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Figure 22.6 Water and urea contacts to CI2 core residues as a function of simulation time accompanied by snapshots of unfolding. Simulation of CI2 in 7.15 M urea: (a) The number of heavy atom contacts between CI2 's Val 47 and water (cyan) and urea (red) as the MD simulation progresses. (b) The number of heavy atom contacts between CI2's Pro 61 and water (cyan) and urea (red) vs simulation time. (c) Snapshots of CI2 showing hydration waters and urea within 5.0 Â of Val 47 and Pro 61. The protein is shown as ribbons with two of the hydrophobic residues of the core shown in space filling. At the beginning of the simulation, there are no urea to Val 47 or Pro 61 contacts, although several water contacts can be observed (a and c). After water attacks the core at the TS (vertical bar in a and b at 5.426 ns), urea molecules are observed entering into the hydrophobic nucleus. By the end of the simulation (50 ns) the protein is denatured and the core is solvated by urea.

Start

1 Tj

Val 47

50 ns

Val 47

50 ns

Figure 22.6 Water and urea contacts to CI2 core residues as a function of simulation time accompanied by snapshots of unfolding. Simulation of CI2 in 7.15 M urea: (a) The number of heavy atom contacts between CI2 's Val 47 and water (cyan) and urea (red) as the MD simulation progresses. (b) The number of heavy atom contacts between CI2's Pro 61 and water (cyan) and urea (red) vs simulation time. (c) Snapshots of CI2 showing hydration waters and urea within 5.0 Â of Val 47 and Pro 61. The protein is shown as ribbons with two of the hydrophobic residues of the core shown in space filling. At the beginning of the simulation, there are no urea to Val 47 or Pro 61 contacts, although several water contacts can be observed (a and c). After water attacks the core at the TS (vertical bar in a and b at 5.426 ns), urea molecules are observed entering into the hydrophobic nucleus. By the end of the simulation (50 ns) the protein is denatured and the core is solvated by urea.

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