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An unusual helix turn helix motif in the catalytic core of HIV-1 integrase binds viral DNA and LEDGF.

Merad H, Porumb H, Zargarian L, René B, Hobaika Z, Maroun RG, Mauffret O, Fermandjian S - PLoS ONE (2009)

Bottom Line: In our motif, in contrast to the conventional HTH (helix-turn-helix), it is the N terminal helix (alpha(4)) which has the role of DNA recognition helix, while the C terminal helix (alpha(5)) would rather contribute to the motif stabilization by interactions with the alpha(4) helix.The motif, termed HTHi (i, for inverted) emerges as a central piece of the IN structure and function.It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.

View Article: PubMed Central - PubMed

Affiliation: LBPA, CNRS (UMR 8113)-Ecole Normale Supérieure de Cachan, Cachan, France.

ABSTRACT

Background: Integrase (IN) of the type 1 human immunodeficiency virus (HIV-1) catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149-186) in the crystal structure of the catalytic core (CC) of the IN-Phe185Lys variant that consists of the alpha(4) and alpha(5) helices connected by a 3 to 5-residue turn. The motif is embedded in a large array of interactions that stabilize the monomer and the dimer.

Principal findings: We describe the conformational and binding properties of the corresponding synthetic peptide. This displays features of the protein motif structure thanks to the mutual intramolecular interactions of the alpha(4) and alpha(5) helices that maintain the fold. The main properties are the binding to: 1- the processing-attachment site at the LTR (long terminal repeat) ends of virus DNA with a K(d) (dissociation constant) in the sub-micromolar range; 2- the whole IN enzyme; and 3- the IN binding domain (IBD) but not the IBD-Asp366Asn variant of LEDGF (lens epidermal derived growth factor) lacking the essential Asp366 residue. In our motif, in contrast to the conventional HTH (helix-turn-helix), it is the N terminal helix (alpha(4)) which has the role of DNA recognition helix, while the C terminal helix (alpha(5)) would rather contribute to the motif stabilization by interactions with the alpha(4) helix.

Conclusion: The motif, termed HTHi (i, for inverted) emerges as a central piece of the IN structure and function. It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.

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Related in: MedlinePlus

Secondary structure predictions.Results provided by: a). Agadir [64] and b). GOR IV [63] for the helical propensities of HTHi (blue), α4 (green) and INH5 (orange). The predictions with Agadir were performed at pH 7, at a temperature of 25°C.
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pone-0004081-g002: Secondary structure predictions.Results provided by: a). Agadir [64] and b). GOR IV [63] for the helical propensities of HTHi (blue), α4 (green) and INH5 (orange). The predictions with Agadir were performed at pH 7, at a temperature of 25°C.

Mentions: The comparison of the GOR IV [63] and AGADIR [64] predictions strongly suggest that long distance interactions–like those stabilizing the protein tertiary structures–are needed besides the short distance interactions in order to keep the helix secondary structure in the HTHi motif (Fig. 2). Examination of the reported crystal structures shows that long range interactions occur in great number inside the HTHi motif itself i.e., between the α4 and the α5 helices (there are 16 such interactions, listed in Table 2), but also between the HTHi motif and other components of the protein (for example, there are 16 interactions between HTHi and the neighboring β-sheet–Table 2). Accordingly, a loss of helicity could be feared upon isolation of the motif from the protein context.


An unusual helix turn helix motif in the catalytic core of HIV-1 integrase binds viral DNA and LEDGF.

Merad H, Porumb H, Zargarian L, René B, Hobaika Z, Maroun RG, Mauffret O, Fermandjian S - PLoS ONE (2009)

Secondary structure predictions.Results provided by: a). Agadir [64] and b). GOR IV [63] for the helical propensities of HTHi (blue), α4 (green) and INH5 (orange). The predictions with Agadir were performed at pH 7, at a temperature of 25°C.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2607020&req=5

pone-0004081-g002: Secondary structure predictions.Results provided by: a). Agadir [64] and b). GOR IV [63] for the helical propensities of HTHi (blue), α4 (green) and INH5 (orange). The predictions with Agadir were performed at pH 7, at a temperature of 25°C.
Mentions: The comparison of the GOR IV [63] and AGADIR [64] predictions strongly suggest that long distance interactions–like those stabilizing the protein tertiary structures–are needed besides the short distance interactions in order to keep the helix secondary structure in the HTHi motif (Fig. 2). Examination of the reported crystal structures shows that long range interactions occur in great number inside the HTHi motif itself i.e., between the α4 and the α5 helices (there are 16 such interactions, listed in Table 2), but also between the HTHi motif and other components of the protein (for example, there are 16 interactions between HTHi and the neighboring β-sheet–Table 2). Accordingly, a loss of helicity could be feared upon isolation of the motif from the protein context.

Bottom Line: In our motif, in contrast to the conventional HTH (helix-turn-helix), it is the N terminal helix (alpha(4)) which has the role of DNA recognition helix, while the C terminal helix (alpha(5)) would rather contribute to the motif stabilization by interactions with the alpha(4) helix.The motif, termed HTHi (i, for inverted) emerges as a central piece of the IN structure and function.It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.

View Article: PubMed Central - PubMed

Affiliation: LBPA, CNRS (UMR 8113)-Ecole Normale Supérieure de Cachan, Cachan, France.

ABSTRACT

Background: Integrase (IN) of the type 1 human immunodeficiency virus (HIV-1) catalyzes the integration of viral DNA into host cellular DNA. We identified a bi-helix motif (residues 149-186) in the crystal structure of the catalytic core (CC) of the IN-Phe185Lys variant that consists of the alpha(4) and alpha(5) helices connected by a 3 to 5-residue turn. The motif is embedded in a large array of interactions that stabilize the monomer and the dimer.

Principal findings: We describe the conformational and binding properties of the corresponding synthetic peptide. This displays features of the protein motif structure thanks to the mutual intramolecular interactions of the alpha(4) and alpha(5) helices that maintain the fold. The main properties are the binding to: 1- the processing-attachment site at the LTR (long terminal repeat) ends of virus DNA with a K(d) (dissociation constant) in the sub-micromolar range; 2- the whole IN enzyme; and 3- the IN binding domain (IBD) but not the IBD-Asp366Asn variant of LEDGF (lens epidermal derived growth factor) lacking the essential Asp366 residue. In our motif, in contrast to the conventional HTH (helix-turn-helix), it is the N terminal helix (alpha(4)) which has the role of DNA recognition helix, while the C terminal helix (alpha(5)) would rather contribute to the motif stabilization by interactions with the alpha(4) helix.

Conclusion: The motif, termed HTHi (i, for inverted) emerges as a central piece of the IN structure and function. It could therefore represent an attractive target in the search for inhibitors working at the DNA-IN, IN-IN and IN-LEDGF interfaces.

Show MeSH
Related in: MedlinePlus