2M3Z

NMR solution structure of HIV-1 nucleocapsid protein in complex with an inhibitor displaying a 2 inhibitors:1 NC stoichiometry

Summary for 2M3Z

• Entry DOI: 10.2210/pdb2m3z/pdb
• Related: 1A1T 1F6U
• NMR Information: BMRB: 18980
• Descriptor: NUCLEOCAPSID PROTEIN P7, ZINC ION, (3E)-3-{(2Z)-[(5Z)-5-(furan-2-ylmethylidene)-4-oxo-1,3-thiazolidin-2-ylidene]hydrazinylidene}-2-oxo-2,3-dihydro-1H-indole-5-sulfonic acid (3 entities in total)
• Functional Keywords: hiv-1 nc, viral protein
• Biological source: Human immunodeficiency virus type 1 (HIV-1)
• Cellular location: Matrix protein p17: Virion (Potential). Capsid protein p24: Virion (Potential). Nucleocapsid protein p7: Virion (Potential). Reverse transcriptase/ribonuclease H: Virion (Potential). Integrase: Virion (Potential): P12497
• Total number of polymer chains: 1
• Total formula weight: 7336.08

Authors

Goudreau, N.,Hucke, O. (deposition date: 2013-01-28, release date: 2013-02-27, Last modification date: 2024-05-15)

Primary citation

Goudreau, N.,Hucke, O.,Faucher, A.M.,Grand-Maitre, C.,Lepage, O.,Bonneau, P.R.,Mason, S.W.,Titolo, S.
Discovery and Structural Characterization of a New Inhibitor Series of HIV-1 Nucleocapsid Function: NMR Solution Structure Determination of a Ternary Complex Involving a 2:1 Inhibitor/NC Stoichiometry.
J.Mol.Biol., 425:1982-1998, 2013

PubMed Abstract: The nucleocapsid (NC) protein is an essential factor with multiple functions within the human immunodeficiency virus type 1 (HIV-1) replication cycle. In this study, we describe the discovery of a novel series of inhibitors that targets HIV-1 NC protein by blocking its interaction with nucleic acids. This series was identified using a previously described capsid (CA) assembly assay, employing a recombinant HIV-1 CA-NC protein and immobilized TG-rich deoxyoligonucleotides. Using visible absorption spectroscopy, we were able to demonstrate that this new inhibitor series binds specifically and reversibly to the NC with a peculiar 2:1 stoichiometry. A fluorescence-polarization-based binding assay was also developed in order to monitor the inhibitory activities of this series of inhibitors. To better characterize the structural aspect of inhibitor binding onto NC, we performed NMR studies using unlabeled and (13)C,(15)N-double-labeled NC(1-55) protein constructs. This allowed the determination of the solution structure of a ternary complex characterized by two inhibitor molecules binding to the two zinc knuckles of the NC protein. To the best of our knowledge, this represents the first report of a high-resolution structure of a small-molecule inhibitor bound to NC, demonstrating sub-micromolar potency and moderate antiviral potency with one analogue of the series. This structure was compared with available NC/oligonucleotide complex structures and further underlined the high flexibility of the NC protein, allowing it to adopt many conformations in order to bind its different oligonucleotide/nucleomimetic targets. In addition, analysis of the interaction details between the inhibitor molecules and NC demonstrated how this novel inhibitor series is mimicking the guanosine nucleobases found in many reported complex structures.

PubMed: 23485336
DOI: 10.1016/j.jmb.2013.02.022

Experimental method

SOLUTION NMR