filling hydrophobic cavity with... methane?

From: Sebastian Stolzenberg (ss629_at_cornell.edu)
Date: Thu Dec 18 2008 - 16:10:00 CST

Dear All,

I need to fill a ~2000A^3 hydrophobic protein cavity with methane or
some other suitable molecule (in reality, people don't know what type of
molecule is in there).

At 310K, methane is a gas with a particle density several orders of
magnitude lower than the one for water - so it is unlikely, that all
niches of this cavity can be entirely filled with methane
- unless...
1.)
In a buried hydrophobic protein cavity environment, how (much) could one
expect the methane density to change? So far, I didn't find any papers
on this highly unusual topic.

2.)
Is there any other molecule that I could use instead? We were thinking
about ethanol, which, however, has hydrophilic parts.

Thank you very much,
Sebastian

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