Table 3.
List of binding partners of the mitochondrial-shaping proteins altered in Parkinson’s disease (Table 2) that are found in the list of proteins modified in the context of Parkinson’s disease (Supplementary Table S1).
| Gene Names | Protein Names |
|---|---|
| ACAD9 | Acyl-CoA dehydrogenase family member 9, mitochondrial (ACAD-9) (EC 1.3.99.-) |
| ACP2 | Lysosomal acid phosphatase (LAP) (EC 3.1.3.2) |
| ACTB | Actin, cytoplasmic 1 (Beta-actin) (Cleaved into: Actin, cytoplasmic 1, N-terminally processed) |
| ACTBL2 | Beta-actin-like protein 2 (Kappa-actin) |
| ACTN1 | Alpha-actinin-1 (Alpha-actinin cytoskeletal isoform) (F-actin cross-linking protein) (Non-muscle alpha-actinin-1) |
| ALB, GIG20, GIG42, PRO0903, PRO1708, PRO2044, PRO2619, PRO2675, UNQ696/PRO1341 | Serum albumin |
| ALDH1B1, ALDH5, ALDHX | Aldehyde dehydrogenase X, mitochondrial (EC 1.2.1.3) (Aldehyde dehydrogenase 5) (Aldehyde dehydrogenase family 1 member B1) |
| ALDOA, ALDA | Fructose-bisphosphate aldolase A (EC 4.1.2.13) (Lung cancer antigen NY-LU-1) (Muscle-type aldolase) |
| ANXA2, ANX2, ANX2L4, CAL1H LPC2D | Annexin A2 (Annexin II) (Annexin-2) (Calpactin I heavy chain) (Calpactin-1 heavy chain) (Chromobindin-8) (Lipocortin II) (Placental anticoagulant protein IV) (PAP-IV) (Protein I) (p36) |
| APOA1 | Apolipoprotein A-I (Apo-AI) (ApoA-I) (Apolipoprotein A1) (Cleaved into: Proapolipoprotein A-I (Proapo A-I); Truncated apolipoprotein A-I (Apolipoprotein A-I(1-242))) |
| ATP5A1, ATP5A, ATP5AL2, ATPM | ATP synthase subunit alpha, mitochondrial |
| ATP5B, ATPMB, ATPSB, | ATP synthase subunit beta, mitochondrial (EC 3.6.3.14) |
| ATP5H, My032 | ATP synthase subunit d, mitochondrial (ATPase subunit d) |
| ATP5I, ATP5K | ATP synthase subunit e, mitochondrial (ATPase subunit e) (Cleaved into: ATP synthase subunit e, mitochondrial, N-terminally processed) |
| BCAP31, BAP31, DXS1357E | B-cell receptor-associated protein 31 (BCR-associated protein 31) (Bap31) (6C6-AG tumor-associated antigen) (Protein CDM) (p28) |
| C1QBP, GC1QBP, HABP1, SF2P32 | Complement component 1 Q subcomponent-binding protein, mitochondrial (ASF/SF2-associated protein p32) (Glycoprotein gC1qBP) (C1qBP) (Hyaluronan-binding protein 1) (Mitochondrial matrix protein p32) (gC1q-R protein) (p33) |
| CALR, CRTC | Calreticulin (CRP55) (Calregulin) (Endoplasmic reticulum resident protein 60) (ERp60) (HACBP) (grp60) |
| CCT5, CCTE, KIAA0098 | T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon) |
| COX4I1, COX4 | Cytochrome c oxidase subunit 4 isoform 1, mitochondrial (Cytochrome c oxidase polypeptide IV) (Cytochrome c oxidase subunit IV isoform 1) (COX IV-1) |
| COX5A | Cytochrome c oxidase subunit 5A, mitochondrial (Cytochrome c oxidase polypeptide Va) |
| COX6C | Cytochrome c oxidase subunit 6C (Cytochrome c oxidase polypeptide VIc) |
| DDAH1, DDAH | N(G),N(G)-dimethylarginine dimethylaminohydrolase 1 (DDAH-1) (Dimethylarginine dimethylaminohydrolase 1) (EC 3.5.3.18) (DDAHI) (Dimethylargininase-1) |
| DDOST, KIAA0115, OST48 OK/SW-cl.45 | Dolichyl-diphosphooligosaccharide—protein glycosyltransferase 48 kDa subunit (DDOST 48 kDa subunit) (Oligosaccharyl transferase 48 kDa subunit) |
