Intrinsically disordered proteins (IDPs) are an abundant class of proteins and protein regions which rapidly change between multiple structures without an equilibrium position. IDPs exist as a series of conformational ensembles of semi-stable conformations that can be adopted based on a hilly landscape of shallow free energy minima. Disordered sequences share characteristic features differentiating them from globular proteins, including low sequence complexity, low occurrence of hydrophobic residues, high polar and charged residue content, and high flexibility. IDPs are commonly involved in regulation in the cell, and frequently function as, or interact with, hub proteins in protein-protein interaction networks, making them an important class of macromolecules for understanding regulatory and other processes. Given their functional importance, these proteins are widely studied. Many analytical techniques are used, though rapid conformational sampling by IDPs makes it difficult to detect many states with NMR or other techniques. Computational approaches such as molecular dynamics are increasingly used to probe the binding and conformational sampling of these proteins, allowing for observation of factors that cannot be observed with traditional analytical methods such as NMR, such as differing conformational ensembles and the dipoles of individual residues. Here, we studied the role of electrostatic interactions in IDP protein-protein interaction using molecular dynamics simulations performed with the Drude-2019 force field (FF), a polarizable model that allows for more accurate representation of electrostatics, an important factor for highly charged systems like IDPs. For this project, a prototypical protein with disordered regions, p53, was simulated with two protein partners, the nuclear coactivator domain of the CREB binding protein (CBP), and the E3 ubiquitin-protein ligase mouse double minute 2 (MDM2). p53 is widely studied, and the p53 transactivation domain (TAD) is disordered and binds to many structurally diverse partners, making this protein domain a useful model for probing the role of electrostatic interactions formed by IDPs at protein-protein binding interfaces. We found that the Drude-2019 FF allows for simulation of the p53 TAD with Cα chemical shifts comparable to those observed with NMR, supporting that the Drude-2019 FF performs well in simulating IDPs. We observed large relative change in sidechain dipole moments when comparing the p53 TAD alone and when bound to either CBP or MDM2. We observed that aliphatic and aromatic amino acids experienced the largest relative change in sidechain dipole moments, and that there is sensitivity to binding shown in this dipole response. The largest percent changes in sidechain dipole moment were found to localize at and around the binding interface. Understanding the binding interactions of IDPs at a fundamental level, including the role of electrostatic interactions, may help with targeting IDPs or their partners for drug design. / Master of Science in Life Sciences / Many proteins adopt one main structure, and these proteins are called ordered proteins. Intrinsically disordered proteins (IDPs) are an abundant category of proteins which adopt multiple structures, and transition between these different structures is based on factors such as the environment around them, modifications, or interactions with other macromolecules. The flexible structures of IDPs allow them to bind to multiple different partners and to regulate processes in the cell. Since IDPs often regulate processes important to cell function, when these proteins are mutated, misfolded, or otherwise mis-regulated the resulting issues are associated with disease states. IDPs are widely studied with analytical techniques, but because IDPs frequently change shape it can be difficult to observe certain behaviors or certain factors with these techniques. Computational approaches, such as molecular dynamics (MD). MD is the study of molecular motion and interaction, and can allow observation of factors that would be difficult or impossible to observe otherwise, such as the varying structures of IDPs or the dipole moments of specific amino acids within the proteins. For this project we wanted to probe the role of dipole moments, which are charge-based interactions, in the binding of IDPs to protein partners, to better understand how IDPs bind to different partners. We used the p53 protein as an example of IDP binding and simulated it alone and bound to two other proteins, the CREB binding protein (CBP), and the E3 ubiquitin-protein ligase mouse double minute 2 (MDM2). We observed that our simulations were comparable to experiments done with nuclear magnetic resonance spectroscopy, which served to validate that our simulations were realistic. We observed that the dipole moments of the proteins change when simulating the proteins alone and in complex, and that the largest relative changes in dipole are observed for regions of the proteins involved in binding. Probing the role of charge-based interactions in protein-protein binding interactions for IDPs can help us to greater understand these interactions at a more fundamental level and could help with targeting IDPs or their partners for drug design or other problems.
| Identifer | oai:union.ndltd.org:VTETD/oai:vtechworks.lib.vt.edu:10919/112656 |
| Date | 25 May 2021 |
| Creators | Corrigan, Alexsandra Nikol |
| Contributors | Biochemistry, Lemkul, Justin A., Brown, Anne M., Allen, Kylie D. |
| Publisher | Virginia Tech |
| Source Sets | Virginia Tech Theses and Dissertation |
| Detected Language | English |
| Type | Thesis |
| Format | ETD, application/pdf |
| Rights | In Copyright, http://rightsstatements.org/vocab/InC/1.0/ |
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