cancer-associated mutants. Adv Cancer Res
97:1–23
27. Dai C, Gu W (2010) P53 post-translational
modification: deregulated in tumorigenesis.
Trends Mol Med 16:528–536
28. Petty TJ, Emamzadah S, Costantino L et al
(2011) An induced fit mechanism regulates
p53 DNA binding kinetics to confer sequence
specificity. EMBO J 30:2167–2176
29. Cho Y, Gorina S, Jeffrey PD et al (1994)
Crystal structure of a p53 tumor suppressorDNA complex: understanding tumorigenic
mutations. Science 265:346–355
30. Khoo KH, Andreeva A, Fersht AR (2009)
Adaptive evolution of p53 thermodynamic
stability. J Mol Biol 393:161–175
31. Soussi T, Curie M (2014) The TP53 gene
network in a postgenomic era. Hum Mutat
35(6):641–642
32. Soussi T, Wiman KG (2015) TP53: an oncogene in disguise. Cell Death Differ
22:1239–1249
33. Abramo MD, Besker N, Desideri A et al
(2015) The p53 tetramer shows an inducedfit interaction of the C-terminal domain with
the DNA-binding domain. Oncogene
35:3272–3281
34. Chillemi G, Davidovich P, D’Abramo M et al
(2013) Molecular dynamics of the full-length
p53 monomer. Cell Cycle 12:3098–3108
35. Terakawa T, Takada S (2015) p53 dynamics
upon response element recognition explored
by molecular simulations. Sci Rep 5:17107
36. Demir O ¨ , Ieong PU, Amaro RE (2017) Fulllength p53 tetramer bound to DNA and its
quaternary
dynamics.
Oncogene
36:1451–1460
37. Saha T, Kar RK, Sa G (2015) Structural and
sequential context of p53: a review of experimental and theoretical evidence. Prog Biophys Mol Biol 117(2-3):250–263
38. Lu Q, Tan YH, Luo R (2007) Molecular
dynamics simulations of p53 DNA-binding
domain. J Phys Chem B 111:11538–11545
39. Lukman S, Lane DP, Verma CS (2013)
Mapping the structural and dynamical features of multiple p53 DNA binding domains:
insights into loop 1 intrinsic dynamics. PLoS
One 8:e80221
40. Pan Y, Nussinov R (2010) Lysine120 interactions with p53 response elements can allosterically direct p53 organization. PLoS Comput
Biol 6:e1000878
41. Pan Y (2008) p53-induced DNA bending:
the interplay between p53. J Phys Chem B
112:6716–6724
42. Fraser JA, Madhumalar A, Blackburn E et al
(2010) A novel p53 phosphorylation site
within the MDM2 ubiquitination signal
II. A model in which phosphorylation at
SER 269 induces a mutant. J Biol Chem
285:37773–37786
43. Henzler-Wildman KA, Lei M, Thai V et al
(2007) A hierarchy of timescales in protein
dynamics is linked to enzyme catalysis. Nature
450:913–916
44. Tang C, Schwieters CD, Clore GM (2007)
Open-to-closed transition in apo maltosebinding protein observed by paramagnetic
NMR. Nature 449:1078–1082
45. Baldwin AJ, Kay LE (2009) NMR spectroscopy brings invisible protein states into focus.
Nat Chem Biol 5:808–814
46. Papaleo E, Saladino G, Lambrughi M et al
(2016) The role of protein loops and linkers
in conformational dynamics and allostery.
Chem Rev 116:6391–6423
47. Cui Q, Karplus M (2008) Allostery and cooperativity revisited. Protein Sci 17:1295–1307
48. Tsai C-J, Nussinov R (2014) A unified view of
“how allostery works”. PLoS Comput Biol
10:e1003394
49. Ribeiro AAST, Ortiz V (2016) A chemical
perspective on allostery. Chem Rev
116:6488–6502
50. Bray D, Duke T (2004) Conformational
spread: the propagation of allosteric states in
large multiprotein complexes. Annu Rev Biophys Biomol Struct 33:53–73
51. Nussinov R, Tsai C-J (2015) Allostery without a conformational change? Revisiting the
paradigm. Curr Opin Struct Biol 30:17–24
52. Feher VA, Durrant JD, Van Wart AT et al
(2014) Computational approaches to
mapping allosteric pathways. Curr Opin
Struct Biol 25:98–103
53. Dror RO, Dirks RM, Grossman JP et al
(2012) Biomolecular simulation: a computational microscope for molecular biology.
Annu Rev Biophys 41:429–452
54. Papaleo E (2015) Integrating atomistic
molecular dynamics simulations, experiments,
and network analysis to study protein dynamics: strength in unity. Front Mol Biosci 2:28
55. Torchia DA (2015) NMR studies of dynamic
biomolecular conformational ensembles.
Prog
Nucl Magn Reson Spectrosc
84–85:14–32
56. O’Rourke KF, Gorman SD, Boehr DD
(2016) Biophysical and computational methods to analyze amino acid interaction networks
in
proteins.
