83. Lange OF, Grubmu ¨ller H (2006) Can principal components yield a dimension reduced
description of protein dynamics on long time
scales? J Phys Chem B 110:22842–22852
84. Daidone I, Amadei A (2012) Essential
dynamics: foundation and applications. Wiley
Interdiscip Rev Comput Mol Sci 2:762–770
85. Lindorff-Larsen K, Ferkinghoff-Borg J
(2009) Similarity measures for protein ensembles. PLoS One 4:e4203
86. Tiberti M, Papaleo E, Bengtsen T et al (2015)
ENCORE: software for quantitative ensemble
comparison. PLoS Comput Biol 11:
e1004415
87. Martı ´n-Garcı ´a F, Papaleo E, Gomez-Puertas
P et al (2015) Comparing molecular dynamics
force fields in the essential subspace. PLoS
One 10:e0121114
88. Ramanathan A, Savol AJ, Langmead CJ et al
(2011)
Discovering
conformational
sub-states relevant to protein function. PLoS
One 6:e15827
89. Savol AJ, Burger VM, Agarwal PK et al
(2011) QAARM: quasi-anharmonic autoregressive model reveals molecular recognition
pathways in ubiquitin. Bioinformatics 27:
i52–i60
90. Wriggers W, Stafford KA, Shan Y et al (2009)
Automated event detection and activity monitoring in long molecular dynamics simulations. J Chem Theory Comput 5:2595–2605
91. Kohlhoff KJ, Robustelli P, Cavalli A et al
(2009) Fast and accurate predictions of protein NMR chemical shifts from interatomic
distances. J Am Chem Soc 131:13894–13895
92. Sahakyan AB, Vranken WF, Cavalli A et al
(2011) Structure-based prediction of methyl
chemical shifts in proteins. J Biomol NMR
50:331–346
93. Li DW, Bru ¨schweiler R (2012) PPM: a sidechain and backbone chemical shift predictor
for the assessment of protein conformational
ensembles. J Biomol NMR 54:257–265
94. Li D, Bru ¨schweiler R (2015) PPM_One: a
static protein structure based chemical shift
predictor. J Biomol NMR 62:403–409
95. Natan E, Baloglu C, Pagel K et al (2011)
Interaction of the p53 DNA-binding domain
with its n-terminal extension modulates the
stability of the p53 tetramer. J Mol Biol
409:358–368
96. Liu Q, Kaneko S, Yang L et al (2004) AuroraA abrogation of p53 DNA binding and transactivation activity by phosphorylation of serine 215. J Biol Chem 279:52175–52182
97. Fraser JA, Vojtesek B, Hupp TR (2010) A
novel p53 phosphorylation site within the
MDM2
ubiquitination
signal:
I. phosphorylation at SER269 in vivo is linked
to inactivation of p53 function. J Biol Chem
285:37762–37772
98. Invernizzi G, Tiberti M, Lambrughi M et al
(2014) Communication routes in ARID
domains between distal residues in helix
5 and the DNA-binding loops. PLoS Comput
Biol 10:e1003744
99. Lim CP, Cao X (2006) Structure, function,
and regulation of STAT proteins. Mol BioSyst
2:536
100. Abraham MJ, Murtola T, Schulz R et al
(2015) GROMACS: high performance
molecular simulations through multi-level
parallelism from laptops to supercomputers.
SoftwareX 2:19–25
101. Hess B, Kutzner C, van der Spoel D et al
(2008) GROMACS 4: algorithms for highly
efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput
4:435–447
102. Pronk S, Pa ´ll S, Schulz R et al (2013) GROMACS 4.5: a high-throughput and highly
parallel open source molecular simulation
toolkit. Bioinformatics 29:845–854
103. Bonomi M, Branduardi D, Bussi G et al
(2009) PLUMED: a portable plugin for
free-energy calculations with molecular
dynamics.
