Extremely Slow Intramolecular Diffusion in an Unfolded Protein
We have observed, intramolecular diffusion of the B1 domain of protein L during folding using a serpentine microfluidic mixer (top) and Trp-Cys contact quenching.  The  diffusion-limited rate is much faster in high levels of denaturant and slows down about 20-fold during the 250 microsecond mixing time (bottom, left).  Since the protein chain also compacts significantly, the intramolecular diffusion coefficient, D, is about 500 times slower in water than high dentaturant (bottom, right).  This potentially changes the way we think about protein folding as a rapid search process for native contacts or as diffusion on a smooth energy landscape.  (see MSU press release)
Aggregation of a-synuclein is Controlled by Intramolecular Diffusion
By placing Trp and Cys at several locations within the protein sequence, we measured intramolecular diffusion at different temperatures, neutral and low pH and with the the mutation A30P (which accelerates Parkinson's disease).  We find that under conditions that aggregation is more likely (higher temperature and low pH) the protein is more compact and diffusion is slower.  We think aggregation is most likely when the rate of reconfiguration (related to diffusion) is about the same as the rate bimolecular association.  When reconfiguration is faster, the protein is too diffusive to make stabilizing bimolecular contacts.  When reconfiguration is slower, stabilizing contacts (ie hydrophobic residues) are not exposed very often.  But if the protein reconfiguration rate is in a dangerous middle regime, aggregation is likely.  (MSU press release)
Curcumin, a naturally occuring compound in the spice tumeric, binds strongly to monomeric a-synuclein, prevents aggregation and signifcantly increases the reconfiguration rate of the protein, especially at high temperatue.  This suggests curcumin rescues the protein from the dangerous regime by breaking up intramolecular interactions and increasing reconfiguration.
Curcumin Prevents Aggregation of a-synuclein by Increasing Reconfiguration
     Laboratory of Lisa Lapidus
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Evidence for Multiple Folding Pathways in Villin


Most protein folding theories assume the folding kinetics depend only on the final conditions, not the initial conditions.  In this experiment on the fast folding villin HP35 we have found that folding experiments conducted by T-jump (which partially unfolds the protein) and ultrarapid mixing (which partially folds the protein) with the same final conditions have folding rates that differ by ~5X.  This suggests that the unfolded state in the mixing experiments is very different (and probably more diverse) than the unfolded state in the T-jump experiments.  We are exploring new models of protein folding to account for these results.