SOURCES

Chaperone Proteins

[3] Braakman, I., Hebert, D. N. (2013) Protein Folding in the Endoplasmic Reticulum. NCBI. Cold spring Harb Perspect Biol 5(5):a013201. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632058/

Unfolded Protein Response

[1] (2010). BiP Availability Distinguishes States of Homeostasis and Stress in the Endoplasmic Reticulum of Living Cells. Molecular Biology of the Cell 21(12):1909-1921.

[2] (2013). A modified UPR stress sensing system reveals a novel tissue distribution of IRE1/XBP1 activity during normal Drosophila development. Cell Stress and Chaperones 18(3):307-319.

[3] Karp, G. (2010). Cell Biology. 6th ed. Hoboken, N.J.: Wiley.

ER Degradation

[1 ](2014). ER-associated degradation: Protein quality control and beyond. Journal of Cell Biology 204(6):868-878.

[2] (2019). Proteasomal ad lysosomal clearance of faulty secretory proteins: ER associated degradation (ERAD) and ER to lysosome associated degradation (ERLAD) pathways. Critical Reviews in Biochemistry and Molecular Biology 54(2):153-163.

[3](2018). ER-to-lysosome-associated degradation of proteasome-resistant ATZ polymers occurs via receptor-mediated vesicular transport. EMBO Journal 37(17): e99259 doi: https://doi.org/10.15252/embj.201899259

Post Translational Modification

[1] Hubbard, S. R. and Till, J. H. 2000. Protein tyrosine kinase structure and function. Annu Rev Biochem 69, pp. 373-398. doi: 10.1146/annurev.biochem.69.1.373

[2] Edelman, A. M. et al. 1987. Protein serine/threonine kinases. Annu Rev Biochem 56, pp. 567-613. doi: 10.1146/annurev.bi.56.070187.003031

[3] Lindberg, R. A. et al. 1992. Dual-specificity protein kinases: will any hydroxyl do? Trends Biochem Sci 17(3), pp. 114-119. doi: 10.1016/0968-0004(92)90248-8

[4] Chen, D. et al. 1999. Regulation of transcription by a protein methyltransferase. CH3 Science 284(5423), pp. 2174-2177. doi: 10.1126/science.284.5423.2174

[5] Polevoda, B. and Sherman, F. 2000. Nalpha -terminal acetylation of eukaryotic proteins. J Biol Chem 275(47), pp. 36479-36482. doi: 10.1074/jbc.R000023200

[6] iang, H. et al. 2018. Protein Lipidation: Occurrence, Mechanisms, Biological Functions, and Enabling Technologies. Chem Rev 118(3), pp. 919-988. doi: 10.1021/acs.chemrev.6b00750

[7] Hart, G. W. 1992. Glycosylation. Curr Opin Cell Biol 4(6), pp. 1017-1023. doi: 10.1016/0955-0674(92)90134-x

[8] Zurlo, G. et al. 2016. New Insights into Protein Hydroxylation and Its Important Role in Human Diseases. Biochim Biophys Acta 1866(2), pp. 208-220. doi: 10.1016/j.bbcan.2016.09.004

[9] Sipila, K. H. et al. 2018. Proline hydroxylation in collagen supports integrin binding by two distinct mechanisms. J Biol Chem 293(20), pp. 7645-7658. doi: 10.1074/jbc.RA118.002200

[10] Hartley, B. S. 1960. Proteolytic enzymes. Annu Rev Biochem 29, pp. 45-72. doi: 10.1146/annurev.bi.29.070160.000401

[11] Morris, D. P. et al. 1993. Characterization of the purified vitamin K-dependent gamma-glutamyl carboxylase. J Biol Chem 268(12), pp. 8735-8742.

[12] Bradbury, A. F. and Smyth, D. G. 1991. Peptide amidation. Trends Biochem Sci 16(3), pp. 112-115. doi: 10.1016/0968-0004(91)90044-v

[13] Wilkinson, K. D. 2005. The discovery of ubiquitin-dependent proteolysis. Proc Natl Acad Sci U S A 102(43), pp. 15280-15282. doi: 10.1073/pnas.0504842102

COPII Vesicles

[1] Karp, G. (2010). Cell Biology. 6th ed. Hoboken, N.J.: Wiley.

[2] Nie, C., Wang, H., Wang, R., Ginsburg, D. and Xiao-Wei, C. (2018). Dimeric sorting code for concentrative cargo selection by the COPII coat. Proceedings of the National Academy of Sciences of the United States of America 115(14):3155-3162 doi: https://dx.doi.org/10.1073%2Fpnas.1704639115

[3] Sato, K. and Nakano, A. (2007). Mechanisms of COPII vesicle formation and protein sorting. FEBS Letters 581(11):2076-2082.

Transport through the golgi

[1] Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. (2002a). Transport from the Trans Golgi Network to Lysosomes.

[2] Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. and Walter, P. (2002b). Transport from the Trans Golgi Network to the Cell Exterior: Exocytosis.

[5] Glick, B. S., Elston, T. and Oster, G. (1997). A cisternal maturation mechanism can explain the asymmetry of the Golgi stack. FEBS Lett 414(2):177-181.

