Analysis of the RGD sequence in protein structures: comparison to the conformations of the RGDW and (D)RGDW peptides determined by molecular dynamicssimulations

Geometric properties of the RGD sequence in a data set of protein crystal a nd NMR structures deposited in the Protein Data Bank were examined to ident ify structural characteristics that are related to cell adhesion activity. Interatomic distances and dihedral angles are examined. These geometric mea sures are then used in an analysis of the conformations of the RGDW and (D) RGDW peptides obtained from molecular dynamics simulations (Stote RH, et al . (2000) J Phys Chem B 104:1624). This analysis leads to the suggestion tha t differences in the accessible conformations contribute to the difference in biological activity between the RGDW and the,RGDW peptides.