Structural Insight on Functional Regulation of Human MINERVA Protein
Abstract
:1. Introduction
2. Results
2.1. Functional Analyses of Physiological Role of MINERVA
2.2. MINERVA Crystallization and Structure Determination
2.3. Overall Structure of MINERVAΔC
2.4. PH Domain of MINERVA Recognizes Phosphatidic Acid and Phosphatidylinositol 3-Phosphate
2.5. Functional Analyses of N- and C-Terminal Regions of MINERVAFL
3. Discussion
4. Materials and Methods
4.1. Cell Lines
4.2. Antibodies and Reagents
4.3. DNA Construct and siRNA
4.4. Immunoprecipitation
4.5. Cell Proliferation and Viability Assays
4.6. Western Blotting
4.7. Immunofluorescence Analysis
4.8. Cloning, Expression, and Purification of Recombinant MINERVA Constructs for Structure Determination and Affinity Assay
4.9. Cloning, Expression, and Purification of Keap1321–609 for Affinity Assay
4.10. Limited Trypsin Digestion of MINERVA Proteins
4.11. Crystllization, Data Collection, and Structure Determination
4.12. Size-Exclusion Chromatography with Multi-Angle Light Scattering (SEC–MALS)
4.13. In Silico Docking Experiment
4.14. Lipid Dot Blot Assay
4.15. Surface Plasmone Resonance (SPR) Analysis of MINERVA
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
MINERVA | Melanoma invasion by ERK |
PH domain | Pleckstrin homology domain |
PTM | Posttranslational modification |
SAD | Single-wavelength anomalous diffraction |
MRASU | Molecular replacementAsymmetric unit |
PA | Phosphatidic acid |
PI3P | Phosphatidylinositol (3)-phosphate |
ka | Association rate constant |
kd | Dissociation rate constant |
KD | Equilibrium dissociation constant |
References
- Yoon, H.S.; Hajduk, P.J.; Petros, A.M.; Olejniczak, E.T.; Meadows, R.P.; Fesik, S.W. Solution structure of a pleckstrin-homology domain. Nature 1994, 369, 672–675. [Google Scholar] [CrossRef] [PubMed]
- Lemmon, M.A. Pleckstrin homology (PH) domains and phosphoinositides. Biochem. Soc. Symp. 2007, 81–93. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Lemmon, M.A. Pleckstrin homology domains: Not just for phosphoinositides. Biochem. Soc. Trans. 2004, 32, 707–711. [Google Scholar] [CrossRef] [PubMed]
- Bar-Shavit, R.; Grisaru-Granovsky, S.; Uziely, B. PH-domains as central modulators driving tumor growth. Cell Cycle 2016, 15, 615–616. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Scheffzek, K.; Welti, S. Pleckstrin homology (PH) like domains-versatile modules in protein-protein interaction platforms. FEBS Lett. 2012, 586, 2662–2673. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Old, W.M.; Shabb, J.B.; Houel, S.; Wang, H.; Couts, K.L.; Yen, C.Y.; Litman, E.S.; Croy, C.H.; Meyer-Arendt, K.; Miranda, J.G.; et al. Functional proteomics identifies targets of phosphorylation by B-Raf signaling in melanoma. Mol. Cell 2009, 34, 115–131. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Sun, G.D.; Kobayashi, T.; Abe, M.; Tada, N.; Adachi, H.; Shiota, A.; Totsuka, Y.; Hino, O. The endoplasmic reticulum stress-inducible protein Niban regulates eIF2alpha and S6K1/4E-BP1 phosphorylation. Biochem Biophys. Res. Commun. 2007, 360, 181–187. [Google Scholar] [CrossRef] [PubMed]
