Phosphorylation systems

In order to react to their environment living cells use signalling networks to propagate information from receptors, which are often on the surface of the cell, to the nucleus where transcription factors can change the behaviour of the cell by changing the rate of production of different proteins. Signalling networks often make use of phosphorylation systems. These are networks of proteins whose enzymatic activity is switched on or off by phosphorylation or dephosphorylation. When switched on they catalyse the (de-)phophorylation of other proteins. The information passing through the network is encoded in the phosphate groups attached to specific amino acids in the proteins concerned. A frequently occurring example of this type of system is the MAPK cascade discussed in a previous post. There the phosphate groups are attached to the amino acids serine, threonine and tyrosine. Another type of system, which is common in bacteria, are the two-component systems where the phosphate groups are attached to histidine and aspartic acid.

There is a standard mathematical model for the MAPK cascade due to Huang and Ferrell. It consists of three layers, each of which is a simple or dual futile cycle. Numerical and heuristic investigations indicate that the Huang-Ferrell model admits periodic solutions for certain values of the parameters. Together with Juliette Hell we set out to find a rigorous proof of this fact. In the beginning we pursued the strategy of showing that there are relaxation oscillations. An important element of this is to prove that the dual futile cycle exhibits bistability, a fact which is interesting in its own right, and we were able to prove this, as has been discussed here. In the end we shifted to a different strategy in order to prove the existence of periodic solutions. The bistability proof used a quasistationary (Michaelis-Menten) reduction of the Huang-Ferrell system. It applied bifurcation theory to the Michaelis-Menten system and geometric singular perturbation theory to lift this result to the original system. To prove the existence of periodic solutions we used a similar strategy. This time we showed the presence of Hopf bifurcations in a Michaelis-Menten system and lifted those. The details are contained in a paper which is close to being finished. In the meantime we wrote a review article on phosphorylation systems. Here I want to mention some of the topics covered there.

The MAPK cascade, which is the central subject of the paper is not isolated in its natural biological context. It is connected with other biochemical reactions which can be thought of as feedback loops, positive and negative. As already mentioned, the cascade itself consists of layers which are futile cycles. The paper first reviews what is known about the dynamics of futile cycles and the stand-alone MAPK cascasde. The focus is on phenomena such as multistability, sustained oscillations and (marginally) chaos and what can be proved about these things rigorously. The techniques which can be used in proofs of this kind are also reviewed. Given the theoretical results on oscillations it is interesting to ask whether these can be observed experimentally. This has been done for the Raf-MEK-ERK cascade by Shankaran et. al. (Mol. Syst. Biol. 5, 332). In that paper it is found that the experimental results do not fit well to the oscillations in the isolated cascade but they can be modelled better when the cascade is embedded in a negative feedback loop. Two other aspects are also built into the models used – the translocation of ERK from the cytosol to the nucleus (which is what is actually measured) and the fact that when ERK and MEK are not fully phosphorylated they can bind to each other. It is also briefly mentioned in our paper that a negative feedback can arise through the interaction of ERK with its substrates, as explained in Liu et. al. (Biophys. J. 101, 2572). For the cascade as treated in the Huang-Ferrell model with feedback added no rigorous results are known yet. (For a somewhat different system there is result on oscillations due to Gedeon and Sontag, J. Diff. Eq. 239, 273, which uses the strategy based on relaxation oscillations.)

In our paper there is also an introduction to two-component systems. A general conclusion of the paper is that phosphorylation systems give rise to a variety of interesting mathematical problems which are waiting to be investigated. It may also be hoped that a better mathematical understanding of this subject can lead to new insights concerning the biological systems being modelled. Biological questions of interest in this context include the following. Are dynamical features of the MAPK cascade such as oscillations desirable for the encoding of information or are they undesirable side effects? To what extent do feedback loops tend to encourage the occurrence of features of this type and to what extent do they tend to suppress them? What are their practical uses, if any? If the function of the system is damaged by mutations how can it be repaired? The last question is of special interest due to the fact that many cancer cells have mutations in the Raf-MEK-ERK cascade and there have already been many attempts to overcome their negative effects using kinase inhibitors, some of them successful. A prominent example is the Raf inhibitor Vemurafenib which has been used to treat metastatic melanoma.