Poster abstracts

Poster number 38 submitted by Tanping Li

Solvation of Trp in several proteins and the investigation of water in hydration layer

Tanping Li (Biophysics), Ali A. Hassanali (Biophysics), Sherwin J.Singer (Chemistry), Dongping Zhong (Physics)

Abstract:
Molecular dynamics simulations are used to calculate the time
dependent Stokes shift following photoexcitation of Trp-7(W7) in
myoglobin. In agreement with experiment, a long time (∼ 60ps)
component is observed. Since the long time Stokes shift component is absent when we repeat the calculation with protein frozen at the instant of photoexcitation, we firmly establish that protein flexibility is required to observe slow Stokes shift dynamics in this case. A transition between sub-states near the middle of a 30ns ground state trajectory gave us an opportunity to compare solvation dynamics in two different environments. While some of the superficial features are different, we find that the underlying dynamics are shared by the two isomers. It is necessary to look beyond a decomposition of the Stokes shift into protein and water contributions, and probe the underlying dynamics of protein side groups, backbone, and water dynamics to obtain a full picture of the relaxation process. We analyze water residence times, diffusion, and reorientation dynamics in the hydration layer. We find slow components in each of these quantities, and critically examine their origin and how they affect the observed Stokes shift. The solvation of Trp in thioredoxin and Staphylococcus nuclease are also investigated. The coupled motion between protein and water always dominants the slow stokes shift.

Keywords: solvation, stokes shift, Trp