HGT Z O W a peak at 255 A and a lower part at 265 A were noticed At the second

Hgt z o w a peak at 255 a and a lower part at 265 a

This preview shows page 4 - 6 out of 18 pages.

H(GT) Z O (W), a peak at 2.55 A ˚ and a lower part at 2.65 A ˚ were noticed. At the second solvation shell, the RDF of O Z H (GT) Z O(W) shows a peak at 3.65 A ˚ and a lower point at 4.35 A ˚ . For C Z H(GT) Z O(W), a peak at 5.65 A ˚ and a lower part at 5.75 A ˚ were noticed. For N Z H(GT) Z O(W), a peak at 3.55 A ˚ and a lower part at 3.65 A ˚ were noticed. At the first solvation shell of GT, the ratios g O 2 H ð GT Þ ... O ð Water Þ max = g O 2 H ð GT Þ ... O ð Water Þ min ¼ 1 : 123 ; g C 2 H ð GT Þ ... O ð Water Þ max = g C 2 H ð GT Þ ... O ð Water Þ min ¼ 1 : 046 and g N 2 H ð GT Þ ... O ð Water Þ max = g N 2 H ð GT Þ ... O ð Water Þ min ¼ 0 : 947 were observed. At the second solvation shell, the ratios g O 2 H ð GT Þ ... O ð Water Þ max = g O 2 H ð GT Þ ... O ð Water Þ min ¼ 1 : 213 ; g C 2 H ð GT Þ ... O ð Water Þ max = g C 2 H ð GT Þ ... O ð Water Þ min ¼ 1 : 052 and g N 2 H ð GT Þ ... O ð Water Þ max = g N 2 H ð GT Þ ... O ð Water Þ min ¼ 1 : 051 Table 1. The positions of the maxima and minima r max , r min in (A ˚ ) and of the amplitudes r max , r min at the first peak of first and second solvation shells in RDFs of GT. Solvation shell Interaction r max g max r min g min g max / g min First O Z H(GT) Z O(W) 2.15 0.571 2.35 0.46 1.123 C Z H(GT) Z O(W) 3.35 0.748 3.65 0.715 1.046 N Z H(GT) Z O(W) 2.55 0.51 2.65 0.483 0.947 Second O Z H(GT) Z O(W) 3.65 1.092 4.35 0.9 1.213 C Z H(GT) Z O(W) 5.65 0.944 5.75 0.897 1.052 N Z H(GT) Z O(W) 3.55 0.725 3.65 0.69 1.051 Figure 1. O Z H(GT) . . . O(Water), N Z H(GT) . . . O(Water) and C Z H(GT) . . . O(Water) RDFs of GT in water. 944 B. Yogeswari et al. Downloaded by [Thammasat University Libraries] at 03:39 08 October 2014
Image of page 4
were noticed. The order of H-bond strength was found to be O Z H(GT) . . . O(W) . C Z H(GT) . . . O(W) . N Z H (GT) . . . O(W), both at first and second solvation shells of GT. Figure 2 shows the number of water molecules that occupy the first and second solvation shells of GT. On average, four water molecules were often found to interact with GT at the first solvation shell. From Figure 2 , it is interesting to note that a maximum of seven water molecules were found to interact with GT residues at 6228 ps in the first coordination shell. Five water molecules were seldom interacting with GT (only nine times) throughout the simulation for the first 446 ps. On the other hand, nearly 50–82 water molecules were found to occupy in the second solvation shell of GT which were playing a vital role in altering the conformations. The Ramachandran plot for the angles F 2 (C3 Z N9 Z C11 Z C14) and C 2 (N9 Z C11 Z C14 Z N16) of the middle glycine is shown in Figure 3 . The different conformations of GT at different times during the MD simulation (1, 2, 4, 6, 8 and 10 ns) are shown in Figure 4 . The F 2 and C 2 values of GT conformations shown in Figure 3 suggest that the GT exhibits a -helix conformations in the solvation environment. But according to previous studies, it prefers to be in b sheet [18] and planar trans [10] conformations in the gas phase. We have added solvation effect, using water as a solvent to find the GT conformations and arrived at the result which is supported by the previous conformational study of GT in solution. [19] Figure 2. The number of water molecules falling into the first and second solvation shells of GT.
Image of page 5
Image of page 6

You've reached the end of your free preview.

Want to read all 18 pages?

  • Fall '19
  • dr. ahmed

  • Left Quote Icon

    Student Picture

  • Left Quote Icon

    Student Picture

  • Left Quote Icon

    Student Picture

Stuck? We have tutors online 24/7 who can help you get unstuck.
A+ icon
Ask Expert Tutors You can ask You can ask You can ask (will expire )
Answers in as fast as 15 minutes