In an earlier paper we showed that the closed state of Kir1.1, a important potassium ion channel found in the kidneys, was stabilised by a single hydrogen bond. This paper builds on that work by looking for any interactions that stabilise either the open or closed state of the channel by systematically mutating the majority of the residues to alanine. We were surprised to find that 47 mutations destabilised the open state but only 2 destabilised the closed state, one of which was the one we’d found before. Modelling suggests that this is because open conformations of the channel are more optimised and compact hence mutations tend to be more disruptive. The work was partly funded by the Wellcome Trust and hence the paper is free to download.
Our lab has recently bought two Drobo 5Ds to give us some large storage. They work out of the box with Macs but getting them to play nicely with Linux, specifically Ubuntu 12.04, has been a bit more work so I thought I’d share the recipe that, for us at least, appears to work. Much of this has been cobbled together from the drobo-utils page and also from a very helpful earlier blog post. One thing I could not get to work, unfortunately, is USB3. There appeared to be problems with USB3 and Linux when I was trying this out. Finally I should mention that the Drobo here was setup on a Mac, so was formatted HFS+ to begin with and, of course, follow these commands at your own risk. They worked for me, but they might not work for you..
Here we examine by computer simulation what effect adding a small cell-signalling protein does to a model ternary lipid mixture that has been shown before to phase separate. This paper was presented at the 169th Faraday Discussion meeting in Nottingham in May 2014, the theme of which was Molecular simulations and visualization. We followed the progress of the phase separation of the lipid bilayer by measuring the length of the interface using an edge detection algorithm from image processing. An example python script can be downloaded here.
We found that the protein, NRas, indeed slows down the rate at which the bilayer phase separates. The protein also tends to localise to the interface between the domains which is consistent with it acting to reduce the line tension between the phases.
The questions asked during the discussion (and my answers) will be posted on the journal’s website soon. I’ll update this post when that happens. This paper is open access so is free to download.