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Keywords:

  • molecular surface;
  • hydrophobicity;
  • molecular dynamics;
  • patches

Abstract

We present a simple and efficient method called PATCHTRACK, for studying the dynamics of hydrophobic surface patches. It tracks the patches on snapshot structures taken from a Molecular Dynamics simulation. They are connected into so-called patch runs, which are subsequently clustered into so-called recurrent patches. The method is applied to simulations of three different proteins. Protein motion causes addition and removal of one or more atoms to a patch, resulting in size fluctuations of around 25%. The fluctuations eventually lead to the break-up of a patch, and their average life span is therefore remarkably short at around 4 ps. However, some patch runs are much more stable, lasting hundreds of picoseconds. One such case is the largest patch in amicyanin that is known to be biologically relevant. Another case, previously not reported, is found in phospholipase A2, where the functional significance of a large recurrent patch formed by Leu58 and Phe94 seems likely. This patch appears to have been overlooked as it is relatively small in the X-ray structure, demonstrating the utility of the current method. The most frequently occurring patch size is 40–60 Å2, but sizes of up to 500 Å2 are also observed. There is no clear relation between patch run durations and their average size. However, long-lasting patch runs tend not to have large fluctuations. The recurrent patches have alternating periods of “liveness” and “dormancy”; around 25% of them is predominantly in the live state. Proteins 2008. © 2008 Wiley-Liss, Inc.