Now that protein folding is becoming better understood, we can study it in combination with other interactions that proteins make with biomolecules. Proteins in cells and organisms continuously interact with other biomolecules, such as RNA. They are also modified with attachments, such as polyethylene glycol (PEG) molecules that can enhance stability for drug delivery. Finally, domains of larger proteins can interact with one another, modifying the folding process or leading to undesirable aggregation, which can lead to protein diseases. Our long-term objective is to study interactions of proteins with PEG, RNA, and other protein domains, and to characterize these interactions quantitatively. Within that long-term objective, our specific aims are threefold: 1) PEG is used extensively in the pharmaceutical industry to improve the delivery of protein drugs. We study how PEG interacts with protein surfaces, so we can figure out the mechanism by which PEG helps stabilize protein drugs for delivery. We will study several protein systems, including a therapeutic agent for chronic kidney disease. 2) The spliceosome assembles in the cell nucleus to splice and re-assemble messenger RNA, which is necessary to take the information to make new proteins from the nucleus to the ribosomes, where proteins are synthesized. We will study one of the key protein-RNA interactions by making many mutants and comparing them with a new model we just developed, that we think can predict how strongly protein and RNA will bind. This will be important for rational design of drugs to interfere with, or repair, protein-RNA interactions. 3) Large proteins contain many domains, and when they fold things can go wrong. We study these interactions in an expanded phase diagram of pressure and temperature, to better understand their physical origins. We discovered that folding intermediates, which are structures that are not quite properly folded, can appear and disappear in this phase diagram. By learning why this happens we can better suppress such intermediates, which could form harmful aggregates. To achieve our goals, we are developing new fluorescence assays to rapidly and sensitively detect interactions. We are expanding the capabilities of our protein pressurization techniques, so we can study protein under conditions relevant to pressure sterilization of food. And we are making new PEG-labeled proteins to study how important PEG length and attachment sites really are.
As the protein folding problem is getting solved, at least for small proteins, we can now use that knowledge to better understand how folding competes with protein interactions, such as protein-PEG, protein-RNA, and protein-protein domain interactions. Our aims focus on developing new model systems to study these three cases: PEG is used in many pharmaceutical proteins to enhance delivery in the patient, but the mechanism of action is unknown. Protein-RNA interactions and protein domain interactions offer many new drug targets, whose design could be enhanced if the binding mechanisms were better understood.
|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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