13th International Conference on Fracture June 16–21, 2013, Beijing, China -5- decrease trend implies a sustained hydrogen bond formation (see Figure 3(B)), which is an indicator of increasing secondary structure. (3) The cross of hp and hb energy curves show that hydrophobic effect dominate the early folding stage and the hydrogen bonding interaction controls the following stage after a transition state around step 3500. Figure 2. Native and predicted structure of target T619 Figure 3. Simulation results for 10001 steps of target T619. (A) Hydrophobic (hp) energy, hydrogen bond (hb) energy, electrostatic (ele) energy and total energy. (B) Number of hydrogen bond. (C) Predicted structure radius of gyration and RMSD. (D)Structure evaluation parameter The radius of gyration (Rg) and RMSD curves show obvious stages during the folding process. (1) Before update step 300, there is a fast collapse of Rg. This is a reasonable result from fast mainchain collapse driven by hydrophobic effect. In this stage, protein backbone can pivot freely because of relatively less residue repulsive forces. As residues packing to each other, the hydrophobic cores are formed and there are many hydrogen bonds appear. Hydrophobic energy and hydrogen bonding energy have a sharp decrease during the first 300 steps, so as the number of hydrogen bonds in this fast collapse stage (Figure 3(B)). Considering definition of CSAW energy, protein backbone collapse fast to a globular structure containing may hydrophobic cores. This globular shaped structure becomes more stable with the help of hydrogen bonds. (2) From update step 300 to 2000, there is a slow packing process. Protein structure Rg decrease slowly from 30 Å to 20 Å. The decrease of hydrophobic and hydrogen bonding energy also slows down. This means that it become difficult for protein to find a ‘comfortable’ structure with lower energy. As the hydrophobic residue cluster grow to a certain size, the increase of hydrophobic effect will slow down. This is caused by the dewetting effect near large hydrophobic cluster surface. On the contrary, hydrogen bonding interaction keep increasing as more H-bond appear. Hydrogen bond energy take the place of hydrophobic energy. Since hydrophobic effect cannot hold the globular structure as tight as before, protein has more chance to expand in volume and accommodate more hydrogen bonds. Consequently, the radius of gyrations show large fluctuation after step 2000.
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