- Boyd, R.S.; Adam, P.J.; Patel, S.; Loader, J.A.; Berry, J.; Redpath, N.T.; Poyser, H.R.; Fletcher, G.C.; Burgess, N.A.; Stamps, A.C.; et al. Proteomic analysis of the cell-surface membrane in chronic lymphocytic leukemia: Identification of two novel proteins, BCNP1 and MIG2B. Leukemia 2003, 17, 1605–1612. [Google Scholar] [CrossRef] [Green Version]
- Bamford, S.; Dawson, E.; Forbes, S.; Clements, J.; Pettett, R.; Dogan, A.; Flanagan, A.; Teague, J.; Futreal, P.A.; Stratton, M.R.; et al. The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. Br. J. Cancer 2004, 91, 355–358. [Google Scholar] [CrossRef] [PubMed]
- Forbes, S.A.; Beare, D.; Gunasekaran, P.; Leung, K.; Bindal, N.; Boutselakis, H.; Ding, M.; Bamford, S.; Cole, C.; Ward, S.; et al. COSMIC: Exploring the world’s knowledge of somatic mutations in human cancer. Nucleic. Acids Res. 2015, 43, D805–D811. [Google Scholar] [CrossRef]
- Zhou, X.; Yang, F.; Zhang, Q.; Miao, Y.; Hu, X.; Li, A.; Hou, G.; Wang, Q.; Kang, J. FAM129B promoted tumor invasion and proliferation via facilitating the phosphorylation of FAK signaling and associated with adverse clinical outcome of non-small cell lung cancer patients. Onco Targets 2018, 11, 7493–7501. [Google Scholar] [CrossRef] [Green Version]
- Cheng, K.C.; Lin, R.J.; Cheng, J.Y.; Wang, S.H.; Yu, J.C.; Wu, J.C.; Liang, Y.J.; Hsu, H.M.; Yu, J.; Yu, A.L. FAM129B, an antioxidative protein, reduces chemosensitivity by competing with Nrf2 for Keap1 binding. EBioMedicine 2019, 45, 25–38. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Deramaudt, T.B.; Dujardin, D.; Hamadi, A.; Noulet, F.; Kolli, K.; De Mey, J.; Takeda, K.; Ronde, P. FAK phosphorylation at Tyr-925 regulates cross-talk between focal adhesion turnover and cell protrusion. Mol. Biol. Cell 2011, 22, 964–975. [Google Scholar] [CrossRef] [PubMed]
- Oishi, H.; Itoh, S.; Matsumoto, K.; Ishitobi, H.; Suzuki, R.; Ema, M.; Kojima, T.; Uchida, K.; Kato, M.; Miyata, T.; et al. Delayed cutaneous wound healing in Fam129b/Minerva-deficient mice. J. Biochem. 2012, 152, 549–555. [Google Scholar] [CrossRef]
- Ji, H.; Lee, J.H.; Wang, Y.; Pang, Y.; Zhang, T.; Xia, Y.; Zhong, L.; Lyu, J.; Lu, Z. EGFR phosphorylates FAM129B to promote Ras activation. Proc. Natl. Acad. Sci. USA 2016, 113, 644–649. [Google Scholar] [CrossRef] [Green Version]
- Chen, S.; Evans, H.G.; Evans, D.R. FAM129B/MINERVA, a novel adherens junction-associated protein, suppresses apoptosis in HeLa cells. J. Biol. Chem. 2011, 286, 10201–10209. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Conrad, W.; Major, M.B.; Cleary, M.A.; Ferrer, M.; Roberts, B.; Marine, S.; Chung, N.; Arthur, W.T.; Moon, R.T.; Berndt, J.D.; et al. FAM129B is a novel regulator of Wnt/beta-catenin signal transduction in melanoma cells. F1000Research 2013, 2, 134. [Google Scholar] [CrossRef] [PubMed]
