Error in Biochemistry 39(19) / DynaFit tutorial

Petr Kuzmic pkuzmic at biokin.com
Mon May 15 01:55:35 EST 2000


There is a small but potentially confusing typographical error in the
most recent issue of Biochemistry (v.39, no.19), in the following paper

   "Mechanism of Neomycin and Rev Peptide Binding to the Rev 
    Responsive Element of HIV-1 As Determined by Fluorescence 
    and NMR Spectroscopy"

    Karen A. Lacourciere, James T. Stivers, and John P. Marino
    Biochemistry, 39 (19), 5630 -5641, 2000

The legend for Figure 2 should say "30 nM" instead of "100 nM" for the
concentration of the HIV-1 Rev-Responsive Element.   The problem is that
if one tries to interpret the data in Figure 2, the concentration [RRE]
= 100 nM will give a nonsensical Rev/HIV binding constant.

The authors (Jim Stivers, of NIST) kindly sent me their original
experimental data in a digital format.  I used these data to create a
small on-line tutorial showing how to use DynaFit [P. Kuzmic (1996)
Anal. Biochem. 237, 260-273] in similar cases.  You can look it up at


   http://www.biokin.com/dynafit/tutorial/hivrev.html


Most practicing biochemists will probably appreciate the fact that the
equilibrium binding data can be fit to a model specified in a symbolic
form, as opposed to the algebraic form:


ALGEBRAIC METHOD
----------------

F = Fo - ((Fo-Ff)/(2*[RRE]))*(Kd + [Rev] + [RRE])

    - sqrt((Kd + [Rev] + [RRE])^2 - 4*[RRE]*[Rev]))


   F  ... fluorescence at given [Rev]
   Fo ... fluorescence at [Rev] = 0
   Ff ... fluorescence at [Rev] --> infinity
   Kd ... binding constant


DYNAFIT METHOD
--------------

[task]
   data = equilibria
   task = fit

[mechanism]
   RRE + Rev <==> RRE.Rev  :  Kd  dissoc.

[constants]
   Kd = 15 ? 


Compared with the algebraic model, the DynaFit symbolic description of
the reaction mechanism is probably more easy to derive by most
experimentalists. 

DynaFit is a freeware that can be downloaded from


   http://www.biokin.com/dynafit/


_____________________________________________________________________
Petr Kuzmic, Ph.D. * BioKin, Ltd. * Consulting & Software Development
http://www.biokin.com * (608) 256-4790 * (608) 256-1269 FAX





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