43. DiPaola L, DeRuvo M, Paci P, Santoni D,
Giuliani A (2013) Protein contact networks:
an emerging paradigm in chemistry. Chem
Rev 113:1598–1613
44. Dokholyan NV (2016) Controlling allosteric
networks
in
proteins.
Chem
Rev
116:6463–6487
45. Livi L, Maiorino E, Pinna A, Sadeghian A,
Rizzi A, Giuliani A (2016) Analysis of heat
kernel highlights the strongly modular and
heat-preserving structure of proteins. Physica
A 441:199–214
46. Livi L, Maiorino E, Giuliani A, Rizzi A, Sadeghian A (2016) A generative model for protein contact networks. J Biomol Struct
Dynamics 34:1441–1454
47. Khor S (2017) Comparing local search paths
with global search paths on protein residue
networks: allosteric communication. J Complex Networks 5:409–432
48. Khor S (2016) Protein residue networks from
a local search perspective. J Complex Networks 4:245–278
49. Avd V, Lorkowski A, Ma N, Gray GM (2017)
Computer simulations of the retinoid X
receptor: conformational dynamics and allosteric networks. Curr Top Med Chem
17:731–741
50. Amor BRC, Schaub MT, Yaliriki SN, Barahona M (2016) Prediction of allosteric sites
and mediating interactions through bond-tobond propensities. Nat Commun 7:12477.
https://doi.org/10.1038/ncomms12477
51. Censoni L, dosSantosMuniz H, Martı ´nez L
(2017) A network model predicts the intensity of residue-protein thermal coupling. Bioinformatics.
https://doi.org/10.1093/
bioinformatics/btx124
52. Banerji A, Ghosh I (2011) Fractal symmetry
of protein interior: what have we learned? Cell
Mol Life Sci 68:2711–2737
53. Reuveni S, Klafter J, Granek R (2012)
Dynamic structure factor of vibrating fractals.
Phys Rev Lett 108:068101
54. Reuveni S, Granek R, Klafter J (2010)
Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure. Proc Natl Acad Sci U S A
107:13696–13670
55. Granek R (2011) Proteins as fractals: role of
the hydrodynamic interaction. Phys Rev E
83:020902
56. Enright MB, Yu X, Leitner DM (2006)
Hydration dependence of the mass fractal
dimension and anomalous diffusion of vibrational energy in proteins. Phys Rev E
73:051905
57. Enright MB, Leitner DM (2005) Mass fractal
dimension and the compactness of proteins.
Phys Rev E 71:011912
58. Yu X, Leitner DM (2003) Anomalous diffusion of vibrational energy in proteins. J Chem
Phys 119:12673–12679
59. Leitner DM (2008) Energy flow in proteins.
Ann Rev Phys Chem 59:233–259
60. Chowdary P, Gruebele M (2009) Molecules:
what kind of bag of atoms? J Phys Chem A
113:13139–13143
61. Suel GM, Lockless SW, Wall MA, Ranganathan R (2003) Evolutionarily conserved
networks of residues mediate allosteric communication in proteins. Nat Struct Biol
10:59–69
62. Ota N, Agard DA (2005) Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J Mol Biol
351:345–354
63. Sharp K, Skinner JJ (2006) Pump-probe
molecular dynamics as a tool for studying protein motion and long range coupling. Proteins 65:347–361
64. Lu C, Knecht V, Stock G (2016) Long-range
conformational response of a PDZ domain to
ligand binding and release: a molecular
dynamics study. J Chem Theor Comput
12:870–878
65. Buchenberg S, Knecht V, Walser R, Hamm P,
Stock G (2014) Long-range conformational
transition of a photoswitchable allosteric protein: molecular dynamics simulation study. J
Phys Chem B 118:13468–13476. https://
doi.org/10.1021/jp506873y
66. Cui Q, Karplus M (2008) Allostery and cooperativity revisited. Protein Sci 17:1295–1307.
https://doi.org/10.1110/ps.03259908
67. Tsai C-J, delSol A, Nussinov R (2009) Protein
allostery, signal transmission and dynamics: a
classification scheme of allosteric mechanisms.
Mol BioSystems 5:207–216
68. Changeux J-P (2012) Allostery and the
Monod-Wyman-Changeux
model
after
50 years. Annu Rev Biophys 41:103–133
69. Diaz-Franulic I, Poblete H, Min ˜o-Galaz G,
Gonza ´lez C, Latorre R (2016) Allosterism
and structure in thermally activated transient
receptor potential channels. Annu Rev Biophys 45:371–398
70. Smock RG, Gierasch LM (2009) Sending signals dynamically. Science 324:198–203
71. Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways of energetic
connectivity in protein families. Science
286:295–299
Locating and Navigating Energy Transport Networks in Proteins
55
Giuliani A (2013) Protein contact networks:
an emerging paradigm in chemistry. Chem
Rev 113:1598–1613
44. Dokholyan NV (2016) Controlling allosteric
networks
in
proteins.
