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Originally published In Press as doi:10.1074/jbc.M203172200 on May 25, 2002

J. Biol. Chem., Vol. 277, Issue 34, 30968-30975, August 23, 2002
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Rapid Mapping of Protein Structure, Interactions, and Ligand Binding by Misincorporation Proton-Alkyl Exchange*

Joshua A. SilvermanDagger and Pehr B. Harbury§

From the Department of Biochemistry, Stanford University, Stanford, California 94305

Understanding protein conformation, interactions, and ligand binding is essential to all biological inquiry. We report a novel biochemical technique, called misincorporation proton-alkyl exchange (MPAX), that can be used to footprint protein structure at single amino acid resolution. MPAX exploits translational misincorporation of cysteine residues to generate probes for physical analysis. We apply MPAX to the triosephosphate isomerase (beta /alpha )8 barrel, accurately determining its substrate-binding site, a protein-protein interaction surface, the solvent-accessible protein surface, and the stability of the barrel. Because MPAX requires only microgram quantities of material and is not limited by protein size, it is ideally suited for proteins not amenable to conventional structural methods, such as membrane proteins, partially folded or insoluble proteins, and large protein complexes.

* This work was supported by a grant from the Chicago Community Trust (to P. B. H.) and a Terman fellowship (to P. B. H.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.

Dagger Supported by the Paul and Mildred Berg Stanford Graduate Fellowship.

§ To whom correspondence should be addressed: Dept. of Biochemistry, Stanford University, 279 Campus Dr. W., Stanford, CA 94305. E-mail: harbury@cmgm.stanford.edu.

Copyright © 2002 by The American Society for Biochemistry and Molecular Biology, Inc.


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