From owner-chemistry@ccl.net Tue May 16 13:37:00 2006 From: "Spencer Snyder Ericksen spencer_ericksen _ hotmail.com" To: CCL Subject: CCL: polypeptide tethers to span protein subunits Message-Id: <-31764-060516130608-28910-ONy0kkO/oLyKBxBsU+uX9A.:.server.ccl.net> X-Original-From: "Spencer Snyder Ericksen" Date: Tue, 16 May 2006 13:06:07 -0400 Sent to CCL by: "Spencer Snyder Ericksen" [spencer_ericksen,,hotmail.com] I'm interested in constructing concatenated monomers of a heteropentameric ion channel. I'm linking tandem monomers using polypeptides of different sequence and length. Using a homology model, Ive tested these linkers to span two fixed monomers within a fixed pentameric assembly by comparing the molecular mechanics energy of certain isomeric arrangements (after many cycles of simulated annealing and optimization in vacuo). When the linker length is too short for a given arrangement, the strain energy increases abruptly. I then deem the linker a poor choice for application. Sometimes, however, when examining different adjacent arrangements of the tandem (clockwise vs. counterclockwise) within the pentamer, I see little difference in relative strain energies (MM) for the systems. These arrangements present significantly different distances for spanning, yet there is no discernible difference in molecular mechanical strain in the configurations. In wet-lab experiments, we see almost no expression of the CCW arrangement. If my calculations are informative, then I conclude that either the dimerization is kinetically controlled such that the CW arrangement is simply more accessible and/or the CW arrangement is favored due to sterically selective dimerization prior to pentameric assembly. Am I leaving something out? It seems that linker length may depend upon the polypeptides free RMS end-to-end distance and or persistence length. I cant seem to find tables in literature for such values for various polypeptide sequences. Could you point me to some? Also, I thought that the relative strain in different configurations would tell me about the influence of the linker on assembly. Is it likely that the neglected entropic contribution to relative free energies of the arrangements is very important here? I am mostly concerned about the ability for a polymer to span two bodies fixed at different positions. Is there a better way to explore this potential theoretically?