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J. Biol. Chem., Vol. 282, Issue 31, 22793-22803, August 3, 2007

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Nucleotide-dependent Allostery within the ABC Transporter ATP-binding Cassette

A COMPUTATIONAL STUDY OF THE MJ0796 DIMER^*

From the Department of Medical and Molecular Biosciences, Faculty of Science, University of Technology Sydney, P. O. Box 123, Broadway, New South Wales 2007, Australia

ATP-binding cassette transporters perform energy-dependent transmembrane solute trafficking in all organisms. These proteins often mediate cellular resistance to therapeutic drugs and are involved in a range of human genetic diseases. Enzymological studies have implicated a helical subdomain within the ATP-binding cassette nucleotide-binding domain in coupling ATP hydrolysis to solute transport in the transmembrane domains. Consistent with this, structural and computational analyses have indicated that the helical subdomain undergoes nucleotide-dependent movement relative to the core of the nucleotide-binding domain fold. Here we use theoretical methods to examine the allosteric nucleotide dependence of helical subdomain transitions to further elucidate its role in interactions between the transmembrane and nucleotide-binding domains. Unrestrained 30-ns molecular dynamics simulations of the ATP-bound, ADP-bound, and apo states of the MJ0796 monomer support the idea that interaction of a conserved glutamine residue with the catalytic metal mediates the rotation of the helical subdomain in response to nucleotide binding and hydrolysis. Simulations of the nucleotide-binding domain dimer revealed that ATP hydrolysis induces a large transition of one helical subdomain, resulting in an asymmetric conformation of the dimer not observed previously. A coarse-grained elastic network analysis supports this finding, revealing the existence of corresponding dynamic modes intrinsic to the contact topology of the protein. The implications of these findings for the coupling of ATP hydrolysis to conformational changes in the transmembrane domains required for solute transport are discussed in light of recent whole transporter structures.

Received for publication, January 29, 2007 , and in revised form, April 30, 2007.

^* The costs of publication of this article were defrayed in part by the payment of page charges. This article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

¹ An Australian Wool Innovation Ltd. Postdoctoral Fellow.

² To whom correspondence should be addressed. Tel.: 612-9514-4158; Fax: 612-9514-8206; E-mail: tony.george{at}uts.edu.au.

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