Chem
Rev
116:6463–6487
45. Livi L, Maiorino E, Pinna A, Sadeghian A,
Rizzi A, Giuliani A (2016) Analysis of heat
kernel highlights the strongly modular and
heat-preserving structure of proteins. Physica
A 441:199–214
46. Livi L, Maiorino E, Giuliani A, Rizzi A, Sadeghian A (2016) A generative model for protein contact networks. J Biomol Struct
Dynamics 34:1441–1454
47. Khor S (2017) Comparing local search paths
with global search paths on protein residue
networks: allosteric communication. J Complex Networks 5:409–432
48. Khor S (2016) Protein residue networks from
a local search perspective. J Complex Networks 4:245–278
49. Avd V, Lorkowski A, Ma N, Gray GM (2017)
Computer simulations of the retinoid X
receptor: conformational dynamics and allosteric networks. Curr Top Med Chem
17:731–741
50. Amor BRC, Schaub MT, Yaliriki SN, Barahona M (2016) Prediction of allosteric sites
and mediating interactions through bond-tobond propensities. Nat Commun 7:12477.
https://doi.org/10.1038/ncomms12477
51. Censoni L, dosSantosMuniz H, Martı ´nez L
(2017) A network model predicts the intensity of residue-protein thermal coupling. Bioinformatics.
https://doi.org/10.1093/
bioinformatics/btx124
52. Banerji A, Ghosh I (2011) Fractal symmetry
of protein interior: what have we learned? Cell
Mol Life Sci 68:2711–2737
53. Reuveni S, Klafter J, Granek R (2012)
Dynamic structure factor of vibrating fractals.
Phys Rev Lett 108:068101
54. Reuveni S, Granek R, Klafter J (2010)
Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure. Proc Natl Acad Sci U S A
107:13696–13670
55. Granek R (2011) Proteins as fractals: role of
the hydrodynamic interaction. Phys Rev E
83:020902
56. Enright MB, Yu X, Leitner DM (2006)
Hydration dependence of the mass fractal
dimension and anomalous diffusion of vibrational energy in proteins. Phys Rev E
73:051905
57. Enright MB, Leitner DM (2005) Mass fractal
dimension and the compactness of proteins.
Phys Rev E 71:011912
58. Yu X, Leitner DM (2003) Anomalous diffusion of vibrational energy in proteins. J Chem
Phys 119:12673–12679
59. Leitner DM (2008) Energy flow in proteins.
Ann Rev Phys Chem 59:233–259
60. Chowdary P, Gruebele M (2009) Molecules:
what kind of bag of atoms? J Phys Chem A
113:13139–13143
61. Suel GM, Lockless SW, Wall MA, Ranganathan R (2003) Evolutionarily conserved
networks of residues mediate allosteric communication in proteins. Nat Struct Biol
10:59–69
62. Ota N, Agard DA (2005) Intramolecular signaling pathways revealed by modeling anisotropic thermal diffusion. J Mol Biol
351:345–354
63. Sharp K, Skinner JJ (2006) Pump-probe
molecular dynamics as a tool for studying protein motion and long range coupling. Proteins 65:347–361
64. Lu C, Knecht V, Stock G (2016) Long-range
conformational response of a PDZ domain to
ligand binding and release: a molecular
dynamics study. J Chem Theor Comput
12:870–878
65. Buchenberg S, Knecht V, Walser R, Hamm P,
Stock G (2014) Long-range conformational
transition of a photoswitchable allosteric protein: molecular dynamics simulation study. J
Phys Chem B 118:13468–13476. https://
doi.org/10.1021/jp506873y
66. Cui Q, Karplus M (2008) Allostery and cooperativity revisited. Protein Sci 17:1295–1307.
https://doi.org/10.1110/ps.03259908
67. Tsai C-J, delSol A, Nussinov R (2009) Protein
allostery, signal transmission and dynamics: a
classification scheme of allosteric mechanisms.
Mol BioSystems 5:207–216
68. Changeux J-P (2012) Allostery and the
Monod-Wyman-Changeux
model
after
50 years. Annu Rev Biophys 41:103–133
69. Diaz-Franulic I, Poblete H, Min ˜o-Galaz G,
Gonza ´lez C, Latorre R (2016) Allosterism
and structure in thermally activated transient
receptor potential channels. Annu Rev Biophys 45:371–398
70. Smock RG, Gierasch LM (2009) Sending signals dynamically. Science 324:198–203
71. Lockless SW, Ranganathan R (1999) Evolutionarily conserved pathways of energetic
connectivity in protein families. Science
286:295–299
Locating and Navigating Energy Transport Networks in Proteins
55