Protein folding and aggregation are processes that constantly interact, sometimes leading to disease. Both protein folding and protein aggregation are sensitive to pressure, a thermodynamically simpler variable than temperature or solvent additives. We develop a new pressure jump simultaneously capable of >2500 atm pressure drops in <700 nanoseconds on <1 nM of protein sample. The experiment will be used to study the interplay of folding and aggregation of the Syrian hamster prion ShPrP, which is known to have very fast pressure-jump kinetic phases that could not be resolved by conventional instruments. Pressure- and concentration-dependent studies will reveal how formation of early folding intermediates and subsequent formation of the native state compete with transient aggregation that could eventually lead to formation of protofibrils. As a second pressure jump project, we also study in detail the folding of lambda repressor mutants designed to alter the packing and secondary structure propensity of the protein. For folding studies, the pressure drop provides an alternative refolding method that perturbs secondary structure less than temperature jump experiments. We picked lambda repressor because rich T-jump data already exist, and T-jump and P-jump experiments will be interesting to compare. All experiments will be analyzed with a folding or folding/aggregation master equation kinetics model that is useful for comparison with Markov dynamics derived from molecular dynamics simulation. We collaborate with the Schulten and Pande group who will carry out relevant simulations. The goal is to build a good low-resolution model of the folding or folding/aggregation energy landscape of these proteins.
Many diseases are caused by the competition between folding and aggregation of proteins. Very fast and large pressure jumps are a new way of studying the interplay between folding and the earliest aggregation step of a model of the Creutzfeldt-Jakob disease protein.
| Ghaemi, Zhaleh; Guzman, Irisbel; Gnutt, David et al. (2017) Role of Electrostatics in Protein-RNA Binding: The Global vs the Local Energy Landscape. J Phys Chem B 121:8437-8446 |
| Zanetti-Polzi, Laura; Davis, Caitlin M; Gruebele, Martin et al. (2017) Parallel folding pathways of Fip35 WW domain explained by infrared spectra and their computer simulation. FEBS Lett 591:3265-3275 |
| Sukenik, Shahar; Ren, Pin; Gruebele, Martin (2017) Weak protein-protein interactions in live cells are quantified by cell-volume modulation. Proc Natl Acad Sci U S A 114:6776-6781 |
| Kachlishvili, Khatuna; Dave, Kapil; Gruebele, Martin et al. (2017) Eliminating a Protein Folding Intermediate by Tuning a Local Hydrophobic Contact. J Phys Chem B 121:3276-3284 |
| Chao, Shu-Han; Schäfer, Jan; Gruebele, Martin (2017) The Surface of Protein ?6-85 Can Act as a Template for Recurring Poly(ethylene glycol) Structure. Biochemistry 56:5671-5678 |
| Sukenik, Shahar; Pogorelov, Taras V; Gruebele, Martin (2016) Can Local Probes Go Global? A Joint Experiment-Simulation Analysis of ?(6-85) Folding. J Phys Chem Lett 7:1960-5 |
| Dave, Kapil; Jäger, Marcus; Nguyen, Houbi et al. (2016) High-Resolution Mapping of the Folding Transition State of a WW Domain. J Mol Biol 428:1617-36 |
| Gruebele, Martin; Dave, Kapil; Sukenik, Shahar (2016) Globular Protein Folding In Vitro and In Vivo. Annu Rev Biophys 45:233-51 |
| Davtyan, Aram; Platkov, Max; Gruebele, Martin et al. (2016) Stochastic Resonance in Protein Folding Dynamics. Chemphyschem 17:1305-13 |
| Gelman, Hannah; Wirth, Anna Jean; Gruebele, Martin (2016) ReAsH as a Quantitative Probe of In-Cell Protein Dynamics. Biochemistry 55:1968-76 |
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