title: Inhibition of the ferric uptake regulator by peptides derived from anti-FUR peptide aptamers: coupled theoretical and experimental approaches.
abstract: The FUR protein (ferric uptake regulator) is an iron-dependent global transcriptional regulator. Specific to bacteria, FUR is an attractive antibacterial target since virulence is correlated to iron bioavailability. Recently, four anti-FUR peptide aptamers, composed of 13 amino acid variable loops inserted into a thioredoxinA scaffold, were identified, which were able to interact with Escherichia coli FUR (EcFUR), inhibit its binding to DNA and to decrease the virulence of pathogenic E. coli in a fly infection model. The first characterization of anti-FUR linear peptides (pF1 6 to 13 amino acids) derived from the variable part of the F1 anti-FUR peptide aptamer is described herein. Theoretical and experimental approaches, in original combination, were used to study interactions of these peptides with FUR in order to understand their mechanism of inhibition. After modeling EcFUR by homology, docking with Autodock was combined with molecular dynamics simulations in implicit solvent to take into account the flexibility of the partners. All calculations were cross-checked either with other programs or with experimental data. As a result, reliable structures of EcFUR and its complex with pF1 are given and an inhibition pocket formed by the groove between the two FUR subunits is proposed. The location of the pocket was validated through experimental mutation of key EcFUR residues at the site of proposed peptide interaction. Cyclisation of pF1, mimicking the peptide constraint in F1, improved inhibition. The details of the interactions between peptide and protein were analyzed and a mechanism of inhibition of these anti-FUR molecules is proposed.
authors.affiliation: CEA , Laboratoire de Chimie et Biologie des Métaux (LCBM), F-38000 Grenoble, France.
authors.forename: Cheickna
authors.initials: C
authors.lastname: Cissé
authors.forename: Sophie V
authors.initials: SV
authors.lastname: Mathieu
authors.forename: Mohamed B Ould
authors.initials: MB
authors.lastname: Abeih
authors.forename: Lindsey
authors.initials: L
authors.lastname: Flanagan
authors.forename: Sylvia
authors.initials: S
authors.lastname: Vitale
authors.forename: Patrice
authors.initials: P
authors.lastname: Catty
authors.forename: Didier
authors.initials: D
authors.lastname: Boturyn
authors.forename: Isabelle
authors.initials: I
authors.lastname: Michaud-Soret
authors.forename: Serge
authors.initials: S
authors.lastname: Crouzy
mesh_terms: D000595:Amino Acid Sequence; D023181:Antimicrobial Cationic Peptides / Q000138:chemical synthesis / Q000737:chemistry*; D052158:Aptamers, Peptide / Q000138:chemical synthesis / Q000737:chemistry*; D001426:Bacterial Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D004926:Escherichia coli / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015870:Gene Expression; D007501:Iron / Q000737:chemistry* / Q000378:metabolism; D007700:Kinetics; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D011485:Protein Binding; D017433:Protein Structure, Secondary; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013329:Structure-Activity Relationship; D013816:Thermodynamics; D013879:Thioredoxins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D023181:Antimicrobial Cationic Peptides; D052158:Aptamers, Peptide; D001426:Bacterial Proteins; D011994:Recombinant Proteins; D012097:Repressor Proteins; C068477:ferric uptake regulating proteins, bacterial; D013879:Thioredoxins; D007501:Iron