Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones
- PMID: 34735438
- PMCID: PMC8604352
- DOI: 10.1371/journal.pcbi.1009567
Physics-based modeling provides predictive understanding of selectively promiscuous substrate binding by Hsp70 chaperones
Abstract
To help cells cope with protein misfolding and aggregation, Hsp70 molecular chaperones selectively bind a variety of sequences ("selective promiscuity"). Statistical analyses from substrate-derived peptide arrays reveal that DnaK, the E. coli Hsp70, binds to sequences containing three to five branched hydrophobic residues, although otherwise the specific amino acids can vary considerably. Several high-resolution structures of the substrate -binding domain (SBD) of DnaK bound to peptides reveal a highly conserved configuration of the bound substrate and further suggest that the substrate-binding cleft consists of five largely independent sites for interaction with five consecutive substrate residues. Importantly, both substrate backbone orientations (N- to C- and C- to N-) allow essentially the same backbone hydrogen-bonding and side-chain interactions with the chaperone. In order to rationalize these observations, we performed atomistic molecular dynamics simulations to sample the interactions of all 20 amino acid side chains in each of the five sites of the chaperone in the context of the conserved substrate backbone configurations. The resulting interaction energetics provide the basis set for deriving a predictive model that we call Paladin (Physics-based model of DnaK-Substrate Binding). Trained using available peptide array data, Paladin can distinguish binders and nonbinders of DnaK with accuracy comparable to existing predictors and further predicts the detailed configuration of the bound sequence. Tested using existing DnaK-peptide structures, Paladin correctly predicted the binding register in 10 out of 13 substrate sequences that bind in the N- to C- orientation, and the binding orientation in 16 out of 22 sequences. The physical basis of the Paladin model provides insight into the origins of how Hsp70s bind substrates with a balance of selectivity and promiscuity. The approach described here can be extended to other Hsp70s where extensive peptide array data is not available.
Conflict of interest statement
The authors have declared that no competing interests exist.
Figures
Similar articles
-
Selective promiscuity in the binding of E. coli Hsp70 to an unfolded protein.Proc Natl Acad Sci U S A. 2021 Oct 12;118(41):e2016962118. doi: 10.1073/pnas.2016962118. Proc Natl Acad Sci U S A. 2021. PMID: 34625496 Free PMC article.
-
Structural studies on the forward and reverse binding modes of peptides to the chaperone DnaK.J Mol Biol. 2013 Jul 24;425(14):2463-79. doi: 10.1016/j.jmb.2013.03.041. Epub 2013 Apr 2. J Mol Biol. 2013. PMID: 23562829
-
Sequence-dependent peptide binding orientation by the molecular chaperone DnaK.Biochemistry. 2005 Sep 20;44(37):12307-15. doi: 10.1021/bi051145r. Biochemistry. 2005. PMID: 16156644
-
Molecular basis for interactions of the DnaK chaperone with substrates.Biol Chem. 2000 Sep-Oct;381(9-10):877-85. doi: 10.1515/BC.2000.109. Biol Chem. 2000. PMID: 11076019 Review.
-
Interaction of Hsp70 chaperones with substrates.Nat Struct Biol. 1997 May;4(5):342-9. doi: 10.1038/nsb0597-342. Nat Struct Biol. 1997. PMID: 9145101 Review.
Cited by
-
HSP70-binding motifs function as protein quality control degrons.Cell Mol Life Sci. 2023 Jan 7;80(1):32. doi: 10.1007/s00018-022-04679-3. Cell Mol Life Sci. 2023. PMID: 36609589 Free PMC article.
-
Distribution and solvent exposure of Hsp70 chaperone binding sites across the Escherichia coli proteome.Proteins. 2023 May;91(5):665-678. doi: 10.1002/prot.26456. Epub 2023 Jan 1. Proteins. 2023. PMID: 36539330 Free PMC article.
-
Computationally-Aided Modeling of Hsp70-Client Interactions: Past, Present, and Future.J Phys Chem B. 2022 Sep 15;126(36):6780-6791. doi: 10.1021/acs.jpcb.2c03806. Epub 2022 Aug 30. J Phys Chem B. 2022. PMID: 36040440 Free PMC article.
-
Multivalent protein-protein interactions are pivotal regulators of eukaryotic Hsp70 complexes.Cell Stress Chaperones. 2022 Jul;27(4):397-415. doi: 10.1007/s12192-022-01281-1. Epub 2022 Jun 7. Cell Stress Chaperones. 2022. PMID: 35670950 Free PMC article. Review.
References
Publication types
MeSH terms
Substances
Grants and funding
LinkOut - more resources
Full Text Sources
Molecular Biology Databases
Miscellaneous