A Novel Method for Sampling Alpha-Helical Protein Backbones

Abstract

We present a novel technique of sampling the configurations of helical proteins. Assuming knowledge of native secondary structure, we employ assembly rules gathered from a database of existing structures to enumerate the geometrically possible three-dimensional arrangements of the constituent helices. We produce a library of possible folds for twenty-five helical protein cores. In each case, our method finds significant numbers of conformations close to the native structure. In addition we assign coordinates to all atoms for four of the twenty-five proteins and show that this has a small effect on the number of near-native conformations. In the context of database driven exhaustive enumeration our method performs extremely well, yielding significant percentages of structures (between 0.02% and 82%) within 6 Angstroms of the native structure. The method's speed and efficiency make it a valuable tool for predicting protein structure.