[RASMB] time to reach equilibrium

[John Correia]

John

If you have data & papers to reference on slow kinetics then disagree
all you need to - every system I have worked on is far more aggregation
prone?  Seems that stopped flow needs to get rejuvenated as a
complementary technique!  If there are more papers out there let us
know!!!  

I would still caution against the idea that polymerization & slow
kinetics go hand in hand.  Of course I never do equilibrium runs without
a concentration series by sed velocity, so I would see it & maybe skip
the equilibrium run to begin with.

Thus, for global analysis of multiple cells you need to use individual
K's?  or can you actually get equilibrium & global fits?  With some
systems we work on the aggregation & heterogeneity is different from
cell to cell & condition to condition, so its not a frozen system. Thus,
individual K's works better.  How to extract the true K is the hard part
since it depends upon the aggregation model too.

The Antibodies are S-S linked & thus that is disulfide cross-linking &
re-shuffling - thus slow kinetics here are due to covalent bond
reshuffling - NO?

I will point out a previous email from Avi on using C(s) and fitting
for monomer-dimer-tetramer referred to MW's as if the species separated
into independent or slowly equilibrating zones in a velocity run.  Very
slow kinetics will given separate zones that can be fit as if they are
noninteracting.  Rapid requilibration (100 secs or less) should never
give separate zones for the polymers & thus should never be analyzed in
this way.  This appears to be confusing to some new users.

Entropically driven polymers like tubulin polymers are primarily
hydrophobic & the assembly steps are not slow.  Significant
conformational/folding linkages seems more reasonable as a mechanism. 
So is this a linkage to unstable or unfavorable folding kinetics?  Thus,
the small peptide/protein connection?  Any evidence of this in the
coiled-coil field??


-------------------------------------------------------------------
 Dr. John J. "Jack" Correia
 Department of Biochemistry
 University of Mississippi Medical Center
 2500 North State Street
 Jackson, MS  39216
 (601) 984-1522                                 
 fax (601) 984-1501                             
 email address: jcorreia at biochem.umsmed.edu     
 homepage location: http://biochemistry.umc.edu/correia.html
 dept homepage location:    http://biochemistry.umc.edu/
-------------------------------------------------------------------