- Thinon, E.; Serwa, R.A.; Broncel, M.; Brannigan, J.A.; Brassat, U.; Wright, M.H.; Heal, W.P.; Wilkinson, A.J.; Mann, D.J.; Tate, E.W. Global profiling of co- and post-translationally N-myristoylated proteomes in human cells. Nat. Commun. 2014, 5, 4919. [Google Scholar] [CrossRef] [Green Version]
- Furukawa, M.; Xiong, Y. BTB protein Keap1 targets antioxidant transcription factor Nrf2 for ubiquitination by the Cullin 3-Roc1 ligase. Mol. Cell Biol. 2005, 25, 162–171. [Google Scholar] [CrossRef] [Green Version]
- Kensler, T.W.; Wakabayashi, N.; Biswal, S. Cell survival responses to environmental stresses via the Keap1-Nrf2-ARE pathway. Annu. Rev. Pharm. Toxicol. 2007, 47, 89–116. [Google Scholar] [CrossRef]
- Tang, Z.; Li, C.; Kang, B.; Gao, G.; Li, C.; Zhang, Z. GEPIA: A web server for cancer and normal gene expression profiling and interactive analyses. Nucleic Acids Res. 2017, 45, W98–W102. [Google Scholar] [CrossRef] [Green Version]
- Ward, J.J.; McGuffin, L.J.; Bryson, K.; Buxton, B.F.; Jones, D.T. The DISOPRED server for the prediction of protein disorder. Bioinformatics 2004, 20, 2138–2139. [Google Scholar] [CrossRef]
- McGuffin, L.J.; Bryson, K.; Jones, D.T. The PSIPRED protein structure prediction server. Bioinformatics 2000, 16, 404–405. [Google Scholar] [CrossRef] [PubMed]
- Slabinski, L.; Jaroszewski, L.; Rychlewski, L.; Wilson, I.A.; Lesley, S.A.; Godzik, A. XtalPred: A web server for prediction of protein crystallizability. Bioinformatics 2007, 23, 3403–3405. [Google Scholar] [CrossRef] [Green Version]
- Wilkins, M.R.; Gasteiger, E.; Bairoch, A.; Sanchez, J.C.; Williams, K.L.; Appel, R.D.; Hochstrasser, D.F. Protein identification and analysis tools in the ExPASy server. Methods Mol. Biol 1999, 112, 531–552. [Google Scholar] [CrossRef] [PubMed]
- Krissinel, E.; Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 2007, 372, 774–797. [Google Scholar] [CrossRef]
- Holm, L. Benchmarking Fold Detection by DaliLite v.5. Bioinformatics 2019. [Google Scholar] [CrossRef] [PubMed]
- Jackson, S.G.; Zhang, Y.; Haslam, R.J.; Junop, M.S. Structural analysis of the carboxy terminal PH domain of pleckstrin bound to D-myo-inositol 1,2,3,5,6-pentakisphosphate. BMC Struct. Biol. 2007, 7, 80. [Google Scholar] [CrossRef] [Green Version]
- Catimel, B.; Kapp, E.; Yin, M.X.; Gregory, M.; Wong, L.S.; Condron, M.; Church, N.; Kershaw, N.; Holmes, A.B.; Burgess, A.W. The PI(3)P interactome from a colon cancer cell. J. Proteom. 2013, 82, 35–51. [Google Scholar] [CrossRef]
- Friesner, R.A.; Murphy, R.B.; Repasky, M.P.; Frye, L.L.; Greenwood, J.R.; Halgren, T.A.; Sanschagrin, P.C.; Mainz, D.T. Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J. Med. Chem. 2006, 49, 6177–6196. [Google Scholar] [CrossRef] [Green Version]
- Levine, E.M.; Becker, Y.; Boone, C.W.; Eagle, H. Contact Inhibition, Macromolecular Synthesis, and Polyribosomes in Cultured Human Diploid Fibroblasts. Proc. Natl. Acad. Sci. USA 1965, 53, 350–356. [Google Scholar] [CrossRef] [Green Version]
- Wang, X.; Devaiah, S.P.; Zhang, W.; Welti, R. Signaling functions of phosphatidic acid. Prog. Lipid Res. 2006, 45, 250–278. [Google Scholar] [CrossRef] [PubMed]
