CCL: polypeptide tethers to span protein subunits

 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?