Solution structure of apamin determined by nuclear magnetic resonance and distance geometry

Abstract

The solution structure of the bee venom neurotoxin apamin has been determined with a distance geometry program using distance constraints derived from NMR. Twenty embedded structures were generated and refined by using the program DSPACE. After error minimization using both conjugate gradient and dynamics algorithms, six structures had very low residual error. Comparisons of these show that the backbone of the peptide is quite well-defined with the largest rms difference between backbone atoms in these structures of 1.34 A. The side chains have far fewer constraints and show greater variability in their positions. The structure derived here is generally consistent with the qualitative model previously described, with most differences occurring in the loop between the beta-turn (residues 2-5) and the C-terminal alpha-helix (residues 9-17). Comparisons are made with previously derived models from NMR data and other methods.

Model Peptide Studies Demonstrate That Amphipathic Secondary Structures Can Be Recognized by the Chaperonin GroEL (cpn60)

“…The data for residues [17][18][19] are not indicative of a well formed helix, suggesting that they form a frayed terminus to the helix or adopt a turn conformation. These findings are in line with the structure modeled for APA14 and are consistent with the three-dimensional structures determined for other apamin peptides (35). 1 Many of the chemical shifts of oxidized APA14c are found to be very different from random coil values, suggesting that the peptide does adopt a well defined structure.…”

“…These disulfides lock the COOH-terminal half of apamin (residues 9 -16) into a helical conformation (18,35). Various sequences can be substituted into the COOH terminus of apamin and forced into a helical conformation by the presence of these disulfide bridges (19).…”

Structures and related properties of helical, disulfide-stabilized peptides

“…The linear least squares fit of the data from 2SOC to 7 5°C is also shown. The typeS of connectivities observed are exactly the same as those in both apamin (Pease & Wemmer, 1988) and the Apa-S hybrid (Pease, et al, 1990) for the first 16 residues at 0°C and 25°C. These include the aH-NH-NH-NH connectivity characteristic of the type I 13-turn, and i,i+2 connectivity at the beginning of the helix, and the continued NH-NH connectivities in the a-helix from residue 9 through residue 16.…”

“…A summary of the sequential connectivities observed, and longer range contacts in the helix are shown in apamin (Pease & Wemmer, 1988), the Apa-S hybrid (Pease, et al, 1990), and the Apa-M5 hybrid (chapter 3.3) for the frrst 16 residues at 15°C. These include the aH-NH-NH-NH connectivity characteristic of the type lfi-tum, i,i+2 connectivity at the beginning of the helix, and the continued NH-NH connectivities in the a-heijx from residue 9 through .…”

“…The presence of the helix is verified by a number· of i,i+3, aH-NH, and aH-I3H connectivities, which are normally seen in this secondary structure. Additional tertiary NOEs are observed which indicate that the fold of the first 16 residues is very similar to apamin (Pease & Wemmer, 1988) and the Apa-S hybrid (Pease, et al, 1990 are some residues for which the helical NOE connectivities cannot be observed. Given the number of interspersed helical NOE connectivities, it seems most likely that the helix propagates in a cooperative fashion from the section nucleated by the formation of disulfide bonds (residues 9-15).…”