Residence times of water molecules in the hydration sites of myoglobin

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Abstract

Hydration sites are high-density regions in the three-dimensional time-averaged solvent structure in molecular dynamics simulations and diffraction experiments. In a simulation of sperm whale myoglobin, we found 294 such high-density regions. Their positions appear to agree reasonably well with the distributions of waters of hydration found in 38 x-ray and 1 neutron high-resolution structures of this protein. The hydration sites are characterized by an average occupancy and a combination of residence time parameters designed to approximate a distribution of residence times. It appears that although the occupancy and residence times of the majority of sites are rather bulk-like, the residence time distribution is shifted toward the longer components, relative to bulk. The sites with particularly long residence times are located only in the cavities and clefts of the protein. This indicates that other factors, such as hydrogen bonds and hydrophobicity of underlying protein residues, play a lesser role in determining the residence times of the longest-lived sites.

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Makarov, V. A., Andrews, B. K., Smith, P. E., & Pettitt, B. M. (2000). Residence times of water molecules in the hydration sites of myoglobin. Biophysical Journal, 79(6), 2966–2974. https://doi.org/10.1016/S0006-3495(00)76533-7

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