Communication Cite This: Biochemistry 2017, 56, 5866-5869
pubs.acs.org/biochemistry
Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States Dan Nguyen, Zoe A. Hoffpauir, and Junji Iwahara* Department of Biochemistry & Molecular Biology, Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, Texas 77555, United States S Supporting Information *
Arg side chains that directly interact with the DNA bases were found to lose substantial mobility upon binding. To examine whether or not these are general characteristics of basic side chains, other systems should also be studied. For this purpose, we study the dynamics of the basic side chains of the fruit fly Antennapedia (Antp) homeodomain in the free and DNA-bound states. The Antp homeodomain is comprised of 60 residues, 18 of which are basic side chains (12 Arg and 6 Lys residues) (Figure 1). This protein recognizes
ABSTRACT: Basic side chains play crucial roles in protein−DNA interactions. In this study, using NMR spectroscopy, we investigated the dynamics of Arg and Lys side chains of the fruit fly Antennapedia homeodomain in the free state and in the complex with target DNA. We measured 15N relaxation for Arg and Lys side chains at two magnetic fields, from which generalized order parameters for the cationic groups were determined. Mobility of the R5 side chain, which makes hydrogen bonds with a thymine base in the DNA minor groove, was greatly dampened. Several Lys and Arg side chains that form intermolecular ion pairs with DNA phosphates were found to retain high mobility with the order parameter being
