KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Bacterial and virus strains | ||
| Escherichia coli Mach1 | ThermoFisher | Cat# C862003 |
| Escherichia coli Rosetta2 (DE3) | Millipore Sigma/Novagen | Cat# 71400-3 |
| Escherichia coli Rosetta2 (DE3) pLysS | Millipore Sigma/Novagen | Cat# 71403-3 |
| Mycobacterium smegmatis wild-type (mc2155) | Glickman Lab (Memorial Sloan Kettering) | N/A |
| Mycobacterium smegmatis Δdnaj1 | Lupoli et al., 2016 | N/A |
| Mycobacterium smegmatis Δdnaj2 | Lupoli et al., 2016 | N/A |
| Mycobacterium smegmatis ΔdnaK | Fay & Glickman, 2014 | N/A |
| M. smegmatis ΔdnaK attB::Mtb dnaK | This work | N/A |
| Escherichia coli strains for protein overexpression, see Table S3 | Various | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Fmoc-protected natural amino acids | ChemImpex | N/A |
| Fmoc-L-Photo-Leu (Fmoc- photoLeu-OH) | Sigma-Aldrich | CAS: 1360651-24-6 |
| Fmoc-L-tert-leucine (Fmoc-Tle-OH) | ChemImpex | CAS: 132684-60-7 |
| Fmoc-L-cyclohexyl-glycine (Fmoc-Chg-OH) | ChemImpex | CAS: 161321-36-4 |
| Fmoc-L-β-alanine (Fmoc-β-Ala-OH/Fmoc-βA-OH) | ChemImpex | CAS: 35737-10-1 |
| Pyrazine-2-carboxylic acid (Pz) | Sigma-Aldrich | CAS: 98-97-5 |
| Fluorescein isothiocyanate isomer 1 (FL-NCS) | ChemImpex | CAS: 3326-32-7 |
| 4-Benzoylbenzoic Acid (4-BBA) | Sigma-Aldrich | CAS: 611-95-0 |
| Telaprevir | Cayman Chemical | CAS: 402957-28-2 |
| Simeprevir | Cayman Chemical | CAS: 1241946-89-3 |
| Boceprevir | Cayman Chemical | CAS: 394730-60-0 |
| Grazoprevir | Cayman Chemical | CAS: 1350514-68-9 |
| Velpatasvir | Cayman Chemical | CAS: 1377049-84-7 |
| Danoprevir | Celia Schiffer (UMass Medical School) | CAS: 850876-88-9 |
| Paritaprevir | Celia Schiffer (UMass Medical School) | CAS: 1216941-48-8 |
| 2-Cl-IB-MECA | Cayman Chemical | CAS: 163042-96-4 |
| AB-MECA | Cayman Chemical | CAS: 152918-26-8 |
| VER 155008 | Cayman Chemical | CAS: 1134156-31-2 |
| NH2-Asn-Arg-Leu-Leu-Leu-Thr-Gly-OH | Biomatik | N/A |
| FL-β-Ala-Asn-Arg-Leu-Leu-Leu-Thr-Gly-OH | This work | N/A |
| Pz-Chg-Tle-Pro-Leu-OH (1) | This work | N/A |
| Pz-Val-Val-Pro-Leu-OH (2) | This work | N/A |
| 4BB-Val-Val-Pro-Leu-OH (3) | This work | N/A |
| Pz-Chg-Tle-Pro-Leu-OMe (4) | This work | N/A |
| Pz-Val-Val-Pro-Leu-OMe (5) | This work | N/A |
| 4BB-Val-Val-Pro-Leu-OMe (6) | This work | N/A |
| Pz-Val-Val-Pro-photoLeu-OMe (7) | This work | N/A |
| Firefly Luciferase: QuantiLum Recombinant Luciferase | Promega | Cat# E1701 |
| Critical commercial assays | ||
| Luciferase Assay System | Promega | Cat# E1500 |
| ADP-Glo Kinase System | Promega | Cat# V6930 |
| Kinase-Glo Luminescent Kinase Assay | Promega | Cat# V6711 |
| Deposited data | ||
| Raw small molecule screening data from pilot and primary screens | This paper; OSF | https://osf.io/cmqxd/?view_only=a2e3d69e9d404bd598f9f6475b042a77 |
| Analysis of mass spectrometry data of proteolyzed DnaK crosslinked to probe | This paper; SI file | N/A |
| Mass spectrometry raw files of proteolyzed DnaK crosslinked to probe | MassIVE | https://massive.ucsd.edu; MassIVE ID: MSV000088127 |
| Oligonucleotides | ||
| Primers for cloning bacterial and human chaperones into overexpression vectors, see Table S1 | This paper | N/A |
| Primers for inserting mutations into DnaK, see Table S1 | This paper | N/A |
| Recombinant DNA | ||
| Plasmid: pETHisSUMO | Gift from Scott Gradia, University of California, Berkeley | Addgene Plasmid #29711 |
| Plasmid: pHYRS52: overexpression vector for Ulp1 | Gift from Hideo Iwai, University of Helsinki; Muona, M. et al. 2008 | Addgene Plasmid #31122 |
| Plasmid: pET-47b(+) | Millipore Sigma/Novagen | Cat# 71461-3 |
| Plasmid: pcDNA5/FRT/TO HIS HSPA8: contains gene encoding Hsc70 | Gift from Harm Kampinga, University of Groningen; Hageman, J. et al. 2009 | Addgene Plasmid #19541 |
| Plasmid: pcDNA5/FRT/TO DNAJA2: contains gene encoding DnaJA2 | Gift from Harm Kampinga, University of Groningen; Hageman, J. et al. 2009 | Addgene Plasmid #19465 |
| Plasmid: pAJF465: M. tuberculosis dnaK expression in mycobacteria | This work | N/A |
| Plasmids for overexpression of bacterial and human chaperones and mutants in E. coli, see Table S2 | This work | N/A |
| Software and algorithms | ||
| Prism 9 | Mathpad | https://www.graphpad.com/scientific-software/prism/ |
| AFFINImeter | AFFINImeter | https://www.affinimeter.com/site/ |
| Chromeleon 7 | ThermoFisher Scientific | https://www.thermofisher.com/order/catalog/product/CHROMELEON7#/CHROMELEON7 |
| PyMOL 2.0 | Schrodinger | https://www.schrodinger.com/products/pymol |
| Image Lab | Biorad | https://www.bio-rad.com/en-us/product/image-lab-software?ID=KRE6P5E8Z |
| Byonic | Protein Metrics | https://proteinmetrics.com/resources/byonic-advanced-peptide-and-protein-identification-software/ |
| Other | ||
| Compound libraries used for small molecule screens | Various sources; assembled by The Rockefeller University High Throughput and Spectroscopy Center | https://www.rockefeller.edu/htsrc/libraries/ |