Modeling the Accessible Conformations of the Intrinsically Unstructured Transactivation Domain of P53
Document Type
Article
Publication Date
2007
Digital Object Identifier (DOI)
https://doi.org/10.1002/prot.21721
Abstract
Internuclear distances derived from paramagnetic relaxation enhancement (PRE) data were used to restrain molecular dynamics simulations of the intrinsically unstructured transactivation domain of the tumor suppressor protein, p53. About 1000 structures were simulated using ensemble averaging of replicate molecules to compensate for the inherent bias in the PRE-derived distances. Gyration radii measurements on these structures show that the p53 transactivation domain (p53TAD) is statistically predominantly in a partially collapsed state that is unlike the open structure that is found for p53TAD bound to either the E3 ubiquitin ligase, MDM2, or the 70 kDa subunit of replication protein A, RPA70. Contact regions that potentially mediate the collapse were identified and found to consist of mostly hydrophobic residues. The identified contact regions preferentially place the MDM2 and RPA70 binding regions in close proximity. We show that our simulations thoroughly sample the available range of conformations and that a fraction of the molecules are in an open state that would be competent for binding either MDM2 or RPA70. We also show that the Stokes radius estimated from the average gyration radius of the ensemble is in good agreement with the value determined using size exclusion chromatography. Finally, the presence of a persistent loop localized to a PXP motif was identified. Serine residues flanking the PXP motif become phosphorylated in response to DNA damage, and we postulate that this will perturb the equilibrium population to more open conformations. Proteins 2008. © 2007 Wiley-Liss, Inc.
Was this content written or created while at USF?
Yes
Citation / Publisher Attribution
Proteins: Structure, Function, and Bioinformatics, v. 71, issue 2, p. 587-598
Scholar Commons Citation
Lowry, David F.; Stancik, Amber; Shrestha, Ranjay M.; and Daughdrill, Gary W., "Modeling the Accessible Conformations of the Intrinsically Unstructured Transactivation Domain of P53" (2007). Molecular Biosciences Faculty Publications. 157.
https://digitalcommons.usf.edu/bcm_facpub/157
