13th International Conference on Fracture June 16–21, 2013, Beijing, China -2- 2. “Crank” model of Amino acid Amino acids are molecules containing an amine group, a carboxylic acid group and a side chain that varies between different amino acids. The amine and carboxylic acid groups of amino acids react to form amide bonds. One amino acid molecule can react with another and become joined through an amide linkage. This polymerization of amino acids yields the newly formed peptide bond and a molecule of water. The protein is a linear polymer of the 20 different kinds of amino acid, which are linked by peptide bonds. All of the 20 amino acids have in common a central carbon atom (Cα) to which are attached a hydrogen atom, an amino group, and a carboxyl group (COOH). What distinguishes one amino acid from another is the side chain attached to the Cα. The main-chain atoms are a carbon atom Cα, an NH group bound to Cα, and a carbonyl group C’=O, where the carbon atom C’ is attached to Cα. The basic repeating unit along the main chain is thus (NH- Cα-C’=O), which is the residue of the common parts of amino acids after peptide bonds have been formed. Figure 1. Crank chain model of protein backbone structure The peptide bond tend to be planar and the rigid peptide dihedral angle (the bond between C’ and N) is always close to 180 degrees (Figure 1). Here C’ indicate the carbon atom bonded to Cα. Because of the double-bond unrotatable feature of peptide bond, the atoms Cα-C’=O-N are constrained in a rigid plane, called peptide plane. There are obvious repeating patterns -Cα-C'=N-Cα in protein backbone. The interlink within these atoms form a crank-shaped rigid body. Thus, we introduce a ‘crank’ unit –Cα-C1=N- in CSAW. Crank is a simplification of amino acid residues. The Cα atom is located at origin point. 3. Add sidechain atoms to residue What distinguish protein from common polymers are the diversity of residue sidechains. There are 20 natural amino acid residues in protein. They can be classified into several groups, such as hydrophobic, charged, polar and so on. Some works show that hydrophobic/hydrophilic residue types are enough to create secondary structures (such as alpha helix). However, the importance of other subtle properties of amino acid sidechains are still underestimated. The delicate sidechain differences may shed light to the folding of native structure. As for coarse-grained model, all atom sidechains are substantially important. The single sphere sidechain model is good. But sometimes spurious overlaps happen when anisotropic residue sidechains come close to each other. In single ball sidechain model, many important dense configurations will be ignored, which prevent protein structure from search correct folding path in conformation space. Protein folding simulations of real proteins make demand of an all-atom
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