry 9, 3471–3479.Google Scholar
- Momany, F. A., McGuire, R. F., Burgess, A. W., and Scheraga, H. A. (1975). Energy parameters in polypeptides. 7. Geometrical parameters, partial atomic charges, nonbonded interactions, hydrogen bond interactions, and intrinsic torsional potentials for the naturally occurring amino acids,J. Phys. Chem. 79, 2361–2381.Google Scholar
- Vásquez, M., Némethy, G., and Scheraga, H. A. (1983). Computed conformational states of the 20 naturally occurring amino acid residues and of the prototype residueα-aminobutyric acid,Macromolecules 16, 1043–1049.Google Scholar