A key driving force in determination of protein structural classes

The three-dimensional structure of a protein is uniquely dictated by its pr imary 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-ac id composition. This suggests that the interaction among the components of amino acid composition may play a considerable role in determining the stru ctural class of a protein. To quantitatively test such a hypothesis at a de eper level, three potential functions, U-(0), U-(1), and U-(2), were formul ated that respectively represent the 0th-order, 1st-order, and 2nd-order ap proximations for the interaction among the components of the amino acid com position in a protein. It was observed that the correct rates in recognizin g protein structural classes by U-(2) are significantly higher than those b y U-(0) and U-(1), indicating that an algorithm that can more completely in corporate the interaction contributions will yield better recognition quali ty, 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) 199 9 Academic Press.