[6] Glick, B. S. and Luini, A. (2011). Models for Golgi Traffic: A Critical Assessment. In: Cold Spring Harb Perspect Biol. Vol. 3.

[7] Gomez-Navarro, N. and Miller, E. (2016). Protein sorting at the ER-Golgi interface. In: J Cell Biol. Vol. 215. pp. 769-778.

[8] Hua, Z. and Graham, T. R. (2013). The Golgi Apparatus.

[9] Lodish, H., Berk, A., Zipursky, S. L., Matsudaira, P., Baltimore, D. and Darnell, J. (2000). Protein Glycosylation in the ER and Golgi Complex.

COP1 Vesicles

[1] Arakel EC, Schwappach B. Formation of COPI-coated vesicles at a glance. Journal of cell science. 2018;131(5).

[2] Beck R, Ravet M, Wieland FT, Cassel D. The COPI system: Molecular mechanisms and function. FEBS Letters. 2009;583(17):2701-9.

Exocytosis

[1] Karp G. Cell biology. 7th ed. / International student version. ed. Hoboken, N.J.: Hoboken, N.J. : Wiley; 2014.

[2] Alberts B. Molecular biology of the cell. Sixth edition. ed. Johnson A, Lewis J, Morgan D, Raff MC, Roberts K, Walter P, editors: New York, NY ; Abingdon : Garland Science, Taylor and Francis Group; 2014.

[3] Gerber SH, Südhof TC. Molecular determinants of regulated exocytosis. Diabetes. 2002;51 Suppl 1:S3.

[4] Chia PZC, Gleeson PA. Membrane tethering. F1000prime reports. 2014;6:74.

[5] Berg JM. Biochemistry. 7th ed. / International ed. ed. Tymoczko JL, Stryer L, editors. New York : Basingstoke: New York : W. H. Freeman ; Basingstoke : Palgrave Macmillan; 2012.

[6] Han J, Pluhackova K, Böckmann RA. The Multifaceted Role of SNARE Proteins in Membrane Fusion. Frontiers in Physiology. 2017;8.

[7] Bombardier JP, Munson M. Three steps forward, two steps back: mechanistic insights into the assembly and disassembly of the SNARE complex. Current Opinion in Chemical Biology. 2015;29:66-71.

[8] Roche S, Albertini A, Lepault J, Bressanelli S, Gaudin Y. Structures of vesicular stomatitis virus glycoprotein: membrane fusion revisited. Cellular and Molecular Life Sciences. 2008;65(11):1716-28.

[9] Dirk F, Sutton RB, Axel TB, Reinhard J. Conserved structural features of the synaptic fusion complex: SNARE proteins reclassified as Q- and R-SNAREs. Proceedings of the National Academy of Sciences of the United States of America. 1998;95(26):15781.

[10] Ungermann C, Langosch D. Functions of SNAREs in intracellular membrane fusion and lipid bilayer mixing. Journal Of Cell Science. 2005;118(17):3819-28.

Rabs

[9] Yang, X., Li, X., Zhang, Y., Rodriguez, L., Xiang, M., Wang, H., Zheng, X.F.S. (2016) Rab1 in cell signalling cancer and other diseases. Oncogene ;35(44):5699-5704. Available at: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5396462/

[10] Alfrink, H.L., Zwart,R., Cavanillas,M.L., ScgindlermA.J., Baas, f., Scheper, W. (2012) Rab6 is a modulator of the unfolded ptron response: implications on alzheimers disease. J Alzheimers Dis 28(4):917-29. Available at: https://www.ncbi.nlm.nih.gov/pubmed/22124028

[11] Hoozemans, J.J., Veerhuis, R., Van Haastert, E.S., Rozemuller, J.M., Baas, F., Eikelenboom, P., Scheper, W. (2005) The unfolded response is activated in alzheimers disease. Acta Neuropathol 110#(2):165-72. Available at: https://www.ncbi.nlm.nih.gov/pubmed/15973543

[12] Walworth, N.C., Brennwald, P., Kabcenell, A.K., Garrett, M., Novick, P (1992) hydrolysis is GTP by Sec4 protein plays an important role in vesicular transport and is stimulated by a GTPase-activating protein in Saccharomyces Cervisiae. Mol Cell Biol 12(5):2017-28. Available at: https://www.ncbi.nlm.nih.gov/pubmed/1569938

SNAREs

[13] Rebane, A.A., Wang, B., Ma. L., Auclair, S,M., Qu, H., Coleman, J., Krishankumar, S., Rothman, J.E., Zhang, Y (no date) Twodisease causing SNAP-25B mutations Selectively impair SNARE C-terminal Assembly. Department of cellbiology, Yale School of medicine. Available at: https://discovery.ucl.ac.uk/id/eprint/10049829/1/Rebane%20et%20al_JMB%202018.pdf

[10] Ungermann C, Langosch D. Functions of SNAREs in intracellular membrane fusion and lipid bilayer mixing. Journal Of Cell Science. 2005;118(17):3819-28.

Prokaryotic Secretion

[16] Depluverez, S., Devos, S., Devreese, B. (2016) the role of bacterial secretion systems in the virulence of gram-negative airway pathogens associated with cystic fibrosis. Front Microbiol. Available at: https://www.frontiersin.org/articles/10.3389/fmicb.2016.01336/full