Comput
Struct
Biotechnol J 14:245–251
Dynamics of p53
241
97:1–23
27. Dai C, Gu W (2010) P53 post-translational
modification: deregulated in tumorigenesis.
Trends Mol Med 16:528–536
28. Petty TJ, Emamzadah S, Costantino L et al
(2011) An induced fit mechanism regulates
p53 DNA binding kinetics to confer sequence
specificity. EMBO J 30:2167–2176
29. Cho Y, Gorina S, Jeffrey PD et al (1994)
Crystal structure of a p53 tumor suppressorDNA complex: understanding tumorigenic
mutations. Science 265:346–355
30. Khoo KH, Andreeva A, Fersht AR (2009)
Adaptive evolution of p53 thermodynamic
stability. J Mol Biol 393:161–175
31. Soussi T, Curie M (2014) The TP53 gene
network in a postgenomic era. Hum Mutat
35(6):641–642
32. Soussi T, Wiman KG (2015) TP53: an oncogene in disguise. Cell Death Differ
22:1239–1249
33. Abramo MD, Besker N, Desideri A et al
(2015) The p53 tetramer shows an inducedfit interaction of the C-terminal domain with
the DNA-binding domain. Oncogene
35:3272–3281
34. Chillemi G, Davidovich P, D’Abramo M et al
(2013) Molecular dynamics of the full-length
p53 monomer. Cell Cycle 12:3098–3108
35. Terakawa T, Takada S (2015) p53 dynamics
upon response element recognition explored
by molecular simulations. Sci Rep 5:17107
36. Demir O ¨ , Ieong PU, Amaro RE (2017) Fulllength p53 tetramer bound to DNA and its
quaternary
dynamics.
Oncogene
36:1451–1460
37. Saha T, Kar RK, Sa G (2015) Structural and
sequential context of p53: a review of experimental and theoretical evidence. Prog Biophys Mol Biol 117(2-3):250–263
38. Lu Q, Tan YH, Luo R (2007) Molecular
dynamics simulations of p53 DNA-binding
domain. J Phys Chem B 111:11538–11545
39. Lukman S, Lane DP, Verma CS (2013)
Mapping the structural and dynamical features of multiple p53 DNA binding domains:
insights into loop 1 intrinsic dynamics. PLoS
One 8:e80221
40. Pan Y, Nussinov R (2010) Lysine120 interactions with p53 response elements can allosterically direct p53 organization. PLoS Comput
Biol 6:e1000878
41. Pan Y (2008) p53-induced DNA bending:
the interplay between p53. J Phys Chem B
112:6716–6724
42. Fraser JA, Madhumalar A, Blackburn E et al
(2010) A novel p53 phosphorylation site
within the MDM2 ubiquitination signal
II. A model in which phosphorylation at
SER 269 induces a mutant. J Biol Chem
285:37773–37786
43. Henzler-Wildman KA, Lei M, Thai V et al
(2007) A hierarchy of timescales in protein
dynamics is linked to enzyme catalysis. Nature
450:913–916
44. Tang C, Schwieters CD, Clore GM (2007)
Open-to-closed transition in apo maltosebinding protein observed by paramagnetic
NMR. Nature 449:1078–1082
45. Baldwin AJ, Kay LE (2009) NMR spectroscopy brings invisible protein states into focus.
Nat Chem Biol 5:808–814
46. Papaleo E, Saladino G, Lambrughi M et al
(2016) The role of protein loops and linkers
in conformational dynamics and allostery.
Chem Rev 116:6391–6423
47. Cui Q, Karplus M (2008) Allostery and cooperativity revisited. Protein Sci 17:1295–1307
48. Tsai C-J, Nussinov R (2014) A unified view of
“how allostery works”. PLoS Comput Biol
10:e1003394
49. Ribeiro AAST, Ortiz V (2016) A chemical
perspective on allostery. Chem Rev
116:6488–6502
50. Bray D, Duke T (2004) Conformational
spread: the propagation of allosteric states in
large multiprotein complexes. Annu Rev Biophys Biomol Struct 33:53–73
51. Nussinov R, Tsai C-J (2015) Allostery without a conformational change? Revisiting the
paradigm. Curr Opin Struct Biol 30:17–24
52. Feher VA, Durrant JD, Van Wart AT et al
(2014) Computational approaches to
mapping allosteric pathways. Curr Opin
Struct Biol 25:98–103
53. Dror RO, Dirks RM, Grossman JP et al
(2012) Biomolecular simulation: a computational microscope for molecular biology.
Annu Rev Biophys 41:429–452
54. Papaleo E (2015) Integrating atomistic
molecular dynamics simulations, experiments,
and network analysis to study protein dynamics: strength in unity. Front Mol Biosci 2:28
55. Torchia DA (2015) NMR studies of dynamic
biomolecular conformational ensembles.
Prog
Nucl Magn Reson Spectrosc
84–85:14–32
56. O’Rourke KF, Gorman SD, Boehr DD
(2016) Biophysical and computational methods to analyze amino acid interaction networks
in
proteins.
Comput
Struct
Biotechnol J 14:245–251
Dynamics of p53
241