A key driving force in determination of protein structural classes

The three-dimensional structure of a protein is uniquely dictated by its primary sequence. However, owing to the very high degenerative nature of the sequence-structure relationship, proteins are generally folded into one of only a few structural classes that are closely correlated with the amino-acid composition. This suggests that the interaction among the components of amino acid composition may play a considerable role in determining the structural class of a protein. To quantitatively test such a hypothesis at a deeper level, three potential functions, U-(0), U-(1), and U-(2), were formulated that respectively represent the 0th-order, 1st-order, and 2nd-order approximations for the interaction among the components of the amino acid composition in a protein. It was observed that the correct rates in recognizing protein structural classes by U-(2) are significantly higher than those by U-(0) and U-(1), indicating that an algorithm that can more completely incorporate the interaction contributions will yield better recognition quality, and hence further demonstrate that the interaction among the components of amino acid composition is an important driving force in determining the structural class of a protein during the sequence folding process. (C) 1999 Academic Press.