A study on separation of the protein structural types in amino acid sequence feature spaces

Proteins are diverse with their sequences, structures and functions, it is important to study the relations between the sequences, structures and functions. In this paper, we conduct a study that surveying the relations between the protein sequences and their structures. In this study, we use the natural vector (NV) and the averaged property factor (APF) features to represent protein sequences into feature vectors, and use the multi-class MSE and the convex hull methods to separate proteins of different structural classes into different regions. We found that proteins from different structural classes are separable by hyper-planes and convex hulls in the natural vector feature space, where the feature vectors of different structural classes are separated into disjoint regions or convex hulls in the high dimensional feature spaces. The natural vector outperforms the averaged property factor method in identifying the structures, and the convex hull method outperforms the multi-class MSE in separating the feature points. These outcomes convince the strong connections between the protein sequences and their structures, and may imply that the amino acids composition and their sequence arrangements represented by the natural vectors have greater influences to the structures than the averaged physical property factors of the amino acids.