| DNM1L, DLP1, DRP1 | Dynamin-1-like protein (EC 3.6.5.5) (Dnm1p/Vps1p-like protein) (DVLP) (Dynamin family member proline-rich carboxyl-terminal domain less) (Dymple) (Dynamin-like protein) (Dynamin-like protein 4) (Dynamin-like protein IV) (HdynIV) (Dynamin-related protein 1) |
| DYNC1H1, DHC1, DNCH1, DNCL, DNECL, DYHC, KIAA0325 | Cytoplasmic dynein 1 heavy chain 1 (Cytoplasmic dynein heavy chain 1) (Dynein heavy chain, cytosolic) |
| EEF1A1, EEF1A, EF1A, LENG7 | Elongation factor 1-alpha 1 (EF-1-alpha-1) (Elongation factor Tu) (EF-Tu) (Eukaryotic elongation factor 1 A-1) (eEF1A-1) (Leukocyte receptor cluster member 7) |
| EEF1B2, EEF1B, EF1B | Elongation factor 1-beta (EF-1-beta) |
| EIF5A | Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-5A1) (Eukaryotic initiation factor 5A isoform 1) (eIF-5A) (Rev-binding factor) (eIF-4D) |
| FKBP4, FKBP52 | Peptidyl-prolyl cis-trans isomerase FKBP4 (PPIase FKBP4) (EC 5.2.1.8) (51 kDa FK506-binding protein) (FKBP51) (52 kDa FK506-binding protein) (52 kDa FKBP) (FKBP-52) (59 kDa immunophilin) (p59) (FK506-binding protein 4) (FKBP-4) (FKBP59) (HSP-binding immunophilin) (HBI) (Immunophilin FKBP52) (Rotamase) (Cleaved into: Peptidyl-prolyl cis-trans isomerase FKBP4, N-terminally processed) |
| FLNC, ABPL, FLN2 | Filamin-C (FLN-C) (FLNc) (ABP-280-like protein) (ABP-L) (Actin-binding-like protein) (Filamin-2) (Gamma-filamin) |
| FLOT1 | Flotillin-1 |
| FUBP1 | Far upstream element-binding protein 1 (FBP) (FUSE-binding protein 1) (DNA helicase V) (hDH V) |
| GARS | Glycine-tRNA ligase (EC 3.6.1.17) (EC 6.1.1.14) (Diadenosine tetraphosphate synthetase) (AP-4-A synthetase) (Glycyl-tRNA synthetase) (GlyRS) |
| GSTK1, HDCMD47P | Glutathione S-transferase kappa 1 (EC 2.5.1.18) (GST 13-13) (GST class-kappa) (GSTK1-1) (hGSTK1) (Glutathione S-transferase subunit 13) |
| GSTO1, GSTTLP28 | Glutathione S-transferase omega-1 (GSTO-1) (EC 2.5.1.18) (Glutathione S-transferase omega 1-1) (GSTO 1-1) (Glutathione-dependent dehydroascorbate reductase) (EC 1.8.5.1) (Monomethylarsonic acid reductase) (MMA(V) reductase) (EC 1.20.4.2) (S-(Phenacyl)glutathione reductase) (SPG-R) |
| HSP90AB1, HSP90B HSPC2, HSPCB | Heat shock protein HSP 90-beta (HSP 90) (Heat shock 84 kDa) (HSP 84) (HSP84) |
| HSPA1L | Heat shock 70 kDa protein 1-like (Heat shock 70 kDa protein 1L) (Heat shock 70 kDa protein 1-Hom) (HSP70-Hom) |
| HSPA5, GRP78 | 78 kDa glucose-regulated protein (GRP-78) (Endoplasmic reticulum lumenal Ca(2+)-binding protein grp78) (Heat shock 70 kDa protein 5) (Immunoglobulin heavy chain-binding protein) (BiP) |
| HSPA8, HSC70, HSP73, HSPA10 | Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8) (Lipopolysaccharide-associated protein 1) (LAP-1) (LPS-associated protein 1) |
| HSPA9, GRP75, HSPA9B, mt-HSP70 | Stress-70 protein, mitochondrial (75 kDa glucose-regulated protein) (GRP-75) (Heat shock 70 kDa protein 9) (Mortalin) (MOT) (Peptide-binding protein 74) (PBP74) |
| HSPB1, HSP27, HSP28 | Heat shock protein beta-1 (HspB1) (28 kDa heat shock protein) (Estrogen-regulated 24 kDa protein) (Heat shock 27 kDa protein) (HSP 27) (Stress-responsive protein 27) (SRP27) |
| HSPD1, HSP60 | 60 kDa heat shock protein, mitochondrial (EC 3.6.4.9) (60 kDa chaperonin) (Chaperonin 60) (CPN60) (Heat shock protein 60) (HSP-60) (Hsp60) (HuCHA60) (Mitochondrial matrix protein P1) (P60 lymphocyte protein) |