Comput
Phys
Commun
180:1961–1972
104. Tribello GA, Bonomi M, Branduardi D et al
(2014) PLUMED 2: new feathers for an old
bird. Comput Phys Commun 185:604–613
105. Seeber M, Felline A, Raimondi F et al (2011)
Wordom: a user-friendly program for the
analysis of molecular structures, trajectories,
and free energy surfaces. J Comput Chem
32:1183–1194
106. Pasi M, Tiberti M, Arrigoni A et al (2012)
xPyder: a PyMOL plugin to analyze coupled
residues and their networks in protein structures. J Chem Inf Model 279:1–6
107. Baspinar A, Cukuroglu E, Nussinov R et al
(2014) PRISM: a web server and repository
for prediction of protein-protein interactions
and modeling their 3D complexes. Nucleic
Acids Res 42:W285–W289
108. Tuncbag N, Gursoy A, Nussinov R et al
(2011) Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces
using PRISM. Nat Protoc 6:1341–1354
109. Cho Y, Gorina S, Jeffrey PD et al (1994)
Crystal structure of p53 tumor suppressorDNA complex: understanding tumorigenic
mutations. Science 265(5170):346–355
Dynamics of p53
243
description of protein dynamics on long time
scales? J Phys Chem B 110:22842–22852
84. Daidone I, Amadei A (2012) Essential
dynamics: foundation and applications. Wiley
Interdiscip Rev Comput Mol Sci 2:762–770
85. Lindorff-Larsen K, Ferkinghoff-Borg J
(2009) Similarity measures for protein ensembles. PLoS One 4:e4203
86. Tiberti M, Papaleo E, Bengtsen T et al (2015)
ENCORE: software for quantitative ensemble
comparison. PLoS Comput Biol 11:
e1004415
87. Martı ´n-Garcı ´a F, Papaleo E, Gomez-Puertas
P et al (2015) Comparing molecular dynamics
force fields in the essential subspace. PLoS
One 10:e0121114
88. Ramanathan A, Savol AJ, Langmead CJ et al
(2011)
Discovering
conformational
sub-states relevant to protein function. PLoS
One 6:e15827
89. Savol AJ, Burger VM, Agarwal PK et al
(2011) QAARM: quasi-anharmonic autoregressive model reveals molecular recognition
pathways in ubiquitin. Bioinformatics 27:
i52–i60
90. Wriggers W, Stafford KA, Shan Y et al (2009)
Automated event detection and activity monitoring in long molecular dynamics simulations. J Chem Theory Comput 5:2595–2605
91. Kohlhoff KJ, Robustelli P, Cavalli A et al
(2009) Fast and accurate predictions of protein NMR chemical shifts from interatomic
distances. J Am Chem Soc 131:13894–13895
92. Sahakyan AB, Vranken WF, Cavalli A et al
(2011) Structure-based prediction of methyl
chemical shifts in proteins. J Biomol NMR
50:331–346
93. Li DW, Bru ¨schweiler R (2012) PPM: a sidechain and backbone chemical shift predictor
for the assessment of protein conformational
ensembles. J Biomol NMR 54:257–265
94. Li D, Bru ¨schweiler R (2015) PPM_One: a
static protein structure based chemical shift
predictor. J Biomol NMR 62:403–409
95. Natan E, Baloglu C, Pagel K et al (2011)
Interaction of the p53 DNA-binding domain
with its n-terminal extension modulates the
stability of the p53 tetramer. J Mol Biol
409:358–368
96. Liu Q, Kaneko S, Yang L et al (2004) AuroraA abrogation of p53 DNA binding and transactivation activity by phosphorylation of serine 215. J Biol Chem 279:52175–52182
97. Fraser JA, Vojtesek B, Hupp TR (2010) A
novel p53 phosphorylation site within the
MDM2
ubiquitination
signal:
I. phosphorylation at SER269 in vivo is linked
to inactivation of p53 function. J Biol Chem
285:37762–37772
98. Invernizzi G, Tiberti M, Lambrughi M et al
(2014) Communication routes in ARID
domains between distal residues in helix
5 and the DNA-binding loops. PLoS Comput
Biol 10:e1003744
99. Lim CP, Cao X (2006) Structure, function,
and regulation of STAT proteins. Mol BioSyst
2:536
100. Abraham MJ, Murtola T, Schulz R et al
(2015) GROMACS: high performance
molecular simulations through multi-level
parallelism from laptops to supercomputers.
SoftwareX 2:19–25
101. Hess B, Kutzner C, van der Spoel D et al
(2008) GROMACS 4: algorithms for highly
efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput
4:435–447
102. Pronk S, Pa ´ll S, Schulz R et al (2013) GROMACS 4.5: a high-throughput and highly
parallel open source molecular simulation
toolkit. Bioinformatics 29:845–854
103. Bonomi M, Branduardi D, Bussi G et al
(2009) PLUMED: a portable plugin for
free-energy calculations with molecular
dynamics.
Comput
Phys
Commun
180:1961–1972
104. Tribello GA, Bonomi M, Branduardi D et al
(2014) PLUMED 2: new feathers for an old
bird. Comput Phys Commun 185:604–613
105. Seeber M, Felline A, Raimondi F et al (2011)
Wordom: a user-friendly program for the
analysis of molecular structures, trajectories,
and free energy surfaces. J Comput Chem
32:1183–1194
106. Pasi M, Tiberti M, Arrigoni A et al (2012)
xPyder: a PyMOL plugin to analyze coupled
residues and their networks in protein structures. J Chem Inf Model 279:1–6
107. Baspinar A, Cukuroglu E, Nussinov R et al
(2014) PRISM: a web server and repository
for prediction of protein-protein interactions
and modeling their 3D complexes. Nucleic
Acids Res 42:W285–W289
108. Tuncbag N, Gursoy A, Nussinov R et al
(2011) Predicting protein-protein interactions on a proteome scale by matching evolutionary and structural similarities at interfaces
using PRISM. Nat Protoc 6:1341–1354
109. Cho Y, Gorina S, Jeffrey PD et al (1994)
Crystal structure of p53 tumor suppressorDNA complex: understanding tumorigenic
mutations. Science 265(5170):346–355
Dynamics of p53
243