13th International Conference on Fracture June 16–21, 2013, Beijing, China -4- into water is energetically costly. Thus the burial of hydrophobic sidechains in the folding reaction is energetically favorable. In order to model this folding process, energy decrease caused by hydrophobic residue aggregation is simulated by residue contact degree. The hydrophobicity of amino acids are represented by h. When h is positive, the residue is hydrophobic. Otherwise, it is hydrophilic. Table 1 shows the hydropobic properties of 20 amino acids. If residue m has multiple contact neighbors, the hydrophobic energy variation is the summation of residue hydrophobicities. Table 1. Hydrophobicity of 20 amino acids Amino acid 3-letter codes 1-letter codes Hydropho bicity Amino acid 3-letter codes 1-letter codes Hydropho bicity Alanine Ala A 0.05 Leucine Leu L 0.15 Arginine Arg R -0.42 Lysine Lys K -0.21 Asparagine Asn N -0.28 Methionine Met M 0.04 Aspartic Acid Asp D -0.35 Phenylalanine Phe F 0.06 Cysteine Cys C 0.01 Proline Pro P Glutamic Acid Glu E -0.25 Serine Ser S -0.21 Glutamine Gln Q -0.21 Threonine Thr T -0.15 Glycine Gly G 0.00 Tryptophan Trp W 0.03 Histidine His H -0.17 Tyrosine Tyr Y -0.03 Isoleucine Ile I 0.15 Valine Val V 0.13 Hydrophilicity at 25℃ is relative to glycine, and is based on the partitioning of a sidechain analogue between the two states [5-8]. Hydrogen bond (H-bond) contains both positive (H-donor) and negative (H-acceptor) partial charges. It represents a combination of covalent and electrostatic interactions, but the main component is the electrostatic attraction between hydrogen donor and acceptor. Hydrogen bonding interactions between backbone O atom and N-H atoms has different stabilities in different situations. The Gibbs energy contributions per hydrogen bond in the interior of proteins are estimated to be 10-60 kJ/mol[5, 9, 10]. While the hydrogen bond interaction in protein structure is much weaker at the surface, where the relative permittivity of water is close to 80. 6. Example of CASP09 target simulation Here we show the CASP09 target T619 (3NRW) as an folding simulation example. T619 has 111 amino acids and is composed of five helices (Figure 3(A)). The initial structure is unfolded long chain. The final predicted 3-D structure by CSAW is shown in Figure 3(B). In addition to the final structure, we calculate many other important parameters for the whole folding process. The hydrophobic energy and hydrogen bond energy are shown in Figure 3(A). Although the electrostatic energy is not involved in current AA-CSAW as a driving force, we do calculate it for charged residues through Coulomb’s law. The interesting features of energy curves are (1) Hydrophobic (hp) energy decreases fast within first 300 steps. Then hp curve fluctuates around a stable value. This indicates a fast structure collapse in the very early folding stage. Afterwards the hydrophobic residue clusters do not grow greatly. (2) Hydrogen bond (hb) energy curve descends continuously during the whole folding process. The
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