The coiled-coil of the human Rad50 DNA repair protein contains specific segments of increased flexibility

^*Department of Nanoscience and Delft Institute of Microelectronics and Submicrontechnology, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands; ^‡Department of Cell Biology and Genetics, Erasmus Medical Center, PO Box 1738, 3000 DR Rotterdam, The Netherlands; and ^§Department of Radiation Oncology, Erasmus Medical Center/Daniel den Hoed Cancer Center, 3000 DR Rotterdam, The Netherlands

Edited by Nancy Kleckner, Harvard University, Cambridge, MA, and approved April 21, 2003 (received for review February 6, 2003)

Abstract

Protein structural features are usually determined by defining regularities in a large population of homogeneous molecules. However, irregular features such as structural variation and flexibility are likely to be missed, despite their vital role for their biological function. In this paper, we report the observation of striking irregularities in the flexibility of the coiled-coil region of the human Rad50 DNA repair protein. Existing methods to quantitatively analyze flexibility are applicable to homogeneous polymers only. Because protein coiled-coils cannot be assumed to be homogeneous, we develop a method to quantify the local flexibility from high-resolution atomic force microscopy images. Indeed, in Rad50 coiled-coils, two positions of increased flexibility are observed. We discuss how this dynamic structural feature is integral to Rad50 function.

Footnotes

↵ † To whom correspondence should be addressed. E-mail: noort{at}mb.tn.tudelft.nl.
This paper was submitted directly (Track II) to the PNAS office.
Abbreviations: R/M, Rad50 and Mre11; SMC, structural maintenance of chromosome; AFM, atomic force microscopy.