KANPHOS: A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain
Abstract
:1. Introduction
2. Materials and Methods
2.1. System Configuration and Application Software
2.2. Data Collection, Management and Analysis Tool
2.3. Preparation and Incubation of Coronal Slices
2.4. Mass Spectrometry
2.5. SDS-PAGE and Immunoblotting
3. Results
3.1. Construction and Content of the KANPHOS Database
3.2. Data Accessibility and KANPHOS Workflow
3.3. Case Study: Identification of Adenosine-A2A Receptor Signaling and MAPK-Mediated Signaling Molecules Using KANPHOS
3.4. Pathway Analysis Using KANPHOS Revealed That HCN and Calcium Channel Proteins Are Involved in the MEK-MAPK Pathway Downstream of A2AR
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Method/Stimulation | Kinase | No. of Phos. Site |
---|---|---|
KIOSS (1433z)/Forskolin | PKA, MAPK and other | 278 |
KIOSS (1433z)/OA&U0126 | MAPK and other | 324 |
KIOSS (1433z)/D1R Agonist | PKA, MAPK and other | 185 |
KIOSS (1433z)/A2AR Agonist | PKA, MAPK and other | 62 |
KISS | CaMKI, CDK5, FYN, LYN, MAPK1, PAK7, PKA, PKN, ROCK2 | 3597 |
Protoarray | AKT1, CaMK2A, CDK5, LRRK2, LYN, MAPK1, PRKCA, PRKACA, ROCK2 | 1782 |
Outsource | AurA, AurB, CaMKI, CaMKII, CaMK4, CDK5, GSK3B, LYN, MAPK, MARK1, PKA, AMPK, PRKCA, PRKCE, ROCK, STK11(LKB1) | 3736 |
Motif | Identified Phosphoprotein and Phosphorylation Site | |||||
---|---|---|---|---|---|---|
PKA | Arhgap21 | Arhgap21 | Arhgap21 | Arhgap23 | Brsk1 | Brsk2 |
S472 | S851 | S875 | S401 | S324 | S383 | |
Bsn | Bsn | Cacna1b | Ccdc177 | Ccny | Cdk17 | |
S1987 | S2860 | S2219 | S303 | S301 | S180 | |
Chrna4 | Fam126b | Gpr75 | Hcn2 | Kcnh7 | Kif21b | |
S540 | S521 | S317 | S840 | S174 | S1150 | |
Madd | Mark1 | Nedd4l | Nf1 | Prickle2 | Prrt3 | |
S1038 | S394 | T353 | S2524 | S752 | S846 | |
Rap1gap | Rims1 | Sik3 | Syn1 | Taf4b | Ttc32 | |
S245 | S887 | S454 | S427 | S707 | S24 | |
MAPK | Ablim1 | Arhgap21 | Bsn | Cacna1e | Ccdc177 | Cdk17 |
S89 | S42 | Y3020 | S791 | S308 | T11 | |
Chrna4 | Chrna4 | Hcn3 | Lrfn4 | Madd | Madd | |
S540 | S543 | S633 | S627 | S1038 | T1045 | |
Nedd4l | Prrt3 | Rap1gap | Sipa1l1 | Sorbs2 | Spata2 | |
S329 | S834 | S213 | S1528 | S944 | S247 | |
Syn1 | ||||||
S427 | ||||||
Others | Arhgap21 | Atp6v1h | Cep170 | Gpr75 | Kcnh2 | Khnyn |
S856 | Y125 | S353 | T313 | S322 | S43 | |
Madd | Mapk8 | Rsl1d1 | Rsl1d1 | Sh2d5 | Ttc32 | |
