Important note: Information in this article was accurate in 2000. The state of the art may have changed since the publication date.
Mechanism of neomycin and Rev peptide binding to the Rev responsive element of HIV-1 as determined by fluorescence and NMR spectroscopy.
Biochemistry. 2000 May 16;39(19):5630-41. Unique Identifier : AIDSLINE MED/20263481 Lacourciere KA; Stivers JT; Marino JP; Center for Advanced Research in Biotechnology, University of; Maryland and National Institute for Standards and Technology,; 9600 Gudelsky Drive, Rockville, Maryland 20850, USA.
Abstract:
Rev is an essential HIV-1 regulatory protein that binds the Rev responsive element (RRE) within the env gene of the HIV-1 RNA genome and is involved in transport of unspliced or partially spliced viral mRNA from the cell nucleus to the cytoplasm. Previous studies have shown that a short alpha-helical peptide derived from Rev (Rev 34-50), and a truncated form of the RRE sequence provide a useful in vitro system to study this interaction while still preserving the essential aspects of the native complex. We have selectively incorporated the fluorescent probe 2-aminopurine 2'-O-methylriboside (2-AP) into the RRE sequence in nonperturbing positions (A68 and U72) such that the binding of both Rev peptide and aminoglycoside ligands could be characterized directly by fluorescence methods. Rev peptide binding to the RRE-72AP variant resulted in a 2-fold fluorescence increase that provided a useful signal to monitor this binding interaction (K(D) = 20 +/- 7 nM). Using stopped-flow kinetic measurements, we have shown that specific Rev peptide binding occurs by a two-step process involving diffusion-controlled encounter, followed by isomerization of the RNA. Using the RRE-68AP and -72AP constructs, three classes of binding sites for the aminoglycoside neomycin were unambiguously detected. The first site is noninhibitory to Rev binding (K(D) = 0.24 +/- 0.040 microM), the second site inhibited Rev binding in a competitive fashion (K(D) = 1. 8 +/- 0.8 microM), and the third much weaker site (or sites) is attributed to nonspecific binding (K(D) >/= 40 microM). Complementary NMR measurements have shown that neomycin forms both a specific binary complex with RRE and a specific ternary complex with RRE and Rev. NMR data further suggest that neomycin occupies a similar high-affinity binding site in both the binary and ternary complexes, and that this site is located in the lower stem region of RRE.
Keywords: JOURNAL ARTICLE Amino Acid Sequence Antibiotics, Aminoglycoside/METABOLISM Binding, Competitive/GENETICS Framycetin/*METABOLISM Gene Products, rev/ANTAGONISTS & INHIB/*GENETICS/*METABOLISM HIV-1/*GENETICS/*METABOLISM Kinetics Molecular Sequence Data Nuclear Magnetic Resonance, Biomolecular Peptide Fragments/ANTAGONISTS & INHIB/GENETICS/*METABOLISM Protein Binding/GENETICS *Response Elements Spectrometry, Fluorescence Support, Non-U.S. Gov't Support, U.S. Gov't, P.H.S. Thermodynamics 2-Aminopurine/CHEMISTRY
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Important note: Information in this article was accurate in 2000. The state of the art may have changed since the publication date.
