G2C::Proteomics

Targeted tandem affinity purification of PSD-95 recovers core
postsynaptic complexes and schizophrenia susceptibility proteins
Esperanza Fernandez, Mark O Collins, Rachel T Uren, Maksym V Kopanitsa, Noboru H Komiyama,
Mike DR Croning, Lysimachos Zografos, J Douglas Armstrong, Jyoti S Choudhary and Seth GN Grant


Table 1. Functional classification of PSD-95-associated proteins in at least three out of four tandem purifications.

Approved gene symbols and protein names, and UniProt accession numbers are shown. Number of approved peptides for each protein identified by LC-MS/MS in the four tandem purifications are indicated as T1, T2, T3 and T4. More information of these proteins is listed in Supplementary Table 1.

MGI SymbolApproved NameUniProt Acc
Number of peptides
Cluster
Adaptor/ RegulatoryT1T2T3T4
Anks1ankyrin repeat and SAM domain containing 1P59672433
Anks1bankyrin repeat and sterile alpha motif domain containing 1BQ8BZM21751010
Baiap2brain-specific angiogenesis inhibitor 1-associated protein 2Q8BKX120121313
d
Begainbrain-enriched guanylate kinase-associatedQ68EF6481216
a
Dlg1Synapse-associated protein 97Q3UP6124423442
a
Dlg2Postsynaptic density protein 93Q91XM949676980
a
Dlg3Synapse-associated protein 102Q52KF727171422
a
Dlg4Postsynaptic density protein 95Q6210842576464
a
Dlgap1SAP90/PSD-95-associated protein 1Q9D4151191424
a
Dlgap2SAP90/PSD-95-associated protein 2Q8BJ4218121924
a
Dlgap3SAP90/PSD-95-associated protein 3A2A7T7168715
a
Dlgap4SAP90/PSD-95-associated protein 4A2BDU3149714
a
Receptors/ Channels/ Transporters
Gria1glutamate receptor, ionotropic, AMPA 1Q5NBY123513
b
Gria2glutamate receptor, ionotropic, AMPA 2P23819481020
b
Gria3glutamate receptor, ionotrophic, AMPA 3Q9Z2W92918
b
Gria4glutamate receptor, ionotrophic, AMPA 4Q9Z2W82259
b
Grik2glutamate receptor, ionotropic, kainate 2 (beta 2)P39087246
b
Grik5glutamate receptor, ionotropic, kainate 5 (gamma 2)Q61626237
b
Grin1glutamate receptor, ionotropic, NMDA1 (zeta 1)A2AI2129405055
a
Grin2aglutamate receptor, ionotropic, NMDA2A (epsilon 1)P3543624313646
a
Grin2bglutamate receptor, ionotropic, NMDA2B (epsilon 2)Q0109744546778
a
Grin2dglutamate receptor, ionotropic, NMDA2D (epsilon 4)Q0339136910
a
Gpr123G protein-coupled receptor 123Q52KJ62333
Cacng2calcium channel, voltage-dependent, gamma subunit 2O886022223
b
Kcna1K+ voltage-gated channel, shaker-related subfamily, member 1P163886556
c
Kcna2K+ voltage-gated channel, shaker-related subfamily, member 2P631414576
c
Kcna3K+ voltage-gated channel, shaker-related subfamily, member 3P163903465
c
Kcna4K+ voltage-gated channel, shaker-related subfamily, member 4Q8CBF82355
c
Kcnab1K+ voltage-gated channel, shaker-related subfamily, beta member 1P631433346
c
Kcnab2K+ voltage-gated channel, shaker-related subfamily, beta member 2P62482561011
c
Kcnj10K+ inwardly-rectifying channel, subfamily J, member 10Q9JM633346
a
Kcnj4K+ inwardly-rectifying channel, subfamily J, member 4P521894668
a
Vdac1voltage-dependent anion channel 1Q609324455
f
Vdac2voltage-dependent anion channel 2Q609304234
Atp1b1ATPase, Na+/K+ transporting, beta 1 polypeptide1P140943363
Atp6v0d1ATPase, H+ transporting, V0 subunit d isoform 1P518633342
Sfxn3sideroflexin 3Q91V613343
Slc1a2solute carrier family, member 2P430063244
Slc25a4ADP/ATP translocase 1P48962236
g
Slc25a5ADP/ATP translocase 2P518812236
g
Slc4a4solute carrier family 4 (anion exchanger), member 4O88343364
Cytoskeletal/ Structural/ Cell adhesion
Ablim1actin binding LIM protein 1Q8K4G520101822
Adam22a disintegrin and metallopeptidase domain 22Q9R1V612162431
e
Arcactivity regulated cytoskeletal-associated proteinQ9WV318132019
Arpc4actin related protein 2/3 complex, subunit 4P59999224
Capza2capping protein (actin filament) muscle Z-line, alpha 2P47754222
Cfl1cofilin 1, non-muscleP187602234
DstndestrinQ9R0P52566
Fscn1fascin homolog 1, actin bundling protein (Strongylocentrotus purpuratus)Q61553223
