Three-dimensional structure of the RGD-containing snake toxin albolabrin in solution, based on 1H NMR spectroscopy and simulated annealing calculations.

Abstract

Albolabrin is a snake toxin that contains a RGD-(Arg-Gly-Asp) sequence motif and competes with fibrinogen to bind to the integrin alpha IIb beta 3 (GpIIb-IIIa) on platelets. It thus inhibits platelet aggregation and cell-cell adhesion. It shows a high sequence similarity to other disintegrins, yet the reported disulfide bonding pattern for this peptide differs from that of others in this family. Recently we reported the assignment of the 1H-NMR spectrum of albolabrin and a preliminary description of its secondary structure [Jaseja, M., Smith, K.J., Lu, X. Williams, J.A., Trayer, H., Trayer, I.P. & Hyde, E.I. (1993) Eur. J. Biochem. 218, 853-860]. Here we present a more detailed description of the secondary and the tertiary structure, based on the 1H NMR results and simulated annealing methods. The structure of albolabrin in solution was calculated using 318 distance and 18 dihedral angle restraints. The average atomic RMS deviation between 12 refined structures and the mean structure was 3.1 A for the backbone. The protein appears to be highly mobile. Its structure is dominated by a series of turns and by three hairpins, each with a short region of distorted antiparallel beta-pleated sheet, held together by six disulfide bridges. The most well defined area is the hydrophobic core, residues 21-47 and 57-67, which is clustered around F40 and has a backbone atomic RMS deviation of only 1.3 A from the mean structure. The RGD adhesion sequence is found at the highly mobile tip of one of the beta-hairpins, protruding from the body of the protein. Many of these structural features are similar to those of other disintegrins, and differences in the disulfide bonding pattern of the disintegrins can be accomodated without significant energy penalty. Comparison of this structure with other proteins of similar function suggests that it is the RGD-loop, rather than the precise technology of the proteins, that is important to antagonist activity.