likely to be only the tip of the iceberg of other complex and
interconnected layers of regulation.
The long-range communication from DNA binding loops to
distal regions of the protein that act as cofactor recruitment hotspots can be a broader mechanism, as we recently showed also in
the DBD of the ARID family of transcription factors [98]. Also,
p53 is not the unique case of known transcription factors for which
transcription-independent cytosolic or membrane-associated functions have been identified [99] so that the conformational selection
mechanisms proposed for p53 could be an example of a more
general scenario.
More in general, the methodology illustrated here can be
extended to other proteins to understand how long-range communication occurs from distal sites and which regions interested by the
allosteric effects can act as cofactor recruitment interface. As an
example, we recently applied the same tools to the study of the
MZF1 SCAN domain [76].
2 Materials
The software and tools listed below are needed with a Linux/Unix
working environment and access to HPC resources is recommended for the classical and metadynamics simulations.
1. Pymol (www.pymol.org) or similar software for structure visualization, superimposition, and manipulation.
2. Gromacs version 4 or higher to run unbiased MD simulations
[100–102].
3. Gromacs version 4 or higher patched with Plumed 1.3 or 2 to
perform the metadynamics simulations [103, 104].
4. PyInteraph [68] or Wordom [105] to calculate the PSN and the
paths of long-range communication.
5. Xpyder plugin [106] for Pymol for visualization of the PSN
results and PyKnife to assess convergence of the PSN properties or automatize the collection of the network [75].
6. PRISM [107, 108] to predict the protein-protein complexes.
3 Methods
For the sake of clarity, we will illustrate the example of the analyses
for p53 DBD in its wild-type variant comparing DNA-bound and
DNA-unbound states, inspired by our recent work [14]. The protocol can be translated and adjusted to any other case of study and
also not necessarily to study DNA-induced effects, but more
broadly long-range effects induced by a biological partner that
binds to a biomolecule of interest.
Dynamics of p53
231
interconnected layers of regulation.
The long-range communication from DNA binding loops to
distal regions of the protein that act as cofactor recruitment hotspots can be a broader mechanism, as we recently showed also in
the DBD of the ARID family of transcription factors [98]. Also,
p53 is not the unique case of known transcription factors for which
transcription-independent cytosolic or membrane-associated functions have been identified [99] so that the conformational selection
mechanisms proposed for p53 could be an example of a more
general scenario.
More in general, the methodology illustrated here can be
extended to other proteins to understand how long-range communication occurs from distal sites and which regions interested by the
allosteric effects can act as cofactor recruitment interface. As an
example, we recently applied the same tools to the study of the
MZF1 SCAN domain [76].
2 Materials
The software and tools listed below are needed with a Linux/Unix
working environment and access to HPC resources is recommended for the classical and metadynamics simulations.
1. Pymol (www.pymol.org) or similar software for structure visualization, superimposition, and manipulation.
2. Gromacs version 4 or higher to run unbiased MD simulations
[100–102].
3. Gromacs version 4 or higher patched with Plumed 1.3 or 2 to
perform the metadynamics simulations [103, 104].
4. PyInteraph [68] or Wordom [105] to calculate the PSN and the
paths of long-range communication.
5. Xpyder plugin [106] for Pymol for visualization of the PSN
results and PyKnife to assess convergence of the PSN properties or automatize the collection of the network [75].
6. PRISM [107, 108] to predict the protein-protein complexes.
3 Methods
For the sake of clarity, we will illustrate the example of the analyses
for p53 DBD in its wild-type variant comparing DNA-bound and
DNA-unbound states, inspired by our recent work [14]. The protocol can be translated and adjusted to any other case of study and
also not necessarily to study DNA-induced effects, but more
broadly long-range effects induced by a biological partner that
binds to a biomolecule of interest.
Dynamics of p53
231