3D Protein Structure Modeling

Abstract

Proteins are complex macromolecules that perform vital function in all living beings. They are composed of a chain of amino acids. The biological function of a protein is determined by the way it is folded into a specific 3D structure, known as native conformation. The high resolution 3D structure of a protein is the key to the understanding and manipulating of its biochemical and cellular functions. Protein structure could be calculated from knowledge of its sequence and our understanding of the sequence-structure realizations. Various methods have been applied to solve protein folding problem. In this paper the protein is represented like a sequence over 3 letter alphabet according the specific functions of amino acids. After that the folding problem is defined like optimization problem. Our protein model is multifunctional: it can be used to predict the 3D structure of the protein from its amino acid sequence; the model can predict the changes in the protein folding when several amino acids are mutated; by it can be constructed a protein with needed 3D folding.

Keywords

• Protein folding
• Hydrophobic and hydrophilic amino acids
• Destructor