Looking for packing units of the protein structure

Abstract

Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure foldability. Keeping such conserved specific contacts in mind, we examine contacts made by two secondary structure elements of different helices or sheets and look for possible 'packing units' of the protein structure. Two short backbone fragments of width five centred at the C? atoms in contact is called an H-form, which serves as a candidate for the packing units. The structural alignment of protein family members or even across families indicates that there are conservative H-forms which are similar both in their sequences and local geometry, and consistent with the structural alignment. Carrying strong sequence signals, such packing units would provide 3D constraints as a complement of the potential functions for the structure prediction.