Team:TU-Eindhoven/Project/Background
Our project includes different proteins and an underlying concept seen in nature. In this section we will provide some additional information about the parts and principles on which our project is based.
Gelation and Liquid-Liquid Phase Separation
As the name of our project (GUPPI) states, we are making a system that forms a gel based on protein protein interactions. This principle is already known to most cells, for example, nucleolus, P-bodies and stress granules. The cell uses them to create a desired environment, for concentrating molecules and as protection.[1]
Classical views on cellular organisation show that this is carried out by membrane surrounded organelles like the Golgi and Endoplasmic Reticulum. In recent years a lot has become clear about a new type of organizer, called membraneless organelles. These organelles are phase separated from their surrounding environment and separation and concentration of biological macromolecules can be achieved within these structures.
Examples of membraneless organelles are nucleolus, P bodies and stress granules. There is a wide range of the biological functions that membraneless organelles facilitate. The nucleolus is an example of a membraneless organelle and it produces ribosomes. P-bodies, also membraneless, are required for the translation and transport of mRNA (lack of P-bodies results in large amounts of untranslated mRNA). Next to the protein processing, protein storage and transport, the organelles are also important for signalling. An example is the activation of MAP kinase by the clustering of binding partners to a phosphorylated TCR.[2]
Examples of membraneless organelles are nucleolus, P bodies and stress granules. There is a wide range of the biological functions that membraneless organelles facilitate. The nucleolus is an example of a membraneless organelle and it produces ribosomes. P-bodies, also membraneless, are required for the translation and transport of mRNA (lack of P-bodies results in large amounts of untranslated mRNA). Next to the protein processing, protein storage and transport, the organelles are also important for signalling. An example is the activation of MAP kinase by the clustering of binding partners to a phosphorylated TCR.[2]
Phase separation is a phenomenon seen when molecules reach their miscibility limit in solution. i.e. if a molecule concentration is too high it will phase separate. A well known example being oil droplets in water. What we know of membraneless organelles is that these often contain multivalent macromolecules which have either intra- or inter-molecular interactions. Multivalent molecules inherently assembly into larger structures leading to high local concentrations driving phase separation of membraneless organelles into liquid-like droplets [1,3-4]. In other words, phase separation is a consequence of high molecular concentration i.e. clustering of molecules. Since our system consists out of two proteins which undergo intermolecular interactions, we expect them to cluster and phase separate.
[1] S. F. Banani, H. O. Lee, A. A. Hyman, and M. K. Rosen, “Biomolecular condensates: organizers of cellular biochemistry,” Nat. Rev. Mol. Cell Biol., vol 18, pp 285-298 2017.
[2] X. Su, X. Su, J. A. Ditlev, E. Hui, W. Xing, S. Banjade, J. Okrut, D. S. King, J. Taunton, M. K. Rosen, and R. D. Vale, “Phase separation of signaling molecules promotes T cell receptor signal transduction,” Nature, vol. 9964, no. April, pp. 1–9, 2016.
[3] L. Bergeron-Sandoval, N. Safaee and S.W. Michnick, “Mechanisms and Consequences of Macromolecular Phase Separation”, Cell, vol. 165, issue 5, pp. 1067-1079, 2016.
[4] Y. Lin, D.S.W. Protter, M.K. Rosen and R. Parker, “Formation and Maturation of Phase-Separated Liquid Droples by RNA-Binding Proteins”, Molecular Cell, vol. 60, no. 2, pp. 208-219, 2015.
[2] X. Su, X. Su, J. A. Ditlev, E. Hui, W. Xing, S. Banjade, J. Okrut, D. S. King, J. Taunton, M. K. Rosen, and R. D. Vale, “Phase separation of signaling molecules promotes T cell receptor signal transduction,” Nature, vol. 9964, no. April, pp. 1–9, 2016.
[3] L. Bergeron-Sandoval, N. Safaee and S.W. Michnick, “Mechanisms and Consequences of Macromolecular Phase Separation”, Cell, vol. 165, issue 5, pp. 1067-1079, 2016.
[4] Y. Lin, D.S.W. Protter, M.K. Rosen and R. Parker, “Formation and Maturation of Phase-Separated Liquid Droples by RNA-Binding Proteins”, Molecular Cell, vol. 60, no. 2, pp. 208-219, 2015.
