produce 3D representation of the community network structures by employing a visualization software, such as the Visual
Molecular Dynamics tool [55].
References
1. Fenton AW (2008) Allostery: an illustrated
definition for the ‘second secret of life’. Trends
Biochem Sci 33(9):420–425
2. Changeux JP (2013) 50 years of allosteric
interactions: the twists and turns of the models.
Nat Rev Mol Cell Biol 14(12):819–829
3. Hilser VJ, Wrabl JO, Motlagh HN (2012)
Structural and energetic basis of allostery.
Annu Rev Biophys 41:585–609
4. Tsai CJ, Nussinov R (2014) A unified view of
“how allostery works”. PLoS Comput Biol 10
(2):e1003394
5. Wodak SJ, Paci E, Dokholyan NV, Berezovsky
IN, Horovitz A, Li J, Hilser VJ, Bahar I,
Karanicolas J, Stock G, Hamm P, Stote RH,
Eberhardt J, Chebaro Y, Dejaegere A,
Cecchini M, Changeux J-P, Bolhuis PG,
Vreede J, Faccioli P, Orioli S, Ravasio R,
Yan L, Brito C, Wyart M, Gkeka P, Rivalta I,
Palermo G, McCammon JA, PaneckaHofman J, Wade RC, Di Pizio A, Niv MY,
Nussinov R, Tsai C-J, Jang H, Padhorny D,
Kozakov D, McLeish T (2019) Allostery in its
many disguises: from theory to applications.
Structure 27(4):566–578
6. Wootten D, Christopoulos A, Sexton PM
(2013) Emerging paradigms in gpcr allostery:
implications for drug discovery. Nat Rev Drug
Discov 12(8):630–644
7. Taly A, Corringer PJ, Guedin D, Lestage P,
Changeux JP (2009) Nicotinic receptors: allosteric transitions and therapeutic targets in the
nervous system. Nat Rev Drug Discov 8
(9):733–750
8. Nussinov R, Tsai CJ (2013) Allostery in disease
and in drug discovery. Cell 153(2):293–305
9. Christopoulos A (2002) Allosteric binding
sites on cell-surface receptors: novel targets
for drug discovery. Nat Rev Drug Discov 1
(3):198–210
10. Gohara DW, Di Cera E (2011) Allostery in
trypsin-like proteases suggests new therapeutic
strategies. Trends Biotechnol 29(11):577–585
11. Makhlynets OV, Raymond EA, Korendovych
IV (2015) Design of allosterically regulated
protein
catalysts.
Biochemistry
54
(7):1444–1456
12. Lisi GP, Manley GA, Hendrickson H, Rivalta I,
Batista VS, Loria JP (2016) Dissecting dynamic
allosteric pathways using chemically related
small-molecule activators. Structure 24
(7):1155–1166
13. Suel GM, Lockless SW, Wall MA, Ranganathan
R (2003) Evolutionarily conserved networks of
residues mediate allosteric communication in
proteins. Nat Struct Biol 10(1):59–69
14. Amaro RE, Sethi A, Myers RS, Davisson VJ,
Luthey-Schulten ZA (2007) A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase.
Biochemistry 46(8):2156–2173
15. Bruschweiler S, Schanda P, Kloiber K,
Brutscher B, Kontaxis G, Konrat R, Tollinger
M (2009) Direct observation of the dynamic
process underlying allosteric signal transmission. J Am Chem Soc 131(8):3063–3068
16. del Sol A, Tsai CJ, Ma B, Nussinov R (2009)
The origin of allosteric functional modulation:
multiple pre-existing pathways. Structure 17
(8):1042–1050
17. Feher VA, Durrant JD, Van Wart AT, Amaro
RE (2014) Computational approaches to
mapping allosteric pathways. Curr Opin Struct
Biol 25:98–103
18. Martin NE, Malik S, Calimet N, Changeux JP,
Cecchini M (2017) Un-gating and allosteric
modulation of a pentameric ligand-gated ion
channel captured by molecular dynamics. PLoS
Comput Biol 13(10):e1005784
19. Markwick PR, McCammon JA (2011) Studying functional dynamics in bio-molecules using
accelerated molecular dynamics. Phys Chem
Chem Phys 13(45):20053–20065
20. De Vivo M, Masetti M, Bottegoni G, Cavalli A
(2016) Role of molecular dynamics and related
methods in drug discovery. J Med Chem 59
(9):4035–4061
21. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
22. Di Paola L, De Ruvo M, Paci P, Santoni D,
Giuliani A (2013) Protein contact networks: an
emerging paradigm in chemistry. Chem Rev
113(3):1598–1613
23. Rivalta I, Sultan MM, Lee NS, Manley GA,
Loria JP, Batista VS (2012) Allosteric pathways
in imidazole glycerol phosphate synthase. Proc
Natl Acad Sci U S A 109(22):E1428–E1436
Community Network Analysis of Allosteric Proteins
149
Molecular Dynamics tool [55].