f
Lgi1leucine-rich repeat LGI family, member 1Q9JIA16121915
e
Neflneurofilament, light polypeptide 68kDaP08551336
a
Nrxn1neurexin 1Q9CS848171223
Plp1proteolipid protein (myelin) 1P602022345
Sept11septin 11Q8C1B72222
Sept5septin 5Q9Z2Q6224
Spnb2spectrin beta 2Q62261225
a
Tuba1a*tubulin, beta polypeptideP05213,11142020
Tubb2b*tubulin, beta 2bQ7TMM919212427
Tubb6tubulin, beta 6Q922F4881313
Vesicular/ Trafficking/ Transport
Arf3ADP-ribosylation factor 3P612052234
Cltcclathrin, heavy chain (Hc)Q5SXR610412
a
Cpne4*copine IVQ8BLR2423
Cpne7copine VII7Q0VE824323
Iqsec1IQ motif and Sec7 domain 1Q8R0S2117615
Iqsec2IQ motif and Sec7 domain 2Q5DU2534252436
NsfN-ethylmaleimide sensitive fusion proteinP464604479
Stx1b2syntaxin 1B2P612643432
Stxbp1syntaxin binding protein 1O085995344
Syt1synaptotagmin IP460965222
Vamp2*Synaptobrevin 2P63024242
Enzymes
Acat1acetyl-Coenzyme A acetyltransferase 1Q8QZT1233
Aco2aconitase 2, mitochondrialQ99KI0332
Acot7acyl-CoA thioesterase 7Q91V123334
Aldocaldolase C, fructose-bisphosphateP05063424
Atp5c1ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptide 1Q91VR2334
g
Atp5bATP synthase, H+ transporting mitochondrial F1 complex, beta subunitP56480265
g
Atp5oATP synthase, H+ transporting, mitochondrial F1 complex, O subunitQ9DB202244
g
Atp5a1ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1Q032655101411
g
Cnp2',3'-cyclic nucleotide 3' phosphodiesteraseP163301031110
Gapdhglyceraldehyde-3-phosphate dehydrogenaseP1685898910
f
Gdaguanine deaminaseQ9R11129262931
a
Glulglutamate-ammonia ligase (glutamine synthetase)P151055172119
Gpx4glutathione peroxidase 4O70325222
Msrb2methionine sulfoxide reductase B2Q78J03274
Pdha1pyruvate dehydrogenase E1 alpha 1P354864385
Pdhbpyruvate dehydrogenase (lipoamide) betaQ9D0514446
Pgk1phosphoglycerate kinase 1P0941123138
f
Pkm2pyruvate kinase, muscleP52480761112
Ppap2bphosphatidic acid phosphatase type 2BQ99JY8225
Prdx1peroxiredoxin 1P35700471014
Prdx2peroxiredoxin 2Q61171223
Sdhasuccinate dehydrogenase complex, subunit A, flavoprotein (Fp)Q8K2B37686
Sucla2succinate-CoA ligase, ADP-forming, beta subunitQ9Z2I94256
Kinases
Camk2acalcium/calmodulin-dependent protein kinase II alphaP11798113411
a
Camk2bcalcium/calmodulin-dependent protein kinase II betaQ5SVI310557
a
Mapk1mitogen activated protein kinase 1P630853349
Phosphatases
Ppap2bphosphatidic acid phosphatase type 2BQ99JY8225
Ppp3caprotein phosphatase 3, catalytic subunit, alpha isoformP63328126711
a
Ppp3cbprotein phosphatase 3, catalytic subunit, beta isoformP484537324
G-protein signaling
Abractive BCR-related geneQ6PCY1226
Gnao1guanine nucleotide binding protein, alpha oP18872871516
Kalrnkalirin, RhoGEF kinaseA2CG522328
Rac1RAS-related C3 botulinum substrate 1Q3TLP82233
d
Syngap1synaptic Ras GTPase activating protein 1 homolog (rat)Q9QUH621151738
a
Transcription/ Translation
Park7Parkinson disease (autosomal recessive, early onset) 7A2A817333
Rps14ribosomal protein S14P62264232
Rps3ribosomal protein S3P62908234
Uba52*ubiquitin A-52 residue ribosomal protein fusion product 1Q66JP13356
Signal transduction
Btbd11BTB (POZ) domain containing 11Q6GQW05323
Phb2prohibitin 2O35129254
Ywhaetyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, epsilon polypeptideP62259322
Pcbp1poly(rC) binding protein 1P60335335
Unclassified
Fam81afamily with sequence similarity 81, member AQ3UXZ6762118
AI662250expressed sequence AI662250Q3UKV2222
B630019K06RikRIKEN cDNA B630019K06 geneQ7TNS56789
Frmpd3FERM and PDZ domain containing 3Q8BXG0255
Pgam5phosphoglycerate mutase family member 5Q3UK1977810
Prrt1proline-rich transmembrane protein 1O354492223
Slc9a3r1solute carrier family 9 (sodium/hydrogen exchanger), member 3 regulator 1P704414372

Genes marked with an asterisk represent genes whose peptides are common to other genes:
Cpne4*: Cpne5, Cpne8. Tuba1a*: Tuba1b, Tuba4c, Tuba1b. Tubb2b*:Tubb5, Tubb2a, Tubb2c, Tubb4. Uba52*: Ubc, Ubb. Vamp2*: Vamp3.