REAGENT or RESOURCE | SOURCE | IDENTIFIER |
---|---|---|
Bacterial and Virus Strains | ||
ArcticExpress (DE3) competent E.coli | Agilent | Cat#230192 |
Chemicals, Peptides, and Recombinant Proteins | ||
Brequinar sodium salt hydrate | Sigma Aldrich | Cat#SML0113 |
n-Dodecyl-N,N-Dimethylamine-N-Oxide (LDAO) | Anatrace | Cat#D360 |
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE) | Avanti Polar Lipids | Cat#850757P |
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) | Avanti Polar Lipids | Cat#850457P |
1',3'-bis[1,2-dioleoyl-sn-glycero-3-phospho]-sn-glycerol (CDL) | Avanti Polar Lipids | Cat#710335P |
Dimethylsulfoxide (DMSO) | Sigma Aldrich | Cat#276855 |
Ammonium acetate | Sigma Aldrich | Cat#5.43834 |
H. sapiens DHODHNΔ30 | Ullrich et al., 2001 | N/A |
3,4-Dimethoxy-5-Methyl-p-Benzoquinone | Sigma Aldrich | Cat#D9150 |
Deposited Data | ||
Crystal structure of hDHODH with 3-amido-5-biphenyl-benzoic acid | Hurt et al., 2006 | PDB: 2B0M https://www.rcsb.org/pdb/explore/explore.do?structureId=2B0M |
Crystal structure of hDHODH with brequinar analogue | Liu et al., 2000 | PDB: 1D3G https://www.rcsb.org/pdb/explore/explore.do?structureId=1d3g |
Crystal structure of ligand-free DHODH | Walse et al., 2008 | PDB: 2PRM https://www.rcsb.org/pdb/explore/explore.do?structureId=2prm |
Recombinant DNA | ||
pNIC28-Bsa4 | Savitsky et al., 2010 | Addgene plasmid # 26103 |
H. sapiens DHODHNΔ30 coding sequence (Liu et al., 2000) | GeneArt | N/A |
Software and Algorithms | ||
PULSAR | Allison et al., 2015 | http://www.pulsar.chem.ox.ac.uk |
UniDec | Marty et al., 2015 | http://www.unidec.chem.ox.ac.uk |
IMPACT | Marklund et al., 2015 | http://www.impact.chem.ox.ac.uk |
mMass | Strohalm et al., 2010 | http://www.mmass.org |
Xcalibur | Thermo Scientific | N/A |
UCSF Chimera v1.11.02 | Pettersen et al., 2004 | http://www.cgl.ucsf.edu/chimera |
PyMol | Schrödinger, LLC Version 1.8 | www.sourceforge.net/projects/pymol |
GROMACS 2016.1 | Abraham et al., 2015 | http://www.gromacs.org |
MemGen | Knight and Hub, 2015 | http://memgen.uni-goettingen.de |
ModLoop | Fiser and Sali, 2003 | https://modbase.compbio.ucsf.edu/modloop/ |
AMBER99SB-ILDN force field | Lindorff-Larsen et al., 2010 | http://ambermd.org/#ff |
FMN force field parameters | Schneider and Sühnel, 1999 | http://research.bmh.manchester.ac.uk/bryce/amber |
POPE force field parameters and coordinates | Jämbeck and Lyubartsev, 2012b | http://www.fos.su.se/∼sasha/SLipids/Downloads.html |
Other | ||
Medium nanoES capillaries | Thermo Scientific | Cat#ES380 |