References
1. Fenton AW (2008) Allostery: an illustrated
definition for the ‘second secret of life’. Trends
Biochem Sci 33(9):420–425
2. Changeux JP (2013) 50 years of allosteric
interactions: the twists and turns of the models.
Nat Rev Mol Cell Biol 14(12):819–829
3. Hilser VJ, Wrabl JO, Motlagh HN (2012)
Structural and energetic basis of allostery.
Annu Rev Biophys 41:585–609
4. Tsai CJ, Nussinov R (2014) A unified view of
“how allostery works”. PLoS Comput Biol 10
(2):e1003394
5. Wodak SJ, Paci E, Dokholyan NV, Berezovsky
IN, Horovitz A, Li J, Hilser VJ, Bahar I,
Karanicolas J, Stock G, Hamm P, Stote RH,
Eberhardt J, Chebaro Y, Dejaegere A,
Cecchini M, Changeux J-P, Bolhuis PG,
Vreede J, Faccioli P, Orioli S, Ravasio R,
Yan L, Brito C, Wyart M, Gkeka P, Rivalta I,
Palermo G, McCammon JA, PaneckaHofman J, Wade RC, Di Pizio A, Niv MY,
Nussinov R, Tsai C-J, Jang H, Padhorny D,
Kozakov D, McLeish T (2019) Allostery in its
many disguises: from theory to applications.
Structure 27(4):566–578
6. Wootten D, Christopoulos A, Sexton PM
(2013) Emerging paradigms in gpcr allostery:
implications for drug discovery. Nat Rev Drug
Discov 12(8):630–644
7. Taly A, Corringer PJ, Guedin D, Lestage P,
Changeux JP (2009) Nicotinic receptors: allosteric transitions and therapeutic targets in the
nervous system. Nat Rev Drug Discov 8
(9):733–750
8. Nussinov R, Tsai CJ (2013) Allostery in disease
and in drug discovery. Cell 153(2):293–305
9. Christopoulos A (2002) Allosteric binding
sites on cell-surface receptors: novel targets
for drug discovery. Nat Rev Drug Discov 1
(3):198–210
10. Gohara DW, Di Cera E (2011) Allostery in
trypsin-like proteases suggests new therapeutic
strategies. Trends Biotechnol 29(11):577–585
11. Makhlynets OV, Raymond EA, Korendovych
IV (2015) Design of allosterically regulated
protein
catalysts.
Biochemistry
54
(7):1444–1456
12. Lisi GP, Manley GA, Hendrickson H, Rivalta I,
Batista VS, Loria JP (2016) Dissecting dynamic
allosteric pathways using chemically related
small-molecule activators. Structure 24
(7):1155–1166
13. Suel GM, Lockless SW, Wall MA, Ranganathan
R (2003) Evolutionarily conserved networks of
residues mediate allosteric communication in
proteins. Nat Struct Biol 10(1):59–69
14. Amaro RE, Sethi A, Myers RS, Davisson VJ,
Luthey-Schulten ZA (2007) A network of conserved interactions regulates the allosteric signal in a glutamine amidotransferase.
Biochemistry 46(8):2156–2173
15. Bruschweiler S, Schanda P, Kloiber K,
Brutscher B, Kontaxis G, Konrat R, Tollinger
M (2009) Direct observation of the dynamic
process underlying allosteric signal transmission. J Am Chem Soc 131(8):3063–3068
16. del Sol A, Tsai CJ, Ma B, Nussinov R (2009)
The origin of allosteric functional modulation:
multiple pre-existing pathways. Structure 17
(8):1042–1050
17. Feher VA, Durrant JD, Van Wart AT, Amaro
RE (2014) Computational approaches to
mapping allosteric pathways. Curr Opin Struct
Biol 25:98–103
18. Martin NE, Malik S, Calimet N, Changeux JP,
Cecchini M (2017) Un-gating and allosteric
modulation of a pentameric ligand-gated ion
channel captured by molecular dynamics. PLoS
Comput Biol 13(10):e1005784
19. Markwick PR, McCammon JA (2011) Studying functional dynamics in bio-molecules using
accelerated molecular dynamics. Phys Chem
Chem Phys 13(45):20053–20065
20. De Vivo M, Masetti M, Bottegoni G, Cavalli A
(2016) Role of molecular dynamics and related
methods in drug discovery. J Med Chem 59
(9):4035–4061
21. Di Paola L, Giuliani A (2015) Protein contact
network topology: a natural language for allostery. Curr Opin Struct Biol 31:43–48
22. Di Paola L, De Ruvo M, Paci P, Santoni D,
Giuliani A (2013) Protein contact networks: an
emerging paradigm in chemistry. Chem Rev
113(3):1598–1613
23. Rivalta I, Sultan MM, Lee NS, Manley GA,
Loria JP, Batista VS (2012) Allosteric pathways
in imidazole glycerol phosphate synthase. Proc
Natl Acad Sci U S A 109(22):E1428–E1436
Community Network Analysis of Allosteric Proteins
149