| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Peroxidase Anti-peroxidase Soluble Complex antibody produced in rabbit | Sigma | Cat: P1291; RRID: AB_1079562 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Trifluoroacetic acid UHPLC-MS (Optigrade) | LGC | Cat# SO-9668-B001 |
| Water for LC-MS (Optigrade) | LGC | Cat# SO-9368-B025 |
| Acetonitrile for LC-MS (Optigrade) | LGC | Cat# SO-9340-B025 |
| Formic Acid | Thermo-Fisher Scientific | Cat# F-1850-PB08 |
| WT: VQLKRPASVLALNDL | AQUA peptide from Sigma | Custom synthesis |
| L-5: VQDKRPASVLALNDL) | AQUA peptide from Sigma | Custom synthesis |
| L+4: VQLKRPASVLAANDL | AQUA peptide from Sigma | Custom synthesis |
| WT: GRPRAASFAEK | AQUA peptide from Sigma | Custom synthesis |
| E-3: GGPEAASFAEK | AQUA peptide from Sigma | Custom synthesis |
| E-5: GEPGAASFAEK | AQUA peptide from Sigma | Custom synthesis |
| E-3 E-5: GEPEAASFAEK | AQUA peptide from Sigma | Custom synthesis |
| Deposited Data | ||
| Kinase co-crystal structures | Mir et al., 2018 | https://www.ebi.ac.uk/pdbe/node/1 |
| PKA-peptide complex | Zheng et al., 1993 | PDB: 1ATP |
| DYRK1A-peptide complex | Soundararajan et al., 2013 | PDB: 2WO6 |
| MARK2-cagA complex | Nesić et al., 2010 | PDB: 3IEC |
| Kinase-substrate relationships (PSP) | Hornbeck et al., 2015 | https://www.phosphosite.org/homeAction |
| Kinase-substrate relationships (Phospho.ELM) | Dinkel et al., 2011 | http://phospho.elm.eu.org/ |
| Kinase-substrate relationships (HPRD) | Prasad et al., 2009 | https://hprd.org/ |
| Kinase-substrate relationships (BioGRID) | Sadowski et al., 2013 | https://thebiogrid.org/ |
| Kinase domain HMM | El-Gebali et al., 2019 | https://pfam.xfam.org/ |
| Kinase substrates for benchmarking | Sugiyama et al., 2019 | PMID: 31324866 |
| Peptide library PWMs (yeast) | Mok et al., 2010 | PMID: 20159853 |
| Kinase orthologs | Kersey et al., 2016 | https://ensemblgenomes.org/ |
| Cancer genome data | The Cancer Genome Atlas (TCGA) | https://www.cancer.gov/about-nci/organization/ccg/research/structural-genomics/tcga |
| Representative proteomes (rp35) | Chen et al., 2011 | https://proteininformationresource.org/rps/ |
| Kinase families | Manning et al., 2002 | http://kinase.com/web/current/ |
| Sequence-structure mappings | Velankar et al., 2013 | https://www.ebi.ac.uk/pdbe/docs/sifts/quick.html |
| Experimental Models: Organisms/Strains | ||
| Saccharomyces cerevisiae: SNF1 KO. Yeast strain used to construct SNF1 point mutants. (BY4741 MATa SNF1 KO) | From Yeast KO collection. A gift from Lars Steinmetz Lab (EMBL) | This paper |
| Saccharomyces cerevisiae: SNF1 WT (BY4741 MATa SNF1 KO + [pGAL-SNF1-URA3 plasmid]) | This paper (PBY362) | This paper (PBY362) |
| Saccharomyces cerevisiae: SNF1 A218L (BY4741 MATa SNF1 KO + [pGAL-SNF1A218L-URA3 plasmid]) | This paper (PBY363) | This paper (PBY363) |
| Saccharomyces cerevisiae: SNF1 V244R (BY4741 MATa SNF1 KO + [pGAL-SNF1V244R-URA3 plasmid]) | This paper (PBY364) | This paper (PBY364) |
| Saccharomyces cerevisiae: YPK1 WT (BY4741 MATa YPK1 KO) | From Yeast KO collection. A gift from Lars Steinmetz Lab (EMBL) | This paper |
| Saccharomyces cerevisiae: YPK1 F433H-Q510G (BY4741 MATa + [YPK1F433H-Q510G-TAP-HIS]) | This paper (PBY929) | This paper (PBY929) |
| Saccharomyces cerevisiae: YPK1 F433K-Q510G-E537R (BY4741 MATa + [YPK1F433K-Q510G-E537R-TAP-HIS]) | This paper (PBY1229) | This paper (PBY1229) |
| Oligonucleotides | ||
| Primers to mutate SNF1, see Table S6 | This paper | N/A |
| Primers to mutate YPK1, see Table S6 | This paper | N/A |
| Software and Algorithms | ||
| CD-HIT | Li and Godzik, 2006 | http://weizhongli-lab.org/cd-hit/ |
| APCluster (R package) | Bodenhofer et al., 2011 | https://cran.r-project.org/web/packages/apcluster/index.html |
| GroupSim | Capra and Singh, 2008 | https://compbio.cs.princeton.edu/specificity/ |
| SPEER | Chakrabarti et al., 2007 | http://www.hpppi.iicb.res.in/ss/index.html |
| MultiRelief-3D | Ye et al., 2008 | https://www.ibi.vu.nl/programs/multirelief/ |
| MAFFT L-INS-i | Katoh et al., 2005 | https://mafft.cbrc.jp/alignment/software/ |
| trimAl | Capella-Gutierrez et al., 2009 | http://trimal.cgenomics.org/publications |
| hmmsearch | Eddy, 1998 | https://www.ebi.ac.uk/Tools/hmmer/search/hmmsearch |
| Bio3D (R package) | Skjærven et al., 2016 | http://thegrantlab.org/bio3d/ |
| PDBsum | de Beer et al., 2014 | https://www.ebi.ac.uk/thornton-srv/databases/pdbsum/ |
| NAMD | (Phillips et al., 2005) | https://www.ks.uiuc.edu/Research/namd/ |
| RAxML | Stamatakis, 2014 | https://cme.h-its.org/exelixis/web/software/raxml/ |
| FastML | Ashkenazy et al., 2012 | http://fastml.tau.ac.il/overview.php |
| Xcalibur | Thermo Fisher Scientific | https://www.thermofisher.com/search/results?query=xcalibur%E2%84%A2&navId=12141&persona=Catalog |
| Custom code | This paper | https://github.com/DBradley27/kinase_SDR |
| Other | ||
| EASY-Spray source | Thermo Fisher Scientific | ES801 |
| μ-pre-column: PEPMAP100 C18 5μM 0.3X5MM 5/PK | Thermo Fisher Scientific | 160454 |
| analytical column: EASY-SPRAY RSLC C18 2μM, 50CM X 75μM | Thermo Fisher Scientific | ES803 |
Official websites use .gov
A
.gov website belongs to an official
government organization in the United States.
Secure .gov websites use HTTPS
A lock (
) or https:// means you've safely
connected to the .gov website. Share sensitive
information only on official, secure websites.