Search for low-energy conformations of a neurotoxic protein by means of predictive rules, tests for hard-sphere overlaps, and energy minimization

A method to obtain models for the three-dimensional structure of the neurotoxin alpha from Naja nigricollis from its amino acid sequence is explored here. Empirical predictive rules were used to estimate the positions of helices, extended structures and bends; advantage was taken of the availability of 14 homologous sequences for the neurotoxins in an attempt to increase the reliability of these predictions. Unassigned residues were allowed to take up several possible conformations determined from the frequencies of occurrence of each type of conformation of that residue in x-ray structures of many proteins. The conformational space of the molecule was explored initially by testing for hard-sphere overlaps and approximate closure of disulfide loops with the aid of a computer; this procedure yielded a limited number of conformations, whose conformational energies were then determined and minimized by optimizing the backbone and side-chain dihedral angles of each residue. Five compact conformations with low energy were found for this neurotoxin. The procedure used here provides an illustration as to how empirical protein algorithms may be used to limit the conformational space, in which energy minimization has to be carried out.