Markov State Modeling Analysis Captures Changes in the Temperature-Sensitive N-Terminal and β-Turn Regions of the p53 DNA-Binding Domain

Abstract

The transcription factor p53 is one of the most widely studied cancer proteins. Its temperature-sensitive nature suggests reduction in functionality at physiological temperatures. Temperature-induced conformational variations and their impact on its functional ability still remain unexplored. A total of 20.8 μs molecular dynamics simulations of wildtype p53 in the apo and the DNA-bound states have been performed at 300 K and 310 K. Further, Markov State Modeling (MSM) analyses were performed, considering C α −C α distances as reaction coordinates. Filtering of these distances based on correlation with the time-independent components (tICs) resulted in 16 and 32 distances for apo and DNA-bound systems, respectively. Individual MSM analyses using these filtered distances were performed for both p53 systems. These C α −C α residue pairs belonged to the N-terminal, S6/7 β-turn, loop L2, loop L3, and hydrophobic core residues. At physiological temperatures, apo-p53 exhibits exposure of its hydrophobic core, where the temperature-sensitive hotspot residues were also located. This exposure was the result of the S6/7 β-turn and N-terminal moving apart. In the DNA-bound p53 system, loop L1 attains an open conformation at physiological temperatures, which weakens the DNA binding. It is already known that p53 mutants that lack DNA binding also tend to show similar conformational variations. The S6/7 β-turn along with the already known functionally important loop L2 may pose as regions to be targeted to overcome the loss in binding of temperature-sensitive wildtype p53. Rescue strategies directed toward these temperature-sensitive regions may be useful to recuperate its strong binding at physiological temperatures.

Oncogenic R248W mutation induced conformational perturbation of the p53 core domain and the structural protection by proteomimetic amyloid inhibitor ADH-6

“…Moreover, ADH-6 inhibits the aggregation of R248W p53 in human cancer cells, restoring the transcriptional activity of p53, leading to cell cycle arrest and apoptosis. 19 Molecular dynamics (MD) simulations have been extensively employed to investigate the conformational properties of different domains of the p53 protein and its mutants, 41,42,[63][64][65][66][67][68][69] as well as the interactions between p53 protein domains and small molecules, 70 short peptides, 71 and other proteins. [72][73][74][75] In spite of experimental and computational studies, it remains mostly unknown how the R248W mutation induces destabilization of R248W p53C and how ADH-6 stabilizes R248W p53C.…”

Elucidating the Mechanisms of R248Q Mutation-Enhanced p53 Aggregation and Its Inhibition by Resveratrol

“…Molecular dynamics (MD) simulation has proven to be a powerful tool in p53 research, providing detailed information on p53 structures, conformational dynamics, and interactions with ligands. − For example, the structural features of different mutant variants of p53 have been identified utilizing MD simulations, including the druggable cavity created by Y220X mutations, the “open/closed” states of the turn between strands S6 and S7 in different aggregating p53 mutants, and the L1/S3 pocket that exists in WT p53C and three frequent cancer mutants (R175H, G245S, and R273H) . These findings offered theoretical guidance and support for the development of a series of effective small molecule drugs targeting p53C (such as carbazole-based Y220X binders, PRIMA-1, ATO, SSG, and UCI-LC0023).…”