Table II.

Sepharose bead proteome: other proteins of additional classes

Gene NameDescriptionNP
 % Exp.CP
 % Exp.WC
 % Exp.
ADARDouble-stranded RNA-specific adenosine deaminase54.50.011.1
AHNAKAHNAK nucleoprotein isoform 154.528.655.6
ALBAlbumin100.045.557.1
ANXA1, 2Annexin 1, A2100.0100.077.8
ASCC3L1Activating signal co-integrator 1 complex subunit 3-like 163.60.022.2
ASS1Argininosuccinate synthase0.057.155.6
ATADATPase family, AAA domain containing protein27.30.022.2
ATP5A, 5BATP synthase, H+ transporting, mitochondrial F1 complex81.814.377.8
BAG2BCL2-associated athanogene 227.30.011.1
BOLA2BBolA-like protein 2B22.236.428.6
CADCarbamoylphosphate synthetase 20.085.733.3
CAND1Cullin-associated NEDD8-dissociated protein 19.128.633.3
CAPRIN1Cytoplasmic activation- and proliferation-associated protein 133.345.50
CCTChaperonin containing TCP145.528.655.6
CD180Elongation factor 1-alpha45.557.133.3
CFL1Cofilin63.685.766.7
CHD3, D4Chromodomain-helicase-DNA-binding protein 3, 418.20.011.1
CLEC2DC-type lectin domain family 2, member D36.40.00.0
CLTCCathrin heavy chain 136.485.777.8
COPA, B1Coatomer protein complex, subunits A, B118.228.644.4
CORO1CCoronin, actin binding protein 1C66.727.314.3
CPS1Carbamoyl-phosphate synthetase 154.571.444.4
CRKLCrk-like protein22.29.128.6
CSDACold shock domain-containing protein A55.636.471.4
CSRP2Cysteine and glycine-rich protein 254.528.611.1
DBN1Drebrin 1 (developmentally regulated brain protein)66.736.428.6
DHRS2Dehydrogenase/reductase (SDR family) member 236.414.322.2
DUTdUTP pyrophosphatase22.218.214.3
DYNLL1Dynein light chain 127.328.611.1
EDARRADEDAR-associated death domain9.10.066.7
ELAVL1ELAV-like 163.60.022.2
EMDEmerin36.428.60.0
ENOEnolase 19.114.377.8
EWSR1Ewing sarcoma breakpoint region 127.314.333.3
FARSA,B,FASNPhenylalanyl-tRNA synthetase; Fatty acid synthase36.485.788.9
FBLFibrillarin63.614.322.2
FKSG30FKSG3036.457.166.7
FUSFus-like protein36.414.333.3
G3BP1,2GTPase activating protein (SH3 domain) binding protein 1, 244.418.214.3
G6PDGlucose-6-phosphate 1-dehydrogenase9.128.622.2
GAPDHGlyceraldehyde-3-phosphate dehydrogenase18.242.955.6
GFAPGlial fibrillary acidic protein36.442.955.6
GNASGuanine nucleotide-binding protein G22.29.114.3
GNB2L1Guanine nucleotide binding protein (G protein), beta polypeptide 2-like 136.428.644.4
GNL2,3Guanine nucleotide-binding protein-like 2 (nucleolar)10000
GSRGlutathione reductase36.442.933.3
GSTM3Glutathione S-transferase M318.228.622.2
ILF 2, 3Interleukin enhancer binding factor 2, 354.542.955.6
KHDRBS1,2,3KH domain containing, RNA binding, signal transduction associated45.50.011.1
KHSRPFar upstream element-binding protein 236.40.011.1
KIF2,4Kinesin family member 2, 444.436.414.3
LDHALactate dehydrogenase A9.142.955.6
LGALS1,3Beta-galactoside–binding lectin72.757.155.6
LIMA1LIM domain and actin-binding protein 144.49.114.3
LMNA, BLamin A/C, B90.90.033.3
MATR3Matrin 363.60.044.4
MCM3,5Minichromosome maintenance complex component 3, 554.514.344.4
MIFMacrophage migration inhibitory factor9.128.622.2
MSH2MutS protein homologue 277.8014.3
MTCH2Mitochondrial carrier homologue 236.40.011.1
NACANascent polypeptide-associated complex subunit alpha11.118.214.3
NCLNucleolin72.742.922.2
NESNestin55.69.114.3
NME1, 2Non-metastatic cells protein 1, 218.228.611.1
NONONon-POU domain containing, octamer-binding36.40.011.1
NPM1Nucleophosmin 181.80.044.4
