(13):8637–8641. https://doi.org/10.1073/
pnas.122076099
- Kaczor AA, Rutkowska E, Bartuzi D,
Targowska-Duda KM, Matosiuk D, Selent J
(2016) Computational methods for studying
G protein-coupled receptors (GPCRs). Meth-
ods Cell Biol 132:359–399.https://doi.org/
10.1016/bs.mcb.2015.11.002
- Lee Y, Jeong LS, Choi S, Hyeon C (2011) Link
between allosteric signal transduction and
functional dynamics in a multisubunit enzyme:
S-adenosylhomocysteine hydrolase. J Am
Chem Soc 133(49):19807–19815. https://
doi.org/10.1021/ja2066175
- Lee Y, Choi S, Hyeon C (2014) Mapping the
intramolecular signal transduction of
G-protein coupled receptors. Proteins 82
(5):727–743.https://doi.org/10.1002/prot.
24451
- Lee Y, Choi S, Hyeon C (2015) Communica-
tion over the network of binary switches reg-
ulates the activation of A2A adenosine
receptor. PLoS Comput Biol 11(2):
e1004044.https://doi.org/10.1371/journal.
pcbi.1004044
- Buck M, Bouguet-Bonnet S, Pastor RW, AD
MK Jr (2006) Importance of the CMAP cor-
rection to the CHARMM22 protein force field:
dynamics of hen lysozyme. Biophys J 90(4):
L36–L38. https://doi.org/10.1529/
biophysj.105.078154
- Phillips JC, Braun R, Wang W, Gumbart J,
Tajkhorshid E, Villa E, Chipot C, Skeel RD,
Kale L, Schulten K (2005) Scalable molecular
dynamics with NAMD. J Comput Chem 26
(16):1781–1802. https://doi.org/10.1002/
jcc.20289
- Zoete V, Cuendet MA, Grosdidier A, Michielin
O (2011) SwissParam: a fast force field genera-
tion tool for small organic molecules. J Com-
put Chem 32(11):2359–2368. https://doi.
org/10.1002/jcc.21816
- Humphrey W, Dalke A, Schulten K (1996)
VMD: visual molecular dynamics. J Mol
Graph 14(1):33–38. 27–38
- Bjarnadottir TK, Gloriam DE, Hellstrand SH,
Kristiansson H, Fredriksson R, Schioth HB
(2006) Comprehensive repertoire and phylo-
genetic analysis of the G protein-coupled
receptors in human and mouse. Genomics 88
(3):263–273. https://doi.org/10.1016/j.
ygeno.2006.04.001
- Dima RI, Thirumalai D (2006) Determination
of network of residues that regulate allostery in
protein families using sequence analysis. Pro-
tein Sci 15(2):258–268.https://doi.org/10.
1110/ps.051767306
30. da Silveira CH, Pires DE, Minardi RC,
Ribeiro C, Veloso CJ, Lopes JC, Meira W Jr,
Neshich G, Ramos CH, Habesch R, Santoro
MM (2009) Protein cutoff scanning: a compar-
ative analysis of cutoff dependent and cutoff
free methods for prospecting contacts in pro-
teins. Proteins 74(3):727–743. https://doi.
org/10.1002/prot.22187
31. Freeman LC (1978) Centrality in social net-
works conceptual clarification. Soc Networks
1(79):215–239
32. Borgatti SP (2005) Centrality and network
flow. Soc Networks 27:55–71. https://doi.
org/10.1016/j.socnet.2004.11.008
33. Park K, Kim D (2011) Modeling allosteric sig-
nal propagation using protein structure net-
works. BMC Bioinformatics 12(Suppl 1):S23.
https://doi.org/10.1186/1471-2105-12-S1-
S23
34. Dijkstra EW (1959) A note on two problems in
connexion with graphs. Numerische Math 1
(1):269–271. https://doi.org/10.1007/
bf01386390
35. Newman MEJ (2005) A measure of between-
ness centrality based on random walks. Soc
Networks 27(1):39–54. https://doi.org/10.
1016/j.socnet.2004.11.009
36. Brandes U (2001) A faster algorithm for
betweenness centrality. J Math Sociol 25
(2):163–177
37. Qin J, Xu JJ, Hu D, Sageman M, Chen H
(2005) Analyzing terrorist networks: a case
study of the global salafi jihad network. Lect
Notes Comput Sci 3495:287–304
38. Singer Y (2006) Dynamic measure of network
robustness. In: IEEE 24th convention of elec-
trical and electronics engineers, Israel, 2006,
pp 366–370. https://doi.org/10.1109/
EEEI.2006.321105
39. Albert R, Jeong H, Barabasi AL (2000) Error
and attack tolerance of complex networks.
Nature 406(6794):378–382. https://doi.
org/10.1038/35019019
40. del Sol A, Fujihashi H, Amoros D, Nussinov R
(2006) Residues crucial for maintaining short
paths in network communication mediate sig-
naling in proteins. Mol Syst Biol 2:2006.0019.
https://doi.org/10.1038/msb4100063
41. Fritze O, Filipek S, Kuksa V, Palczewski K,
Hofmann KP, Ernst OP (2003) Role of the
conserved NPxxY(x)5,6F motif in the rhodop-
sin ground state and during activation. Proc
Natl Acad Sci U S A 100(5):2290–2295.
https://doi.org/10.1073/pnas.0435715100
42. Shi L, Liapakis G, Xu R, Guarnieri F, Balles-
teros JA, Javitch JA (2002) Beta2 adrenergic
receptor activation. Modulation of the proline
Molecular Dynamics Approach for Investigation of GPCR Allostery 471