Anisotropic effective interactions in a coarse-grained tube picture of proteins

Recent studies have shown that a coarse-grained description of a protein backbone represented as a tube of non-zero thickness captures many of the common characteristics of small globular proteins. Here we argue that such a physical picture leads to a prediction of inherently anisotropic amino acid interactions. In order to test this prediction, we have carried out an extensive analysis of a data bank made up of 600 proteins with low sequence homology and covering many different three-dimensional folds. This analysis, based on the study of the geometrical properties of the vectors joining next-nearest neighbor C(alpha) atoms along the chain, shows clearly that when amino acids are in contact, the distribution of their relative orientations is not random but exhibits peaks at specific angles whose values reflect, in general, the tubular nature of proteins and, more specifically, the nature of the secondary structure motifs, which are the building blocks of protein structures. Our results suggest that the incorporation of the relative orientation of amino acids in contact could play a vital role in simplified coarse-grained schemes for determining effective interaction parameters for use in folding, threading, and docking.