Chapter 13
Investigating Conformational Dynamics and Allostery
in the p53 DNA-Binding Domain Using Molecular
Simulations
Elena Papaleo
Abstract
The p53 tumor suppressor is a multifaceted context-dependent protein, which is involved in multiple
cellular pathways, with the ability to either keep the cells alive or to kill them through mechanisms such as
apoptosis. To complicate this picture, cancer cells that express mutant p53 becomes addicted to the mutant
activity, so that the mutant variant features a myriad of gain-of-function activities, opening different venues
for therapy. This makes essential to think outside the box and apply new approaches to the study of p53
structure–(mis)function relationship to find new critical components of its pathway or to understand how
known parts are interconnected, compete, or cooperate. In this context, I will here illustrate how to
integrate different computational methods to the identification of possible allosteric effects transmitted
from the DNA binding interface of p53 to regions for cofactor recruitment. The protocol can be extended
to any other cases of study. Indeed, it does not necessarily apply only to the study of DNA-induced effects,
but more broadly to the investigation of long-range effects induced by a biological partner that binds to a
biomolecule of interest.
Key words p53, DNA-binding domain, Transcription factor, Molecular dynamics, Protein structure
network, Allostery, Structural communication, Metadynamics
1 Introduction
To appreciate the protocol illustrated here, a general introduction
to p53 complexity is needed. Indeed, the pathways regulated by the
p53 tumor suppressor are extremely complex. Even if p53 has been
under the radar in the last 40 years, the mechanisms in which it is
involved are still elusive at the molecular and atom level [1, 2]. P53
was originally discovered as an oncogene that is overexpressed in
cancer to realize then that it is one of the most important tumor
suppressors and it was named as the guardian of the human
genome [3].
In recent years, it was revised as the “guardian of homeostatis”
[4]. Indeed, recently, the attention is turned again to the fact that in
Luisa Di Paola and Alessandro Giuliani (eds.), Allostery: Methods and Protocols, Methods in Molecular Biology, vol. 2253,
https://doi.org/10.1007/978-1-0716-1154-8_13, © Springer Science+Business Media, LLC, part of Springer Nature 2021
221
Investigating Conformational Dynamics and Allostery
in the p53 DNA-Binding Domain Using Molecular
Simulations
Elena Papaleo
Abstract
The p53 tumor suppressor is a multifaceted context-dependent protein, which is involved in multiple
cellular pathways, with the ability to either keep the cells alive or to kill them through mechanisms such as
apoptosis. To complicate this picture, cancer cells that express mutant p53 becomes addicted to the mutant
activity, so that the mutant variant features a myriad of gain-of-function activities, opening different venues
for therapy. This makes essential to think outside the box and apply new approaches to the study of p53
structure–(mis)function relationship to find new critical components of its pathway or to understand how
known parts are interconnected, compete, or cooperate. In this context, I will here illustrate how to
integrate different computational methods to the identification of possible allosteric effects transmitted
from the DNA binding interface of p53 to regions for cofactor recruitment. The protocol can be extended
to any other cases of study. Indeed, it does not necessarily apply only to the study of DNA-induced effects,
but more broadly to the investigation of long-range effects induced by a biological partner that binds to a
biomolecule of interest.
Key words p53, DNA-binding domain, Transcription factor, Molecular dynamics, Protein structure
network, Allostery, Structural communication, Metadynamics
1 Introduction
To appreciate the protocol illustrated here, a general introduction
to p53 complexity is needed. Indeed, the pathways regulated by the
p53 tumor suppressor are extremely complex. Even if p53 has been
under the radar in the last 40 years, the mechanisms in which it is
involved are still elusive at the molecular and atom level [1, 2]. P53
was originally discovered as an oncogene that is overexpressed in
cancer to realize then that it is one of the most important tumor
suppressors and it was named as the guardian of the human
genome [3].
In recent years, it was revised as the “guardian of homeostatis”
[4]. Indeed, recently, the attention is turned again to the fact that in
Luisa Di Paola and Alessandro Giuliani (eds.), Allostery: Methods and Protocols, Methods in Molecular Biology, vol. 2253,
https://doi.org/10.1007/978-1-0716-1154-8_13, © Springer Science+Business Media, LLC, part of Springer Nature 2021
221