Moreover, many methods for analyses of MD conformational
ensembles provide information on paths of long-range communications [46, 54, 66–74], such as the ones based on network theory (see Note 4). Recently, their robustness to different force field
descriptions for MD has been shown in proteins of different size
and fold [75, 76].
Despite p53 DBD importance, few studies have been devoted
to unraveling the long-range communication in p53 DBD in its
free, modified or DNA-bound state. However, in recent years,
progress has been made in this field, and the results are promising
[14, 77–79].
We know from NMR and structural studies that p53 DBD does
not appear to undergo significant conformational changes either
upon binding with other proteins or DNA, but a slow conformational exchange in the proximity of the disordered N-terminal
region has been identified by NMR [80]. This NMR study together
with our enhanced sampling and classical MD simulations [14] also
pointed out the need of including at least part of the disordered
region, which is N-terminal to the p53 DBD in the structural
experimental and computational studies of p53 DBD since these
residues tightly modulate p53 DBD conformational propensities.
In other structures of p53 DBD in complex with protein interactors
[22, 81], we are also observing conformational changes that are not
in the shape of the domain but often interest specific residues or
loop regions. These changes should not be underestimated since it
is known, in many protein systems, that rearrangements of short
loops or even cascade of rearrangements in side-chain conformation can have a major impact on the protein activity and function
and that allostery can occur without changes in shape [46, 82].
Recently, my group and coworkers developed a suitable platform to understand long-range effects at distal sites in transcription
factors such as p53 integrating analyses of classical MD and an
enhanced sampling approach, based on metadynamics
[14]. Indeed, classical MD conformational ensembles can be analyzed with dimensionality reduction [83–87] or higher-order statistics techniques [88–90] to generate working hypotheses on
protein regions that are distantly coupled and could be interested
in long-range communication or allostery. Metadynamics [58] can
be then used to test these hypotheses and to unveil with high
accuracy the changes in the free energy landscape of the protein
due to binding, mutations or modifications. Protein Structure
Network approaches can also complement the overall picture suggesting at the atom level the structural pathways from which one
site communicates with the distal one [46, 54, 66–74]. Moreover,
if available, NMR-derived parameters that are probes of protein
dynamics on different time scales can be used for cross-validation,
as we did [14] using backbone chemical shifts of p53 DBD
previously published [22]. Indeed, different and accurate chemical
228
Elena Papaleo
ensembles provide information on paths of long-range communications [46, 54, 66–74], such as the ones based on network theory (see Note 4). Recently, their robustness to different force field
descriptions for MD has been shown in proteins of different size
and fold [75, 76].
Despite p53 DBD importance, few studies have been devoted
to unraveling the long-range communication in p53 DBD in its
free, modified or DNA-bound state. However, in recent years,
progress has been made in this field, and the results are promising
[14, 77–79].
We know from NMR and structural studies that p53 DBD does
not appear to undergo significant conformational changes either
upon binding with other proteins or DNA, but a slow conformational exchange in the proximity of the disordered N-terminal
region has been identified by NMR [80]. This NMR study together
with our enhanced sampling and classical MD simulations [14] also
pointed out the need of including at least part of the disordered
region, which is N-terminal to the p53 DBD in the structural
experimental and computational studies of p53 DBD since these
residues tightly modulate p53 DBD conformational propensities.
In other structures of p53 DBD in complex with protein interactors
[22, 81], we are also observing conformational changes that are not
in the shape of the domain but often interest specific residues or
loop regions. These changes should not be underestimated since it
is known, in many protein systems, that rearrangements of short
loops or even cascade of rearrangements in side-chain conformation can have a major impact on the protein activity and function
and that allostery can occur without changes in shape [46, 82].
Recently, my group and coworkers developed a suitable platform to understand long-range effects at distal sites in transcription
factors such as p53 integrating analyses of classical MD and an
enhanced sampling approach, based on metadynamics
[14]. Indeed, classical MD conformational ensembles can be analyzed with dimensionality reduction [83–87] or higher-order statistics techniques [88–90] to generate working hypotheses on
protein regions that are distantly coupled and could be interested
in long-range communication or allostery. Metadynamics [58] can
be then used to test these hypotheses and to unveil with high
accuracy the changes in the free energy landscape of the protein
due to binding, mutations or modifications. Protein Structure
Network approaches can also complement the overall picture suggesting at the atom level the structural pathways from which one
site communicates with the distal one [46, 54, 66–74]. Moreover,
if available, NMR-derived parameters that are probes of protein
dynamics on different time scales can be used for cross-validation,
as we did [14] using backbone chemical shifts of p53 DBD
previously published [22]. Indeed, different and accurate chemical
228
Elena Papaleo