NUDT16L1Nudix (nucleoside diphosphate linked moiety X)-type motif 16-like 177.8014.3
NUMA1Nuclear mitotic apparatus protein 166.718.242.9
NUP155Nucleoporin 155 kD54.50.011.1
PABPC1,3,4Poly(A) binding protein, cytoplasmic 1, 3, 418.257.133.3
PALLDPalladin, cytoskeletal associated protein45.50.011.1
PARK7DJ-1 protein36.428.644.4
PARP1Poly (ADP-ribose) polymerase family, member 127.30.011.1
PCBP1, 2Poly(rC)-binding protein 1, 263.685.755.6
PCMTProtein-l-isoaspartate(d-aspartate) O-methyltransferase18.257.133.3
PDIA6Protein disulfide-isomerase A663.614.377.8
PDLIM2,4PDZ and LIM domain protein 255.600
PFDN2Prefoldin subunit 29.114.311.1
PFN2Profilin 236.428.633.3
PHB, PHB2Prohibitin, prohibitin 263.642.977.8
PHF5APHD finger protein 5A45.50.011.1
PHGDHPhosphoglycerate dehydrogenase18.271.444.4
PKM2Pyruvate kinase, muscle54.571.466.7
POTE2Protein expressed in prostate, ovary, testis, and placenta 254.542.966.7
PPIAPeptidylprolyl isomerase A (cyclophilin A)66.727.371.4
PRDX1,2,3,4Peroxiredoxin 1, 2, 3, 490.971.4100.0
PRKDCProtein kinase, DNA-activated81.814.344.4
PTBP1,2Polypyrimidine tract-binding protein 1, 263.614.311.1
RALYRNA-binding protein (autoantigenic, hnRNP-associated with lethal, yellow)10027.328.6
RCC2Regulator of chromosome condensation 263.60.011.1
S100A6,9,10,14S100 calcium binding protein A10036.442.9
SAP18Sin3-associated polypeptide, 18 kD44.4014.3
SEC61BProtein transport protein Sec61 beta subunit45.50.011.1
SERBP1SERPINE1 mRNA binding protein 145.50.022.2
SERPINH1,A11Serine (or cysteine) proteinase inhibitor72.728.666.7
SF3BSplicing factor 3B54.50.022.2
SLC25AADP/ATP translocase 2 (solute carrier family 25)100.071.4100.0
THOC4THO complex subunit 444.49.10
TKTTransketolase36.442.933.3
TMPOThymopoietin22.2028.6
TOMM22Translocase of outer membrane 22-kD subunit homologue22.2028.6
TRAP1Tumor necrosis factor type 1 receptor-associated protein (heat shock protein 75)44.427.342.9
TRIM2152-kD Ro protein18.228.633.3
TRIM25Tripartite motif-containing protein 25 (Zinc finger protein 147)18.20.00.0
TTBK2Tau-tubulin kinase18.214.344.4
TUFMTu translation elongation factor, mitochondrial63.614.355.6
TXNThioredoxin27.357.155.6
U2AF1U2 small nuclear RNA auxillary factor 127.30.011.1
UBA52Ubiquitin and ribosomal protein L40 precursor36.457.155.6
UBE2D2,3Ubiquitin-conjugating enzyme E2D 2, E2D 318.214.30.0
UQCRC1Ubiquinol-cytochrome c reductase core protein I63.60.022.2
VAPA/BVAMP (vesicle-associated membrane protein)-associated protein A, B44.427.328.6
VCPValosin-containing protein44.418.242.9
VDAC2,3Voltage-dependent anion channel 2, 363.60.022.2
XPO1Exportin 19.10.022.2
XRCC5, 6ATP-dependent DNA helicase II18.214.30.0
YBX1Y box binding protein 136.428.633.3
YWHAZ,YWHABTyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein27.328.644.4
  • In addition to the common classes of proteins listed in Table I, there are over 100 proteins, shown here, that do not fall into these specific classes yet still bind Sepharose nonspecifically. This list was screened against datasets from 27 independent SILAC immunoprecipitation experiments using either nucleoplasmic (NP; 11 experiments), cytoplasmic (CP; 7 experiments), or whole cell (WC; 9 experiments) extracts to determine the frequency of detection and distribution of these nonspecific binding proteins among these distinct cellular extracts. The frequency is listed as the percentage of experiments in which the protein was detected.