S1089 | S210 | T314 | S316 | S126 | T18 |
Identified MAPK Candidate Substrates List | |||||||
---|---|---|---|---|---|---|---|
2010300C02Rik | Atg9a | Cdk18 | Epb4.1l3 | Lppr3 | Osbpl6 | Rasgrp2 | Ssh2 |
Aak1 | Bai1 | Cdkl5 | Epb49 | Lrfn4 | Pak7 | Rem2 | Stim1 |
Abi1 | Baiap2 | Cep170 | Erc2 | Lrrc7 | Panx2 | Rims1 | Syn1 |
Abi2 | Bcr | Chrna4 | Etl4 | Madd | Pclo | Rims2 | Syn2 |
Agap2 | Begain | Clasp2 | Fam171a1 | Map3k5 | Pfkfb2 | Rph3a | Syn3 |
Agfg1 | Brsk1 | Crtc2 | Fam171a2 | Map4 | Pip5k1c | Rrad | Synpo |
Akap6 | Brsk2 | Ctnnd2 | Fam171b | Mark1 | Pitpnm3 | Sh2d5 | Syt7 |
Als2 | Bsn | Cyth3 | Frmd4a | Mark3 | Plekha5 | Shank3 | Tanc2 |
Ampd2 | C17orf59 | Dab2ip | Gab2 | Mast1 | Plekho2 | Shisa7 | Tpd52 |
Ank2 | C2cd4c | Dennd1a | Git1 | Mast3 | Pola1 | Sipa1l1 | Tpd52l1 |
Ankrd34a | Cacna1b | Dennd4c | Gm1568 | Mbp | Ppfia2 | Sipa1l2 | Tsc2 |
Ankrd34b | Cacna1e | Dgkq | Gm15800 | Mink1 | Ppfia3 | Slc4a4 | Uhrf1bp1l |
Anks1b | Camk2g | Dlgap2 | Gpr158 | Mllt4 | Ppfia4 | Sorbs1 | Ulk1 |
Arhgap21 | Camkk1 | Dlgap3 | Hcn2 | Mprip | Prrt3 | Sorbs2 | Ulk2 |
Arhgap23 | Camkk2 | Dos | Hcn3 | Nav1 | Psd | Spata2 | Usp31 |
Arhgap32 | Camsap2 | Dpysl2 | Iqsec1 | Nav3 | Psd3 | Specc1 | Usp8 |
Arhgap39 | Caskin1 | Dpysl5 | Kcnb1 | Ndel1 | Rab11fip2 | Speg | Wdr47 |
Arhgef2 | Ccdc22 | Dstn | Kiaa0284 | Nelf | Ralgapa1 | Srcin1 | |
Arhgef6 | Ccny | Dtna | Kiaa0528 | Nhsl2 | Rap1gap | Srgap3 | |
Atat1 | Ccnyl1 | Eif3d | Kiaa1211 | Nyap2 | Rapgef2 | Ssfa2 | |
Total 157 |
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Ahammad, R.U.; Nishioka, T.; Yoshimoto, J.; Kannon, T.; Amano, M.; Funahashi, Y.; Tsuboi, D.; Faruk, M.O.; Yamahashi, Y.; Yamada, K.; et al. KANPHOS: A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain. Cells 2022, 11, 47. https://doi.org/10.3390/cells11010047
Ahammad RU, Nishioka T, Yoshimoto J, Kannon T, Amano M, Funahashi Y, Tsuboi D, Faruk MO, Yamahashi Y, Yamada K, et al. KANPHOS: A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain. Cells. 2022; 11(1):47. https://doi.org/10.3390/cells11010047
Chicago/Turabian StyleAhammad, Rijwan Uddin, Tomoki Nishioka, Junichiro Yoshimoto, Takayuki Kannon, Mutsuki Amano, Yasuhiro Funahashi, Daisuke Tsuboi, Md. Omar Faruk, Yukie Yamahashi, Kiyofumi Yamada, and et al. 2022. "KANPHOS: A Database of Kinase-Associated Neural Protein Phosphorylation in the Brain" Cells 11, no. 1: 47. https://doi.org/10.3390/cells11010047