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62. Sutto L, Gervasio FL (2013) Effects of oncogenic mutations on the conformational freeenergy landscape of EGFR kinase. Proc Natl
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63. Papaleo E, Sutto L, Gervasio FL et al (2014)
Conformational changes and free energies in a
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populated conformations on a complex
energy landscape. elife 5:e17505
65. Palazzesi F, Barducci A, Tollinger M et al
(2013) The allosteric communication pathways in KIX domain of CBP. Proc Natl Acad
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Conserved amino acids participate in the
structure networks deputed to intramolecular
communication in the lutropin receptor. Cell
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(2012) Paths of long-range communication
in the E2 enzymes of family 3: a molecular
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Phys 14:12515–12525
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understanding long-range intra-protein communication. Curr Protein Pept Sci
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Protein contact networks: an emerging paradigm
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72. Ribeiro AAST, Ortiz V (2015) Energy propagation and network energetic coupling in proteins. J Phys Chem A 119:1835–1846
73. Papaleo E, Renzetti G, Tiberti M (2012)
Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl
peptidase: a molecular dynamics investigation.
PLoS One 7:e35686
74. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
75. Salamanca Viloria J, Allega MF, Lambrughi M
et al (2016) An optimal distance cutoff for
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using side chain center of masses. Sci Rep
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76. Nygaard M, Terkelsen T, Olsen AV et al
(2016) The mutational landscape of the oncogenic MZF1 SCAN domain in cancer. Front
Mol Biosci 3:78
77. Ng JWK, Lama D, Lukman S et al (2015)
R248Q mutation—beyond p53-DNA binding. Proteins 83:2240–2250
78. Thayer KM, Quinn TR (2016) p53 R175H
hydrophobic patch and H-bond reorganization observed by MD simulation. Biopolymers 105:176–185
79. Calhoun S, Daggett V (2011) Structural
effects of the L145Q, V157F, and R282W
cancer-associated mutations in the p53
DNA-binding core domain. Biochemistry
50:5345–5353
80. Bista M, Freund SM, Fersht AR (2012)
Domain-domain interactions in full-length
p53 and a specific DNA complex probed by
methyl NMR spectroscopy. Proc Natl Acad
Sci U S A 109:15752–15756
81. Bethuyne J, De Gieter S, Zwaenepoel O et al
(2014) A nanobody modulates the p53 transcriptional program without perturbing its
functional architecture. Nucleic Acids Res
42:12928–12938
82. Tsai CJ, del Sol A, Nussinov R (2008) Allostery: absence of a change in shape does not
imply that allostery is not at play. J Mol Biol
378:1–11
242
Elena Papaleo
(2009) Hidden alternative structures of proline isomerase essential for catalysis. Nature
462:669–673
58. Laio A, Gervasio FL (2008) Metadynamics: a
method to simulate rare events and reconstruct the free energy in biophysics, chemistry
and material science. Rep Prog Phys
71:126601
59. Abrams C, Bussi G (2013) Enhanced sampling in molecular dynamics using metadynamics, replica-exchange, and temperatureacceleration. Entropy 16:163–199
60. Luitz M, Bomblies R, Ostermeir K et al
(2015) Exploring biomolecular dynamics
and interactions using advanced sampling
methods. J Phys Condens Matter 27:323101
61. Marino KA, Sutto L, Gervasio FL (2015) The
effect of a widespread cancer-causing mutation on the inactive to active dynamics of the
B-Raf
kinase.
J
Am
Chem
Soc
137:5280–5283
62. Sutto L, Gervasio FL (2013) Effects of oncogenic mutations on the conformational freeenergy landscape of EGFR kinase. Proc Natl
Acad Sci 110:10616–10621
63. Papaleo E, Sutto L, Gervasio FL et al (2014)
Conformational changes and free energies in a
proline isomerase. J Chem Theory Comput
10:4169–4174
64. Wang Y, Papaleo E, Lindorff-Larsen K (2016)
Mapping transiently formed and sparsely
populated conformations on a complex
energy landscape. elife 5:e17505
65. Palazzesi F, Barducci A, Tollinger M et al
(2013) The allosteric communication pathways in KIX domain of CBP. Proc Natl Acad
Sci U S A 110:14237–14242
66. Csermely P, Korcsma ´ros T, Kiss HJM et al
(2013) Structure and dynamics of molecular
networks: a novel paradigm of drug discovery:
a comprehensive review. Pharmacol Ther
138:333–408
67. Angelova K, Felline A, Lee M et al (2011)
Conserved amino acids participate in the
structure networks deputed to intramolecular
communication in the lutropin receptor. Cell
Mol Life Sci 68:1227–1239
68. Tiberti M, Invernizzi G, Lambrughi M et al
(2014) PyInteraph: a framework for the analysis of interaction networks in structural
ensembles of proteins. J Chem Inf Model
54:1537–1551
69. Papaleo E, Lindorff-larsen K, De Gioia L
(2012) Paths of long-range communication
in the E2 enzymes of family 3: a molecular
dynamics investigation. Phys Chem Chem
Phys 14:12515–12525
70. Whitley MJ, Lee AL (2009) Frameworks for
understanding long-range intra-protein communication. Curr Protein Pept Sci
10:116–127
71. Di Paola L, De Ruvo M, Paci P et al (2013)
Protein contact networks: an emerging paradigm
in
chemistry.
Chem
Rev
113:1598–1613
72. Ribeiro AAST, Ortiz V (2015) Energy propagation and network energetic coupling in proteins. J Phys Chem A 119:1835–1846
73. Papaleo E, Renzetti G, Tiberti M (2012)
Mechanisms of intramolecular communication in a hyperthermophilic acylaminoacyl
peptidase: a molecular dynamics investigation.
PLoS One 7:e35686
74. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
75. Salamanca Viloria J, Allega MF, Lambrughi M
et al (2016) An optimal distance cutoff for
contact-based protein structure networks
using side chain center of masses. Sci Rep
7:2838
76. Nygaard M, Terkelsen T, Olsen AV et al
(2016) The mutational landscape of the oncogenic MZF1 SCAN domain in cancer. Front
Mol Biosci 3:78
77. Ng JWK, Lama D, Lukman S et al (2015)
R248Q mutation—beyond p53-DNA binding. Proteins 83:2240–2250
78. Thayer KM, Quinn TR (2016) p53 R175H
hydrophobic patch and H-bond reorganization observed by MD simulation. Biopolymers 105:176–185
79. Calhoun S, Daggett V (2011) Structural
effects of the L145Q, V157F, and R282W
cancer-associated mutations in the p53
DNA-binding core domain. Biochemistry
50:5345–5353
80. Bista M, Freund SM, Fersht AR (2012)
Domain-domain interactions in full-length
p53 and a specific DNA complex probed by
methyl NMR spectroscopy. Proc Natl Acad
Sci U S A 109:15752–15756
81. Bethuyne J, De Gieter S, Zwaenepoel O et al
(2014) A nanobody modulates the p53 transcriptional program without perturbing its
functional architecture. Nucleic Acids Res
42:12928–12938
82. Tsai CJ, del Sol A, Nussinov R (2008) Allostery: absence of a change in shape does not
imply that allostery is not at play. J Mol Biol
378:1–11
242
Elena Papaleo