[RASMB] Question about the error in determination of kinetic parameters by SedAnal

[John Correia]

Joy
 Sorry for the delay - classes are starting soon.
 When you fit for rates you often find very asymmetric error limits
especially in the range where you approach very fast or very slow.   In
this case your best fit is on the edge of being fast and not kinetically
mediated - thus values that are faster become indistinguishable from
other vales & you see a wide error limit, often unbounded meaning you
can't determine the error limit.  The slower value is well determined
and gives a narrow limit because this is distinguishing between very
different kinetic profiles.   You get the opposite asymmetry at the very slow limit where it is well
limited on the faster side but indistinguishable or unbounded on the
slower side.  Said another way fast is fast and any value fits the data.
 Very, very slow is essentially nonexchangable between species and again
you cannot determine a unique rate.
 The ability to fit for rates depends upon the quality of the data, the
range of the data relative to Kd and the complexity of the system.  For
dimers the edge of the fast range is 5 x 10-3 and the edge of the slow
range is 5 x 10-5.
   -------------------------------------------------------------------
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/ -------------------------------------------------------------------




>>> On 8/9/2007 at 6:58 PM, in message
<68e6eba10708091658h19a3ac73qcd13e814b8d71eaa at mail.gmail.com>, "Joy
Zhao" <joyzhao at gmail.com> wrote:
Hello everyone,
I have a question about the error in determination of kinetic
parameters by SedAnal. When I tried to fit my SV data to obtain kr (or
kf) for a simple monomer-dimer system by using 2A-->A2 model, the
error for the kinetic parameter seems big. I am wondering whether this
is typical for the analyis by SedAnal.

(1).I was using F-statistics, Confidence Interval 68.27%. The rmsd of
the fitting is 4.6771032*10-3 .

(2). This global fitting was performed with four data sets.

(3). Results: kr=0.00238 S-1    min=0.001138 S-1        max=0.099988

S-1(CI=68.27%)

Thank you for your help!

Joy Zhao
Dept of Chem and Biochem
University of Maryland
College Park,MD 20742
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