- Jang, J.H.; Lee, C.S.; Hwang, D.; Ryu, S.H. Understanding of the roles of phospholipase D and phosphatidic acid through their binding partners. Prog. Lipid Res. 2012, 51, 71–81. [Google Scholar] [CrossRef] [PubMed]
- Petiot, A.; Faure, J.; Stenmark, H.; Gruenberg, J. PI3P signaling regulates receptor sorting but not transport in the endosomal pathway. J. Cell Biol. 2003, 162, 971–979. [Google Scholar] [CrossRef]
- Zhang, D.D.; Lo, S.C.; Cross, J.V.; Templeton, D.J.; Hannink, M. Keap1 is a redox-regulated substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex. Mol. Cell Biol. 2004, 24, 10941–10953. [Google Scholar] [CrossRef] [Green Version]
- Kobayashi, A.; Kang, M.I.; Okawa, H.; Ohtsuji, M.; Zenke, Y.; Chiba, T.; Igarashi, K.; Yamamoto, M. Oxidative stress sensor Keap1 functions as an adaptor for Cul3-based E3 ligase to regulate proteasomal degradation of Nrf2. Mol. Cell Biol. 2004, 24, 7130–7139. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Williamson, M.P. The structure and function of proline-rich regions in proteins. Biochem. J. 1994, 297, 249–260. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Aitio, O.; Hellman, M.; Kazlauskas, A.; Vingadassalom, D.F.; Leong, J.M.; Saksela, K.; Permi, P. Recognition of tandem PxxP motifs as a unique Src homology 3-binding mode triggers pathogen-driven actin assembly. Proc. Natl. Acad. Sci. USA 2010, 107, 21743–21748. [Google Scholar] [CrossRef] [Green Version]
- Tobi, D.; Bahar, I. Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state. Proc. Natl. Acad. Sci. USA 2005, 102, 18908–18913. [Google Scholar] [CrossRef] [Green Version]
- Kristensen, A.R.; Gsponer, J.; Foster, L.J. A high-throughput approach for measuring temporal changes in the interactome. Nat. Methods 2012, 9, 907–909. [Google Scholar] [CrossRef]
- Guo, Z.; Neilson, L.J.; Zhong, H.; Murray, P.S.; Zanivan, S.; Zaidel-Bar, R. E-cadherin interactome complexity and robustness resolved by quantitative proteomics. Sci. Signal. 2014, 7, rs7. [Google Scholar] [CrossRef] [Green Version]
- Otwinowski, Z.; Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzym. 1997, 276, 307–326. [Google Scholar]
- Kabsch, W. XDS. Acta Cryst. D Biol. Cryst. 2010, 66, 125–132. [Google Scholar] [CrossRef] [Green Version]
- Adams, P.D.; Afonine, P.V.; Bunkoczi, G.; Chen, V.B.; Davis, I.W.; Echols, N.; Headd, J.J.; Hung, L.W.; Kapral, G.J.; Grosse-Kunstleve, R.W.; et al. PHENIX: A comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D Biol. Cryst. 2010, 66, 213–221. [Google Scholar] [CrossRef] [Green Version]
- Terwilliger, T.C. Automated main-chain model building by template matching and iterative fragment extension. Acta Cryst. D Biol. Cryst. 2003, 59, 38–44. [Google Scholar] [CrossRef] [PubMed]
- Emsley, P.; Lohkamp, B.; Scott, W.G.; Cowtan, K. Features and development of Coot. Acta Cryst. D Biol. Cryst. 2010, 66, 486–501. [Google Scholar] [CrossRef] [PubMed] [Green Version]
