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Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies.

Liebscher M, Roujeinikova A
J Bacteriol 191 1456-62 (2009)
Related entries: 3dpo, 3dpq

Cited: 45 times
EuropePMC logo PMID: 19103929

Abstract

The molecular chaperone DnaK assists protein folding and refolding, translocation across membranes, and regulation of the heat shock response. In Escherichia coli, the protein is a target for insect-derived antimicrobial peptides, pyrrhocoricins. We present here the X-ray crystallographic analysis of the E. coli DnaK substrate-binding domain in complex with pyrrhocoricin-derived peptide inhibitors. The structures show that pyrrhocoricins act as site-specific, dual-mode (competitive and allosteric) inhibitors, occupying the substrate-binding tunnel and disrupting the latch between the lid and the beta-sandwich. Our structural analysis revealed an allosteric coupling between the movements of the lid and the interdomain linker, identifying a previously unknown mechanism of the lid-mediated regulation of the chaperone cycle.

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  2. Allosteric coupling between the lid and interdomain linker in DnaK revealed by inhibitor binding studies. Liebscher M, Roujeinikova A. J Bacteriol 191 1456-1462 (2009)
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Reviews citing this publication (5)

  1. Proline-rich antimicrobial peptides: converging to a non-lytic mechanism of action. Scocchi M, Tossi A, Gennaro R. Cell Mol Life Sci 68 2317-2330 (2011)
  2. HSPA5 Gene encoding Hsp70 chaperone BiP in the endoplasmic reticulum. Wang J, Lee J, Liem D, Ping P. Gene 618 14-23 (2017)
  3. Structural and functional analysis of the Hsp70/Hsp40 chaperone system. Liu Q, Liang C, Zhou L. Protein Sci 29 378-390 (2020)
  4. A History of Molecular Chaperone Structures in the Protein Data Bank. Bascos NAD, Landry SJ. Int J Mol Sci 20 E6195 (2019)
  5. The Link That Binds: The Linker of Hsp70 as a Helm of the Protein's Function. Chakafana G, Zininga T, Shonhai A. Biomolecules 9 E543 (2019)

