Question

.What are protein conformational changes and describe FIVE examples of their involvement in any aspect of signal transduction. One of the examples MUST be the involvement of kinases.

Describe the stages of the cell cycle and what happens in each stage, making sure to include what is happening to the DNA. For M phase, describe all stages. If you were looking at cells under the microscope, what would you use as a distinguishing feature for each stage.

Answer 1

Protein conformational dynamics simultaneously allow promiscuity and specificity in binding. The multiple conformations of the free EphA4 ligand-binding domain observed in two new EphA4 crystal structures provide a unique insight into the conformational dynamics of EphA4 and its signaling pathways. Cell proliferation, differentiation, migration and adhesion are essential processes in development, morphing cells into critical anatomical structures. When cells approach each other, they may have a seemingly simple choice between adhesion and repulsion; however, the precise positioning of cells, as in the case of vascular patterning or in controlling axon growth in the assembly of topographic neural maps, is highly complex.

Conformational selection and population shift in protein binding and signal transduction are receptor, and ligand, concentration-sensitive. Therefore, it is no wonder that nature widely uses conformational dynamics to allow a graded signal response to stimuli. Eph-ephrin binding can lead to cell repulsion or adhesion. Within this framework, between these two extreme responses, Eph-ephrin-guided cell positioning depends on their ability to assemble into signaling complexes according to the concentration and affinities of the Ephs and ephrins.

The conformational states and dynamics observed for EphA4 can help in furthering understanding of the allosteric signal relay in Eph-ephrin signal transduction. These same principles apply more broadly to signaling within and across cells. Examples include the ubiquitination pathway, where E3 ligases mediate ubiquitin transfer from the E2 conjugating enzymes to the substrates. An E2 can bind multiple E3s, and analysis of E2-E3 complexes suggested that loop L1 of E2s is critical. Slightly different conformations of the loop can lead to different specific interactions with E3s, and in this way distinguish between HECT E3s and RING-finger type E3s. Even in the presumably inert cullin scaffolding proteins, it was observed that different loop lengths in the amino-terminal domains confer different dynamical behavior, which allosterically affects the binding site, and thus the choice of partner. Dynamics were also shown to play a prominent role in the protein kinase hub proteins. In protein kinase A (PKA), cAMP acts as a dynamic and allosteric activator, coupling the two lobes of apo PKA, and priming the enzyme for catalysis. NMR and crystallography indicated that a conformational selection rather than an induced-fit mechanism governs substrate recognition.

Signaling across long distances is a multistep pathway. Many of the molecules along the pathway have multiple partners, which bind through the same site. Which partner molecule is selected at a given time is critical in deciding the cellular response. Qin and colleagues provide data that clearly illustrate that the binding sites have multiple pre-existing conformations that can select the partner. The principles described for the Eph/ephrin pathway are general, and can be expected to apply to other signaling pathways.