| ILVBL, AHAS | Acetolactate synthase-like protein (EC 2.2.1.-) (IlvB-like protein) |
| IMMT, HMP, MIC60, MINOS2, PIG4, PIG52 | MICOS Complex subunit MIC60 (Cell proliferation-inducing gene 4/52 protein) (Inner mitochondrial membrane protein) (Mitofilin) (p87/89) |
| LDHB | L-lactate dehydrogenase B chain (LDH-B) (EC 1.1.1.27) (LDH heart subunit) (LDH-H) (Renal carcinoma antigen NY-REN-46) |
| LGALS1 | Galectin-1 (Gal-1) (14 kDa laminin-binding protein) (HLBP14) (14 kDa lectin) (Beta-galactoside-binding lectin L-14-I) (Galaptin) (HBL) (HPL) (Lactose-binding lectin 1) (Lectin galactoside-binding soluble 1) (Putative MAPK-activating protein PM12) (S-Lac lectin 1) |
| LMNA, LMN1 | Prelamin-A/C (Cleaved into: Lamin-A/C (70 kDa lamin) (Renal carcinoma antigen NY-REN-32)) |
| MDH2 | Malate dehydrogenase, mitochondrial (EC 1.1.1.37) |
| MFN2, CPRP1, KIAA0214 | Mitofusin-2 (EC 3.6.5.-) (Transmembrane GTPase MFN2) |
| MYL6 | Myosin light polypeptide 6 (17 kDa myosin light chain) (LC17) (Myosin light chain 3) (MLC-3) (Myosin light chain alkali 3) (Myosin light chain A3) (Smooth muscle and non-muscle myosin light chain alkali 6) |
| NDUFA10 | NADH dehydrogenase (ubiquinone) 1 alpha subcomplex subunit 10, mitochondrial (Complex I-42kD) (CI-42kD) (NADH-ubiquinone oxidoreductase 42 kDa subunit) |
| NDUFA11 | NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 (Complex I-B14.7) (CI-B14.7) (NADH-ubiquinone oxidoreductase subunit B14.7) |
| NDUFA4 | Cytochrome c oxidase subunit NDUFA4 (Complex I-MLRQ) (CI-MLRQ) (NADH-ubiquinone oxidoreductase MLRQ subunit) |
| NDUFS1 | NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-75kD) (CI-75kD) |
| NDUFS3 | NADH dehydrogenase (ubiquinone) iron-sulfur protein 3, mitochondrial (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-30kD) (CI-30kD) (NADH-ubiquinone oxidoreductase 30 kDa subunit) |
| NEDD8 | NEDD8 (Neddylin) (Neural precursor cell expressed developmentally downregulated protein 8) (NEDD-8) (Ubiquitin-like protein Nedd8) |
| NPM1, NPM | Nucleophosmin (NPM) (Nucleolar phosphoprotein B23) (Nucleolar protein NO38) (Numatrin) |
| OAT | Ornithine aminotransferase, mitochondrial (EC 2.6.1.13) (Ornithine delta-aminotransferase) (Ornithine—oxo-acid aminotransferase) (Cleaved into: Ornithine aminotransferase, hepatic form; Ornithine aminotransferase, renal form) |
| OGDH | 2-oxoglutarate dehydrogenase, mitochondrial (EC 1.2.4.2) (2-oxoglutarate dehydrogenase complex component E1) (OGDC-E1) (Alpha-ketoglutarate dehydrogenase) |
| OTUB1, OTB1, OTU1, HSPC263 | Ubiquitin thioesterase OTUB1 (EC 3.4.19.12) (Deubiquitinating enzyme OTUB1) (OTU domain-containing ubiquitin aldehyde-binding protein 1) (Otubain-1) (hOTU1) (Ubiquitin-specific-processing protease OTUB1) |
| PDIA3, ERP57, ERP60, GRP58 | Protein disulfide-isomerase A3 (EC 5.3.4.1) (58 kDa glucose-regulated protein) (58 kDa microsomal protein) (p58) (Disulfide isomerase ER-60) (Endoplasmic reticulum resident protein 57) (ER protein 57) (ERp57) (Endoplasmic reticulum resident protein 60) (ER protein 60) (ERp60) |
| PGK1, PGKA, MIG10, OK/SW-cl.110 | Phosphoglycerate kinase 1 (EC 2.7.2.3) (Cell migration-inducing gene 10 protein) (Primer recognition protein 2) (PRP 2) |
| PHB | Prohibitin |
| PHB2, BAP, REA | Prohibitin-2 (B-cell receptor-associated protein BAP37) (D-prohibitin) (Repressor of estrogen receptor activity) |
