Number sequence representation of protein structures based on the second derivative of a folded tetrahedron sequence

A protein is a sequence of amino-acids of length typically less than 1, 000, where there are 20 kinds of amino-acids. In nature, each protein is folded into a well-defined three-dimensional structure, the native structure, and its functional properties are largely determined by the structure. Since many important cellular functions are carried out by proteins, understanding the native structure of proteins is the key to understanding biology at the molecule level. This paper proposes a new mathematical approach to characterize native protein structures based on the discrete differential geometry of tetrahedron tiles. In the approach, local structure of proteins is classified into finite types according to shape. And one would obtain a number sequence representation of protein structures automatically. As a result, it would become possible to quantify structural preference of amino-acids objectively. And one could use the wide variety of sequence alignment programs to study protein str...

• Type: Journal
• Year: 2006
• Where: CORR
• Authors: Naoto Morikawa
• Keywords: Amino-acids, CORR 2006, Education, Native Structure, Protein