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  3. Insect-derived proline-rich antimicrobial peptides kill bacteria by inhibiting bacterial protein translation at the 70S ribosome. Krizsan A, Volke D, Weinert S, Sträter N, Knappe D, Hoffmann R. Angew Chem Int Ed Engl 53 12236-12239 (2014)
  4. Close and Allosteric Opening of the Polypeptide-Binding Site in a Human Hsp70 Chaperone BiP. Yang J, Nune M, Zong Y, Zhou L, Liu Q. Structure 23 2191-2203 (2015)
  5. Structural studies on the forward and reverse binding modes of peptides to the chaperone DnaK. Zahn M, Berthold N, Kieslich B, Knappe D, Hoffmann R, Sträter N. J Mol Biol 425 2463-2479 (2013)
  6. Structural characterization of the substrate transfer mechanism in Hsp70/Hsp90 folding machinery mediated by Hop. Alvira S, Cuéllar J, Röhl A, Yamamoto S, Itoh H, Alfonso C, Rivas G, Buchner J, Valpuesta JM. Nat Commun 5 5484 (2014)
  7. Crystal structure of the stress-inducible human heat shock protein 70 substrate-binding domain in complex with peptide substrate. Zhang P, Leu JI, Murphy ME, George DL, Marmorstein R. PLoS One 9 e103518 (2014)
  8. Novel apidaecin 1b analogs with superior serum stabilities for treatment of infections by gram-negative pathogens. Berthold N, Czihal P, Fritsche S, Sauer U, Schiffer G, Knappe D, Alber G, Hoffmann R. Antimicrob Agents Chemother 57 402-409 (2013)
  9. ATPase subdomain IA is a mediator of interdomain allostery in Hsp70 molecular chaperones. General IJ, Liu Y, Blackburn ME, Mao W, Gierasch LM, Bahar I. PLoS Comput Biol 10 e1003624 (2014)
  10. The four hydrophobic residues on the Hsp70 inter-domain linker have two distinct roles. Kumar DP, Vorvis C, Sarbeng EB, Cabra Ledesma VC, Willis JE, Liu Q. J Mol Biol 411 1099-1113 (2011)
  11. Intracellular toxicity of proline-rich antimicrobial peptides shuttled into mammalian cells by the cell-penetrating peptide penetratin. Hansen A, Schäfer I, Knappe D, Seibel P, Hoffmann R. Antimicrob Agents Chemother 56 5194-5201 (2012)
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  13. Conformational selection in substrate recognition by Hsp70 chaperones. Marcinowski M, Rosam M, Seitz C, Elferich J, Behnke J, Bello C, Feige MJ, Becker CF, Antes I, Buchner J. J Mol Biol 425 466-474 (2013)
  14. BiPPred: Combined sequence- and structure-based prediction of peptide binding to the Hsp70 chaperone BiP. Schneider M, Rosam M, Glaser M, Patronov A, Shah H, Back KC, Daake MA, Buchner J, Antes I. Proteins 84 1390-1407 (2016)
  15. Targeting the interaction of AIMP2-DX2 with HSP70 suppresses cancer development. Lim S, Cho HY, Kim DG, Roh Y, Son SY, Mushtaq AU, Kim M, Bhattarai D, Sivaraman A, Lee Y, Lee J, Yang WS, Kim HK, Kim MH, Lee K, Jeon YH, Kim S. Nat Chem Biol 16 31-41 (2020)
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  17. Crystallographic and molecular dynamics analysis of loop motions unmasking the peptidoglycan-binding site in stator protein MotB of flagellar motor. Reboul CF, Andrews DA, Nahar MF, Buckle AM, Roujeinikova A. PLoS One 6 e18981 (2011)
  18. A Local Allosteric Network in Heat Shock Protein 70 (Hsp70) Links Inhibitor Binding to Enzyme Activity and Distal Protein-Protein Interactions. Rinaldi S, Assimon VA, Young ZT, Morra G, Shao H, Taylor IR, Gestwicki JE, Colombo G. ACS Chem Biol 13 3142-3152 (2018)
  19. Novel Entropically Driven Conformation-specific Interactions with Tomm34 Protein Modulate Hsp70 Protein Folding and ATPase Activities. Durech M, Trcka F, Man P, Blackburn EA, Hernychova L, Dvorakova P, Coufalova D, Kavan D, Vojtesek B, Muller P. Mol Cell Proteomics 15 1710-1727 (2016)
  20. Absence of in vitro innate immunomodulation by insect-derived short proline-rich antimicrobial peptides points to direct antibacterial action in vivo. Fritsche S, Knappe D, Berthold N, von Buttlar H, Hoffmann R, Alber G. J Pept Sci 18 599-608 (2012)
  21. Mechanism of Escherichia coli resistance to Pyrrhocoricin. Narayanan S, Modak JK, Ryan CS, Garcia-Bustos J, Davies JK, Roujeinikova A. Antimicrob Agents Chemother 58 2754-2762 (2014)
  22. Rational design of novel peptidic DnaK ligands. Liebscher M, Haupt K, Yu C, Jahreis G, Lücke C, Schiene-Fischer C. Chembiochem 11 1727-1737 (2010)
  23. Immunogenicity and pharmacokinetics of short, proline-rich antimicrobial peptides. Holfeld L, Herth N, Singer D, Hoffmann R, Knappe D. Future Med Chem 7 1581-1596 (2015)
  24. New conformational state of NHERF1-CXCR2 signaling complex captured by crystal lattice trapping. Jiang Y, Lu G, Trescott LR, Hou Y, Guan X, Wang S, Stamenkovich A, Brunzelle J, Sirinupong N, Li C, Yang Z. PLoS One 8 e81904 (2013)
  25. Structure-based design of HSPA5 inhibitors: from peptide to small molecule inhibitors. Huang M, Li Z, Li D, Walker S, Greenan C, Kennedy R. Bioorg Med Chem Lett 23 3044-3050 (2013)
  26. An unexpected second binding site for polypeptide substrates is essential for Hsp70 chaperone activity. Li H, Zhu H, Sarbeng EB, Liu Q, Tian X, Yang Y, Lyons C, Zhou L, Liu Q. J Biol Chem 295 584-596 (2020)
  27. Tracking the interplay between bound peptide and the lid domain of DnaK, using molecular dynamics. Azoulay I, Kucherenko N, Nachliel E, Gutman M, Azem A, Tsfadia Y. Int J Mol Sci 14 12675-12695 (2013)
  28. Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future. Nordquist EB, Clerico EM, Chen J, Gierasch LM. J Phys Chem B 126 6780-6791 (2022)
  29. Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones. Nordquist EB, English CA, Clerico EM, Sherman W, Gierasch LM, Chen J. PLoS Comput Biol 17 e1009567 (2021)
  30. Role of the loop L4,5 in allosteric regulation in mtHsp70s: in vivo significance of domain communication and its implications in protein translocation. Samaddar M, Goswami AV, Purushotham J, Hegde P, D'Silva P. Mol Biol Cell 25 2129-2142 (2014)


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