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Published online on November 23, 2005, 10.1073/pnas.0503388102

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Biophysics
Coupled protein domain motion in Taq polymerase revealed by neutron spin-echo spectroscopy

( normal mode analysis | statistical mechanics | protein dynamics | quasielastic neutron scattering )

Zimei Bu *{dagger}, Ralf Biehl {ddagger}, Michael Monkenbusch {ddagger}, Dieter Richter {ddagger}, and David J. E. Callaway *{dagger}{sect}

*Fox Chase Cancer Center, 333 Cottman Avenue, Reimann 414, Philadelphia, PA 19111; {ddagger}Institut für Festkörperforschung, Forschungszentrum Jülich, D-52425 Jülich, Germany; and {sect}Department of Neurology, New York University School of Medicine, 350 Community Drive, Manhasset, NY 11030

Edited by Marshall Fixman, Colorado State University, Fort Collins, CO, and approved October 10, 2005 (received for review April 24, 2005)

Long-range conformational changes in proteins are ubiquitous in biology for the transmission and amplification of signals; such conformational changes can be triggered by small-amplitude, nanosecond protein domain motion. Understanding how conformational changes are initiated requires the characterization of protein domain motion on these timescales and on length scales comparable to protein dimensions. Using neutron spin-echo spectroscopy (NSE), normal mode analysis, and a statistical-mechanical framework, we reveal overdamped, coupled domain motion within DNA polymerase I from Thermus aquaticus (Taq polymerase). This protein utilizes correlated domain dynamics over 70 Å to coordinate nucleotide synthesis and cleavage during DNA synthesis and repair. We show that NSE spectroscopy can determine the domain mobility tensor, which determines the degree of dynamical coupling between domains. The mobility tensor defines the domain velocity response to a force applied to it or to another domain, just as the sails of a sailboat determine its velocity given the applied wind force. The NSE results provide insights into the nature of protein domain motion that are not appreciated by conventional biophysical techniques.

Author contributions: Z.B. and D.J.E.C. designed research; Z.B., R.B., M.M., D.R., and D.J.E.C. performed research; Z.B., R.B., M.M., D.R., and D.J.E.C. contributed new reagents/analytic tools; Z.B., R.B., M.M., D.R., and D.J.E.C. analyzed data; and Z.B. and D.J.E.C. wrote the paper.

Conflict of interest statement: No conflicts declared.

{dagger}To whom correspondence may be addressed.

Zimei Bu, E-mail: zimei.bu{at}fccc.edu
David J. E. Callaway, E-mail: david.callaway{at}fccc.edu

www.pnas.org/cgi/doi/10.1073/pnas.0503388102
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[Abstract] [Full Text] [PDF]