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Re: [Jmol-users] Protein backbone superimposition
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From: David L. <Dav...@gl...> - 2022-04-28 15:05:22
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Bob wrote in relation to superimposition of 1cr6: More thoughts on this: I am wondering -- this correlation is so good -- 0.5 Ang RMSD -- Is that real? Or is that an artifact of the modeling methods used? Why would they be almost identical, down to the identical rotations about side-chain bonds? Well, they are subunits of the same protein. But my interest is in a difference between them. There is a loop motif from 10-15 that has a different conformation in the two: there is a peptide plain flip from betaRalphaL to alphaRalphaR at residues Asp11Gly12 that causes a drastic change of conformation at asp11 in relation to the active site. This is not very visible from the alphaC plot. In all other dimers except one that I have looked at of this family of proteins the loop has betaRalphaL. So I wanted to do a superimposition to see if there were other differences in the vicinity. I think the unstructured missing sections are probably the cause of the unusual alphaRalphaR conformation in one subunit. The history of this structure is a bit odd, in that the enzyme is bifunctional, and the interest was in the other domain (an epoxy domain) and only later was it realized that the other domain was a member of the HAD family of phosphatases. They did some later work directed at this using the human (rather than the mouse) enzyme, but only published one subunit, presumably because they were both ordered and similar there. David _______________________________________________________ Dr. David P. Leader (Honorary Senior Research Fellow) Boyd Orr Building, University of Glasgow, Glasgow G12 8QQ, UK Phone: +44 (0)141 330 5905 http://www.davidleader.net _______________________________________________________ |