- Murshudov, G.N.; Vagin, A.A.; Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Cryst. D Biol. Cryst. 1997, 53, 240–255. [Google Scholar] [CrossRef]
- Afonine, P.V.; Grosse-Kunstleve, R.W.; Echols, N.; Headd, J.J.; Moriarty, N.W.; Mustyakimov, M.; Terwilliger, T.C.; Urzhumtsev, A.; Zwart, P.H.; Adams, P.D. Towards automated crystallographic structure refinement with phenix.refine. Acta Cryst. D Biol. Cryst. 2012, 68, 352–367. [Google Scholar] [CrossRef] [Green Version]
- Vagin, A.; Teplyakov, A. Molecular replacement with MOLREP. Acta Cryst. D Biol. Cryst. 2010, 66, 22–25. [Google Scholar] [CrossRef]
- Chen, V.B.; Arendall, W.B., 3rd; Headd, J.J.; Keedy, D.A.; Immormino, R.M.; Kapral, G.J.; Murray, L.W.; Richardson, J.S.; Richardson, D.C. MolProbity: All-atom structure validation for macromolecular crystallography. Acta Cryst. D Biol. Cryst. 2010, 66, 12–21. [Google Scholar] [CrossRef] [Green Version]
PDB Entry | 7CTP |
---|---|
Diffraction source | SPring-8 BL44XU |
Wavelength (Å) | 1.0000 |
Temperature (K) | 100 |
Space group | P212121 |
a, b, c (Å) | 55.559, 56.283, 201.01 |
α, β, γ (°) | 90, 90, 90 |
Resolution range (Å) a | 49.11–1.80 (1.86–1.80) |
Total No. of reflections a | 443,604 (43,898) |
No. of unique reflections a | 59,470 (5838) |
Completeness (%) a | 99.98 (99.98) |
Redundancy a | 7.5 (7.5) |
〈I/σ(I)〉 a | 18.24 (2.24) |
Rmeasa | 0.063 (0.825) |
Rpima | 0.023 (0.299) |
CC1/2 a | 0.999 (0.799) |
Overall B factor from Wilson plot (Å2) | 30.86 |
No. of reflections, working set a | 59,467 (5838) |
No. of reflections, test set a | 2925 (256) |
Final Rwork b | 0.2038 |
Final Rfree b | 0.2355 |
No. of non-H atoms | 4806 |
Protein | 4519 |
Glycerol | 18 |
Water | 269 |
Root-mean-square deviations | |
Bonds (Å) | 0.007 |
Angles (°) | 1.08 |
Average B factors (Å2) | 37.41 |
Protein | 37.33 |
Glycerol | 45.58 |
Water | 37.33 |
Ramachandran plot c | |
Favored (%) | 99.45 |
Allowed (%) | 0.55 |
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Hahn, H.; Lee, D.-E.; Jang, D.M.; Kim, J.; Lee, Y.; Cheong, H.; Han, B.W.; Kim, H.S. Structural Insight on Functional Regulation of Human MINERVA Protein. Int. J. Mol. Sci. 2020, 21, 8186. https://doi.org/10.3390/ijms21218186
Hahn H, Lee D-E, Jang DM, Kim J, Lee Y, Cheong H, Han BW, Kim HS. Structural Insight on Functional Regulation of Human MINERVA Protein. International Journal of Molecular Sciences. 2020; 21(21):8186. https://doi.org/10.3390/ijms21218186
Chicago/Turabian StyleHahn, Hyunggu, Dong-Eun Lee, Dong Man Jang, Jiyoun Kim, Yeon Lee, Heesun Cheong, Byung Woo Han, and Hyoun Sook Kim. 2020. "Structural Insight on Functional Regulation of Human MINERVA Protein" International Journal of Molecular Sciences 21, no. 21: 8186. https://doi.org/10.3390/ijms21218186
APA StyleHahn, H., Lee, D.-E., Jang, D. M., Kim, J., Lee, Y., Cheong, H., Han, B. W., & Kim, H. S. (2020). Structural Insight on Functional Regulation of Human MINERVA Protein. International Journal of Molecular Sciences, 21(21), 8186. https://doi.org/10.3390/ijms21218186