Program DYNAFIT example problem (PREPRINT)

Petr Kuzmic pkuzmic at biokin.com
Wed Apr 15 13:37:47 EST 1998


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           General Numerical Treatment of Competitive Binding
    Kinetics: Application to Thrombin­Dehydrothrombin­Hirudin

                Analytical Biochemistry, in press (AB97­0614)

                                                  Petr Kuzmic

                                                  BioKin, Ltd.
                                                P.O. Box 8336
                                            Madison, WI 53708

                                          fax (608) 256-1269
                                           pkuzmic at biokin.com

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  Abstract

  This paper describes a general numerical method for the
  determination of rate constants that characterize the
  binding of a ligand L simultaneously and competitively to
  two different receptor molecules, R1 and R2. The
  experimental data consist of changes in the concentration
  of one receptor (e.g., R1) monitored over time. An example
  problem is represented by hirudin (L) binding to thrombin
  (R1) and to a chemical mutant of thrombin (R2). The
  published experimental data [Wedemeyer et al. (1997) Anal.
  Biochem. 248, 130­140], previously analyzed by using an
  approximate algebraic method, were reanalyzed here by
  numerical integration [Kuzmic (1996) Anal. Biochem. 237,
  260­273]. This general numerical method offers the
  following advantages. (1) It provides an estimate for the
  lower limit on feasible values of association rate
  constants. (2) It is many orders of magnitude more
  accurate. (3) It is easily extensible to more complicated
  reaction mechanisms. (4) It uses a simpler formalism and it
  is thus more accessible to non­mathematicians. (5) A
  suitable computer program for the analysis of competitive
  binding kinetics can be obtained via Internet
  (http://www.biokin.com).

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  Full text: http://www.biokin.com/papers/thrombin/index.shtml
  PDF file: http://www.biokin.com/papers/thrombin/thrombin.pdf
  BioKin Home Page: http://www.biokin.com
  Donwload software: http://www.biokin.com/dynafit/index.shtml


 _____________________________________________________________
 Petr Kuzmic Ph.D. * BioKin Ltd. * Madison, WI 53708-8336, USA
 pkuzmic at biokin.com * http://www.biokin.com * 608.256.1269 fax




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