Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States

Dan Nguyen, Zoe A. Hoffpauir, Junji Iwahara

Research output: Contribution to journalArticle

8 Citations (Scopus)

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 <0.6 in the DNA-bound state. Interestingly, some of the interfacial cationic groups in the complex were more mobile than in the free protein. The retained or enhanced mobility of the Arg and Lys side chains in the complex should mitigate the overall loss of conformational entropy in the protein-DNA association and allow dynamic molecular recognition.

Original languageEnglish (US)
Pages (from-to)5866-5869
Number of pages4
JournalBiochemistry
Volume56
Issue number44
DOIs
StatePublished - Nov 7 2017

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DNA
Molecular recognition
Proteins
Thymine
Entropy
Magnetic Fields
Molecular Dynamics Simulation
Fruits
Diptera
Nuclear magnetic resonance spectroscopy
Hydrogen
Fruit
Hydrogen bonds
Magnetic Resonance Spectroscopy
Phosphates
Association reactions
Ions
Magnetic fields

ASJC Scopus subject areas

  • Biochemistry

Cite this

Internal Motions of Basic Side Chains of the Antennapedia Homeodomain in the Free and DNA-Bound States. / Nguyen, Dan; Hoffpauir, Zoe A.; Iwahara, Junji.

In: Biochemistry, Vol. 56, No. 44, 07.11.2017, p. 5866-5869.

Research output: Contribution to journalArticle

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