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Protein Science (2005), 14:735-742. Published by Cold Spring Harbor Laboratory Press. Copyright © 2005 The Protein Society
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Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R1{rho} relaxation experiments

Francesca Massi, Michael J. Grey and Arthur G. Palmer, III

Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, USA

(RECEIVED September 24, 2004; FINAL REVISION September 24, 2004; ACCEPTED November 19, 2004)

NMR spin relaxation experiments are used to characterize the dynamics of the backbone of ubiquitin. Chemical exchange processes affecting residues Ile 23, Asn 25, Thr 55, and Val 70 are characterized using on- and off-resonance rotating-frame 15N R1{rho} relaxation experiments to have a kinetic exchange rate constant of 25,000 sec–1 at 280 K. The exchange process affecting residues 23, 25, and 55 appears to result from disruption of N-cap hydrogen bonds of the {alpha}-helix and possibly from repacking of the side chain of Ile 23. Chemical exchange processes affecting other residues on the surface of ubiquitin are identified using 1H-15N multiple quantum relaxation experiments. These residues are located near or at the regions known to interact with various enzymes of the ubiquitin-dependent protein degradation pathway.

Keywords: protein dynamics; chemical exchange; 15N spin relaxation; multiple-quantum relaxation

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.041139505.

Reprint requests to: Arthur G. Palmer III, Department of Biochemistry and Molecular Biophysics, Columbia University, 630 West 168th Street, New York, NY 10032, USA; e-mail:agp6{at}columbia.edu; fax: (212) 305-6949.


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