BIOPHYSICAL THEORY AND MODELING |
Analyzing Forced Unfolding of Protein Tandems by Ordered
Variates: 2. Dependent Unfolding times
Efstathia Bura 1, Dmitri K Klimov 2 and Valeri Barsegov 3*
1 Department of Statistics, George Washington University
2 Dept. of Bioinformatics & Computational Biology, George Mason University
3 University of Massachusetts
* To whom correspondence should be addressed. E-mail: valeri_barsegov{at}uml.edu.
Submitted on June 16, 2007
Revised on July 30, 2007
Accepted on 8 November 2007
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Abstract |
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Statistical analyses of forced unfolding data for protein tandems, i.e. unfolding forces (force-ramp) and unfolding times (force-clamp) presently used in single-molecule dynamic force spectroscopy, rely on the "iid-assumption" that the unfolding transitions of individual protein domains are independent (uncorrelated) and characterized, respectively, by identically distributed unfolding forces and unfolding times. In our previous work (E. Bura, D. K. Klimov, and V. Barsegov. 2007. Biophys. J. 93: 1100-1115 [1] we showed that in the experimentally accessible pico-Newton force range, the iid-assumption while holds at lower constant force may break at evelated force level, i.e. the unfolding transitions may become correlated when f is increased. In this paper, we develop much needed statistical tests for assessing the independence of the unobserved forced unfolding times for individual protein domains in the tandem and equality of their parent distributions, which are based solely on the observed ordered unfolding times. The use and performance of these tests are illustrated through the analysis of unfolding times for computer models of protein tandems. The proposed tests can be used in force-clamp AFM experiments to obtain accurate information on protein forced unfolding, and to probe data on the presence of interdomain interactions. The order statistics based formalism, introduced in [1], is extended to cover the analysis of correlated unfolding transitions. The use of order statistics leads naturally to the development of new kinetic models, which describe the probabilities of ordered unfolding transitions rather than the populations of chemical species.
Key Words:
correlated unfolding transitions, force-clamp AFM, interdomain interactions, order statistics, protein tandems
