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Published online before print March 7, 2006, 10.1110/ps.051921606
Protein Science (2006), 15:731-743. Published by Cold Spring Harbor Laboratory Press. Copyright © 2006 The Protein Society
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Dynamic motions of free and bound Ø29 scaffolding protein identified by hydrogen deuterium exchange mass spectrometry

Chi-Yu Fu1 and Peter E. Prevelige, Jr.2

1 Department of Biochemistry and Molecular Genetics
2 Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama 35294, USA

(RECEIVED October 19, 2005; FINAL REVISION January 7, 2006; ACCEPTED January 13, 2006)

In the double-stranded DNA containing bacteriophages, hundreds of copies of capsid protein subunits polymerize to form icosahedral shells, called procapsids, into which the viral genome is subsequently packaged to form infectious virions. High assembly fidelity requires the assistance of scaffolding protein molecules, which interact with the capsid proteins to insure proper geometrical incorporation of subunits into the growing icosahedral lattices. The interactions between the scaffolding and capsid proteins are transient and are subsequently disrupted during DNA packaging. Removal of scaffolding protein is achieved either by proteolysis or alternatively by some form of conformational switch that allows it to dissociate from the capsid. To identify the switch controlling scaffolding protein association and release, hydrogen deuterium exchange was applied to Bacillus subtilis phage Ø29 scaffolding protein gp7 in both free and procapsid-bound forms. The H/D exchange experiments revealed highly dynamic and cooperative opening motions of scaffolding molecules in the N-terminal helix-loop-helix (H-L-H) region. The motions can be promoted by destabilizing the hydrophobic contact between two helices. At low temperature where high energy motions were damped, or in a mutant in which the helices were tethered through the introduction of a disulfide bond, this region displayed restricted cooperative opening motions as demonstrated by a switch in the exchange kinetics from correlated EX1 exchange to uncorrelated EX2 exchange. The cooperative opening rate was increased in the procapsid-bound form, suggesting this region might interact with the capsid protein. Its dynamic nature might play a role in the assembly and release mechanism.

Keywords: bacteriophage Ø29; scaffolding proteins; virus assembly; helix-loop-helix structure; hydrogen deuterium exchange; EX1 exchange; mass spectrometry


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