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Analyzing Forced Unfolding of Protein Tandems by Ordered Variates, 1: Independent Unfolding Times

E. Bura ^*, D. K. Klimov  and V. Barsegov 

^* Department of Statistics, George Washington University, Washington, DC; Department of Bioinformatics & Computational Biology, George Mason University, Manassas, Virginia; and Department of Chemistry, University of Massachusetts, Lowell, Massachusetts

Correspondence: Address reprint requests to V. Barsegov, Tel.: 978-934-3661; Fax: 978-934-3013; E-mail: valeri_barsegov{at}uml.edu.

Most of the mechanically active proteins are organized into tandems of identical repeats, (D)_N, or heterogeneous tandems, D₁–D₂–...–D_N. In current atomic force microscopy experiments, conformational transitions of protein tandems can be accessed by employing constant stretching force f (force-clamp) and by analyzing the recorded unfolding times of individual domains. Analysis of unfolding data for homogeneous tandems relies on the assumption that unfolding times are independent and identically distributed, and involves inference of the (parent) probability density of unfolding times from the histogram of the combined unfolding times. This procedure cannot be used to describe tandems characterized by interdomain interactions, or heteregoneous tandems. In this article, we introduce an alternative approach that is based on recognizing that the observed data are ordered, i.e., first, second, third, etc., unfolding times. The approach is exemplified through the analysis of unfolding times for a computer model of the homogeneous and heterogeneous tandems, subjected to constant force. We show that, in the experimentally accessible range of stretching forces, the independent and identically distributed assumption may not hold. Specifically, the uncorrelated unfolding transitions of individual domains at lower force may become correlated (dependent) at elevated force levels. The proposed formalism can be used in atomic force microscopy experiments to infer the unfolding time distributions of individual domains from experimental histograms of ordered unfolding times, and it can be extended to analyzing protein tandems that exhibit interdomain interactions.

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