doi:10.1016/j.cplett.2006.01.012 
Copyright © 2006 Elsevier B.V. All rights reserved.
Tryptophan–water interaction in Monellin: Hydration patterns from molecular dynamics simulation
Priti Hansiaa, Saraswathi Vishveshwaraa and Samir Kumar Palb, 
, 
aMolecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
bUnit for Nano Science and Technology, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake, Kolkata 700 098, India
Received 2 September 2005;
revised 3 January 2006.
Available online 7 February 2006.
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Abstract
Femtosecond spectroscopy carried out earlier on Monellin and some other systems has given insights into the hydration dynamics of the proteins. In the present work, molecular dynamics simulations have been performed on Monellin to study the hydration dynamics. A method has been described to follow up the molecular events of the protein–water interactions in detail. The time constants of the survival correlation function match well with the reported experimental values. This validates the procedure, adapted here for Monellin, to investigate the hydration dynamics in general.
Fig. 1. (a) Monellin in the solvation box. The initial coordinates have been obtained by X-ray-structure (Protein Data Bank entry 4MON). Monellin is centered in a box of 4495 water molecules. Single tryptophan (Trp3) of Monellin (b) with short-lived and (c) long-lived water molecules. The temporal trajectories of water molecules indicated by arrows are discussed in the text.
Fig. 2. Radial distribution of water molecules around Monellin as a function of the distance between water oxygen atoms and the protein atoms, including hydrogen.
Fig. 3. Survival time correlation function, CR(t), of water molecules in various hydration shells with different radii from the single tryptophan (Trp3) of Monellin.
Fig. 4. The temporal trajectories of water molecules in the vicinity of the single tryptophan (Trp3) of Monellin.
Fig. 5. (a) Distribution of residence time of water molecules within a shell of 6 Å from the single tryptophan (Trp3) of Monellin. (b) Trajectories of some of these water molecules with residence time >5 ps black and gray lines represent the trajectories within a shell of 4 and 6 Å, respectively. (c) Schematic representation derived from (b); water molecules interacting with Trp3 with a significant residence time are represented by single arrow; water molecules exchanging with the bulk water and also visiting the 4 Å shell are represented by double arrow.
Table 1.
Short and long time constants extracted by a best fit according to Eq. (2), of the survival time correlation function of water hydration shell at various radial distances from Trp3
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± 60° which is mildly dependent on the anion type present. For all the anions the water molecules in the first shell are strongly oriented with one O–H vector pointing directly towards the anion on average, with an angular spread of 
