Proline-rich antimicrobial peptides optimized for binding to Escherichia coli chaperone DnaK

Daniel Knappe, Tina Goldbach, Marcus P D Hatfield, Nicholas Y. Palermo, Stefanie Weinert, Norbert Strater, Ralf Hoffmann, Sándor Lovas

Research output: Contribution to journalArticle

8 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)1061-1071
Number of pages11
JournalProtein and Peptide Letters
Volume23
Issue number12
DOIs
StatePublished - Dec 1 2016

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Proline
Escherichia coli
Peptides
Protein Refolding
Fluorescence Polarization
Bacterial Proteins
Molecular modeling
Protein Transport
Ribosomes
Proteins
X-Rays
Substitution reactions
Crystal structure
Anti-Bacterial Agents
Ligands
Fluorescence
Polarization
Derivatives
X rays
Substrates

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biochemistry

Cite this

Proline-rich antimicrobial peptides optimized for binding to Escherichia coli chaperone DnaK. / Knappe, Daniel; Goldbach, Tina; Hatfield, Marcus P D; Palermo, Nicholas Y.; Weinert, Stefanie; Strater, Norbert; Hoffmann, Ralf; Lovas, Sándor.

In: Protein and Peptide Letters, Vol. 23, No. 12, 01.12.2016, p. 1061-1071.

Research output: Contribution to journalArticle

Knappe, D, Goldbach, T, Hatfield, MPD, Palermo, NY, Weinert, S, Strater, N, Hoffmann, R & Lovas, S 2016, 'Proline-rich antimicrobial peptides optimized for binding to Escherichia coli chaperone DnaK', Protein and Peptide Letters, vol. 23, no. 12, pp. 1061-1071. https://doi.org/10.2174/0929866523666160719124712
Knappe, Daniel ; Goldbach, Tina ; Hatfield, Marcus P D ; Palermo, Nicholas Y. ; Weinert, Stefanie ; Strater, Norbert ; Hoffmann, Ralf ; Lovas, Sándor. / Proline-rich antimicrobial peptides optimized for binding to Escherichia coli chaperone DnaK. In: Protein and Peptide Letters. 2016 ; Vol. 23, No. 12. pp. 1061-1071.
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