Intrinsic rates and activation free energies from single-molecule pulling experiments

BIOL 36

Olga K Dudko, dudko@mail.nih.gov1, Gerhard Hummer, Gerhard.Hummer@nih.gov2, and Attila Szabo, attilas@nih.gov2. (1) Mathematical & Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, 12 South Drive, Bldg. 12A Room 2007, Bethesda, MD 20892, (2) Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520
We present a unified framework for extracting kinetic information from single-molecule pulling experiments at constant force or constant pulling speed. Our procedure provides estimates of not only i) the intrinsic rate coefficient and ii) the location of the transition state but also iii) the free energy of activation. By analyzing simulated data we show that the resulting rates of force-induced rupture are significantly more reliable than those obtained by the widely used approach based on Bell's formula. We consider the uniqueness of the extracted kinetic information and suggest guidelines to avoid over-interpretation of experiments.
 

Protein Structure and Folding
4:30 PM-6:30 PM, Sunday, 10 September 2006 Moscone Center -- Hall D, Poster

Division of Biological Chemistry

The 232nd ACS National Meeting, San Francisco, CA, September 10-14, 2006