UC Riverside

Oscillations in protein levels or activation state are ubiquitous in eukaryotic signaling pathways, but the function of these oscillations remains unclear. We find that p38α MAPK activation state oscillates at multiple frequencies in response to stress rather than at a singular frequency. Fourier analysis of p38α activation state measured with a novel FRET sensor shows that unique stressors including IL-1β, SARS-CoV-2 Spike protein, and sorbitol induce unique response patterns in the frequency domain. Analysis of statistically over represented frequencies suggests that frequency bins are fixed and organized as harmonics with a fundamental frequency of 0.09 hr−1(p=0.04). Cross spectral dynamics between p38α and a substrate indicate that substrate activation behaves similarly to a forced oscillator system being driven at resonance. We have developed a model that characterizes the MAPK phosphorylation cascade as a chemical resonator that impart multiple frequencies on p38α, allowing the kinase to regulate its substrates through resonance selectivity. Stochastic simulations of substrates being driven on and off-resonance produce spectra comparable to experimental data.

Experiments on E. coli expressing a transposon of the IS200/IS5605 family reveal that expression of transposon protein TnpB leads to a higher excision rate. Furthermore, cells that excise possess TnpB at a significantly higher expression level than cells that don’t, with TnpA expression levels making no discernible difference in excision dynamics.

We present a protocol for purification of SARS-CoV-2 structural proteins using a bacterial expression system, SUMO tags, and affinity purification methods. We further report a method to insert synthesized dimers into a suspended lipid membrane in a homogeneous orientation. AFM and Cryo-EM in tandem with molecular dynamics simulations show membrane thinning around the M protein and a propensity to induce local membrane curvature.