| PIN1 | Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase Pin1) (PPIase Pin1) (Rotamase Pin1) |
| PPIA, CYPA | Peptidyl-prolyl cis-trans isomerase A (PPIase A) (EC 5.2.1.8) (Cyclophilin A) (Cyclosporin A-binding protein) (Rotamase A) (Cleaved into: Peptidyl-prolyl cis-trans isomerase A, N-terminally processed) |
| PRDX4 | Peroxiredoxin-4 (EC 1.11.1.15) (Antioxidant enzyme AOE372) (AOE37-2) (Peroxiredoxin IV) (Prx-IV) (Thioredoxin peroxidase AO372) (Thioredoxin-dependent peroxide reductase A0372) |
| PSMA3, HC8, PSC8 | Proteasome subunit alpha type-3 (EC 3.4.25.1) (Macropain subunit C8) (Multi-catalytic endopeptidase complex subunit C8) (Proteasome component C8) |
| PTPN5 | Tyrosine-protein phosphatase non-receptor type 5 (EC 3.1.3.48) (Neural-specific protein-tyrosine phosphatase) (Striatum-enriched protein-tyrosine phosphatase) (STEP) |
| RAB14 | Ras-related protein Rab-14 |
| RAB2A, RAB2 | Ras-related protein Rab-2A |
| RAC1, TC25, MIG5 | Ras-related C3 botulinum toxin substrate 1 (Cell migration-inducing gene 5 protein) (Ras-like protein TC25) (p21-Rac1) |
| RAPGEF2, KIAA0313, NRAPGEP, PDZGEF1 | Rap guanine nucleotide exchange factor 2 (Cyclic nucleotide ras GEF) (CNrasGEF) (Neural RAP guanine nucleotide exchange protein) (nRap GEP) (PDZ domain-containing guanine nucleotide exchange factor 1) (PDZ-GEF1) (RA-GEF-1) (Ras/Rap1-associating GEF-1) |
| RHOA, ARH12, ARHA, RHO12 | Transforming protein RhoA (Rho cDNA clone 12) (h12) |
| RNH1, PRI, RNH | Ribonuclease inhibitor (Placental ribonuclease inhibitor) (Placental RNase inhibitor) (Ribonuclease/angiogenin inhibitor 1) (RAI) |
| RPN1 | Dolichyl-diphosphooligosaccharide—protein glycosyltransferase subunit 1 (Dolichyl-diphosphooligosaccharide—protein glycosyltransferase 67 kDa subunit) (Ribophorin I) (RPN-I) (Ribophorin-1) |
| RPN2 | Dolichyl-diphosphooligosaccharide—protein glycosyltransferase subunit 2 (Dolichyl-diphosphooligosaccharide—protein glycosyltransferase 63 kDa subunit) (RIBIIR) (Ribophorin II) (RPN-II) (Ribophorin-2) |
| RPS15A, OK/SW-cl.82 | 40S ribosomal protein S15a (Small ribosomal subunit protein uS8) |
| RPS3, OK/SW-cl.26 | 40S ribosomal protein S3 (EC 4.2.99.18) (Small ribosomal subunit protein uS3) |
| S100A10, ANX2LG CAL1L CLP11 | Protein S100-A10 (Calpactin I light chain) (Calpactin-1 light chain) (Cellular ligand of annexin II) (S100 calcium-binding protein A10) (p10 protein) (p11) |
| SAMM50, SAM50 CGI-51 TRG3 | Sorting and assembly machinery component 50 homolog (Transformation-related gene 3 protein) (TRG-3) |
| SELENBP1, SBP | Selenium-binding protein 1 (56 kDa selenium-binding protein) (SBP56) (SP56) |
| SFXN1 | Sideroflexin-1 (Tricarboxylate carrier protein) (TCC) |
| SH3GLB2, KIAA1848, PP578 | Endophilin-B2 (SH3 domain-containing GRB2-like protein B2) |
| SIRT2, SIR2L, SIR2L2 | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) (Regulatory protein SIR2 homolog 2) (SIR2-like protein 2) |
| SLC25A13, ARALAR2 | Calcium-binding mitochondrial carrier protein Aralar2 (Citrin) (Mitochondrial aspartate glutamate carrier 2) (Solute carrier family 25 member 13) |
| SLC25A18, GC2 | Mitochondrial glutamate carrier 2 (GC-2) (Glutamate/H(+) symporter 2) (Solute carrier family 25 member 18) |
