All-Atom CSAW: An Ab Initio Protein Folding Method
by
Weitao Sun(Zhou Pei-Yuan Center for Applied Mathematics, Tsinghua University, Beijing)
→
Europe/Stockholm
122:026
122:026
Description
The biological activity of protein molecules depends on the three-dimensional structure. To understand the biological function of proteins we would like to be able to deduce or predict the three-dimensional structure from the amino acid sequence. In spite of the considered efforts over the past three decades, the protein folding problem is still unsolved, and remains one of the most basic intellectual challenges in molecular biology.
All-Atom Conditioned Self-Avoiding Walk (AA-CSAW) is an ab initio protein folding simulation model based on Monte-Carlo (MC) method. The polypeptide chain is simulated as effectively rigid cranks units lined by covalent bonds. Bond lengths and bond angles are set as fixed optimal values. The structure of polypeptide is fully described by backbone dihedral angles and the sidechain dihedral angles. The number of sidechain angles depends on the type of amino acid. A trial structure is randomly generated by pivoting the polypeptide chain and sidechains. In the pivot algorithm, the backbone dihedral angles for each residue are chosen in Ramachandran plot according to a probability distribution derived from 3-residue fragment set. The effective energy of protein structure is constructed by considering hydrophobic effect, desolvation effect and hydrogen bonding interaction. Examples show that the AA-CSAW method is now ready to simulate protein structures around 300 amino acids.