title: Proline-rich Antimicrobial Peptides Optimized for Binding to Escherichia coli Chaperone DnaK.
abstract: The bacterial protein DnaK promotes folding of newly synthesized polypeptide chains, refolding of misfolded proteins, and protein trafficking. Assisted refolding is especially important under stress conditions induced by antibiotic therapies reducing the desired bactericidal effects. DnaK is supposedly targeted by proline-rich antimicrobial peptides (PrAMPs), but Escherichia coli ΔdnaK mutants and wild type strains are equally susceptible indicating further intracellular targets, such as the 70S ribosome. Crystal structures of PrAMPDnaK- complexes revealed forward and reverse binding modes at the substrate binding domain. Here, we used these ligand-target structures for the first time to rationally optimize peptides using molecular modeling and docking leading to the prediction of four-residue long sequences for improved binding to DnaK. When these sequences were used to replace the original sequence stretch in Onc72, most peptides showed significantly reduced dissociation constants (Kd) determined by fluorescence polarization. In a second approach, the X-ray structures of Api88 and Onc72 bound to DnaK were examined to predict substitutions prone to stronger interactions. Among the 36 peptides obtained from both approaches, six derivatives bound to DnaK with more than 10-fold higher affinities (Kd values in the low micromolar to nanomolar range). Peptides binding stronger to DnaK showed the same minimal inhibitory concentrations against wild type E. coli as the original peptide, but were slightly less active for ΔdnaK mutants. However, one peptide was able to overcome the resistance in an E. coli mutant lacking the SbmA transporter obligatory for the uptake of PrAMPs including Api88 and Onc72. Thus, it´s tempting to speculate that DnaK might be involved in the translocation of PrAMPs into E. coli.
authors.affiliation: Institute für Bioanalytische Chemie, Biotechnologisch-Biomedizinisches Zentrum, Universität Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany. bioanaly@bbz.uni-leipzig.de.
authors.forename: Daniel
authors.initials: D
authors.lastname: Knappe
authors.forename: Tina
authors.initials: T
authors.lastname: Goldbach
authors.forename: Marcus P D
authors.initials: MP
authors.lastname: Hatfield
authors.forename: Nicholas Y
authors.initials: NY
authors.lastname: Palermo
authors.forename: Stefanie
authors.initials: S
authors.lastname: Weinert
authors.forename: Norbert
authors.initials: N
authors.lastname: Sträter
authors.forename: Ralf
authors.initials: R
authors.lastname: Hoffmann
authors.affiliation: Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA. slovas@creighton.edu.
authors.forename: Sándor
authors.initials: S
authors.lastname: Lovas
mesh_terms: D000900:Anti-Bacterial Agents / Q000378:metabolism*; D023181:Antimicrobial Cationic Peptides / Q000737:chemistry / Q000378:metabolism*; D001665:Binding Sites; D004926:Escherichia coli / Q000187:drug effects* / Q000235:genetics / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics / Q000378:metabolism*; D018840:HSP70 Heat-Shock Proteins / Q000235:genetics / Q000378:metabolism*; D007711:Klebsiella pneumoniae / Q000187:drug effects; D026901:Membrane Transport Proteins / Q000235:genetics; D018832:Molecular Chaperones / Q000378:metabolism*; D062105:Molecular Docking Simulation; D011485:Protein Binding; D058849:Protein Refolding; D017434:Protein Structure, Tertiary; D021381:Protein Transport
chemical_list: D000900:Anti-Bacterial Agents; D023181:Antimicrobial Cationic Peptides; D029968:Escherichia coli Proteins; D018840:HSP70 Heat-Shock Proteins; D026901:Membrane Transport Proteins; D018832:Molecular Chaperones; C529573:SbmA protein, E coli; C061361:apidaecin; C063842:dnaK protein, E coli