| SLC25A5, ANT2 | ADP/ATP translocase 2 (ADP, ATP carrier protein 2) (ADP, ATP carrier protein, fibroblast isoform) (Adenine nucleotide translocator 2) (ANT 2) (Solute carrier family 25 member 5) (Cleaved into: ADP/ATP translocase 2, N-terminally processed) |
| SLC9A3R1, NHERF, NHERF1 | Na(+)/H(+) exchange regulatory cofactor NHE-RF1 (NHERF-1) (Ezrin-radixin-moesin-binding phosphoprotein 50) (EBP50) (Regulatory cofactor of Na(+)/H(+) exchanger) (Sodium-hydrogen exchanger regulatory factor 1) (Solute carrier family 9 isoform A3 regulatory factor 1) |
| SSBP1, SSBP | Single-stranded DNA-binding protein, mitochondrial (Mt-SSB) (MtSSB) (PWP1-interacting protein 17) |
| TPD52 | Tumor protein D52 (Protein N8) |
| TPM1, C15orf13, TMSA | Tropomyosin alpha-1 chain (Alpha-tropomyosin) (Tropomyosin-1) |
| TPM2, TMSB | Tropomyosin beta chain (Beta-tropomyosin) (Tropomyosin-2) |
| TPM3 | Tropomyosin alpha-3 chain (Gamma-tropomyosin) (Tropomyosin-3) (Tropomyosin-5) (hTM5) |
| TPM4 | Tropomyosin alpha-4 chain (TM30p1) (Tropomyosin-4) |
| TUBA1A, TUBA3 | Tubulin alpha-1A chain (Alpha-tubulin 3) (Tubulin B-alpha-1) (Tubulin alpha-3 chain) (Cleaved into: Detyrosinated tubulin alpha-1A chain) |
| TUBB, TUBB5, OK/SW-cl.56 | Tubulin beta chain (Tubulin beta-5 chain) |
| TUBB4B, TUBB2C | Tubulin beta-4B chain (Tubulin beta-2 chain) (Tubulin beta-2C chain) |
| TUFM | Elongation factor Tu, mitochondrial (EF-Tu) (P43) |
| UQCRB, UQBP | Cytochrome b-c1 complex subunit 7 (Complex III subunit 7) (Complex III subunit VII) (QP-C) (Ubiquinol-cytochrome c reductase complex 14 kDa protein) |
| UQCRFS1 | Cytochrome b-c1 complex subunit Rieske, mitochondrial (EC 1.10.2.2) (Complex III subunit 5) (Cytochrome b-c1 complex subunit 5) (Rieske iron-sulfur protein) (RISP) (Ubiquinol-cytochrome c reductase iron-sulfur subunit) (Cleaved into: Cytochrome b-c1 complex subunit 11 (Complex III subunit IX) (Ubiquinol-cytochrome c reductase 8 kDa protein)) |
| UQCRFS1P1, UQCRFSL1 | Putative cytochrome b-c1 complex subunit Rieske-like protein 1 (Ubiquinol-cytochrome c reductase Rieske iron-sulfur subunit pseudogene 1) |
| UQCRH | Cytochrome b-c1 complex subunit 6, mitochondrial (Complex III subunit 6) (Complex III subunit VIII) (Cytochrome c1 non-heme 11 kDa protein) (Mitochondrial hinge protein) (Ubiquinol-cytochrome c reductase complex 11 kDa protein) |
| USMG5, DAPIT, HCVFTP2, PD04912 | Upregulated during skeletal muscle growth protein 5 (Diabetes-associated protein in insulin-sensitive tissues) (HCV F-transactivated protein 2) |
| VCP | Transitional endoplasmic reticulum ATPase (TER ATPase) (EC 3.6.4.6) (15S Mg(2+)-ATPase p97 subunit) (Valosin-containing protein) (VCP) |
| VDAC1, VDAC | Voltage-dependent anion-selective channel protein 1 (VDAC-1) (hVDAC1) (Outer mitochondrial membrane protein porin 1) (Plasmalemmal porin) (Porin 31HL) (Porin 31HM) |
| VDAC2 | Voltage-dependent anion-selective channel protein 2 (VDAC-2) (hVDAC2) (Outer mitochondrial membrane protein porin 2) |
| VDAC3 | Voltage-dependent anion-selective channel protein 3 (VDAC-3) (hVDAC3) (Outer mitochondrial membrane protein porin 3) |
| VIM | Vimentin |
| YWHAE | 14-3-3 protein epsilon (14-3-3E) |
| YWHAZ | 14-3-3 protein zeta/delta (Factor activating exoenzyme S) (FAS) (Protein kinase C inhibitor protein 1) (KCIP-1) |