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Nucleic Acids Research 2006 34(2):472-484; doi:10.1093/nar/gkj442
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Published online 24 January 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Article

Complex interactions of HIV-1 nucleocapsid protein with oligonucleotides

Robert J. Fisher*, Matthew J. Fivash1, Andrew G. Stephen, Nathan A. Hagan2, Shilpa R. Shenoy3, Maxine V. Medaglia, Lindsey R. Smith, Karen M. Worthy, John T. Simpson, Robert Shoemaker4, Karen L. McNitt1, Donald G. Johnson5, Catherine V. Hixson5, Robert J. Gorelick5, Daniele Fabris2, Louis E. Henderson5 and Alan Rein6

Protein Chemistry Laboratory, SAIC-Frederick, Inc. NCI Frederick, Frederick, MD 21702, USA 1Data Management Services, Inc. NCI Frederick, Frederick, MD 21702, USA 2Department of Chemistry and Biochemistry, University of Maryland Baltimore County Baltimore, MD 21250, USA 3Molecular Targets Development Program, Basic Research Program, SAIC-Frederick, Inc. NCI Frederick, Frederick, MD 21702, USA 4Screening Technologies Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis NCI Frederick, Frederick, MD 21702, USA 5AIDS Vaccine Program, SAIC-Frederick, Inc. NCI Frederick, Frederick, MD 21702, USA 6HIV Drug Resistance Program, National Cancer Institute at Frederick Frederick, MD 21702, USA

*To whom correspondence should be addressed. Tel: +1 301 846 5154; Fax: +1 301 846 7392; Email: fisher{at}ncifcrf.gov

Received October 7, 2005. Revised December 23, 2005. Accepted December 23, 2005.

The HIV-1 nucleocapsid (NC) protein is a small, basic protein containing two retroviral zinc fingers. It is a highly active nucleic acid chaperone; because of this activity, it plays a crucial role in virus replication as a cofactor during reverse transcription, and is probably important in other steps of the replication cycle as well. We previously reported that NC binds with high-affinity to the repeating sequence d(TG)n. We have now analyzed the interaction between NC and d(TG)4 in considerable detail, using surface plasmon resonance (SPR), tryptophan fluorescence quenching (TFQ), fluorescence anisotropy (FA), isothermal titration calorimetry (ITC) and electrospray ionization Fourier transform mass spectrometry (ESI-FTMS). Our results show that the interactions between these two molecules are surprisngly complex: while the Kd for binding of a single d(TG)4 molecule to NC is only ~5 nM in 150 mM NaCl, a single NC molecule is capable of interacting with more than one d(TG)4 molecule, and conversely, more than one NC molecule can bind to a single d(TG)4 molecule. The strengths of these additional binding reactions are quantitated. The implications of this multivalency for the functions of NC in virus replication are discussed.


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