Computational Drug Discovery and Design

(backadmin) #1
(13):8637–8641. https://doi.org/10.1073/
pnas.122076099


  1. 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

  2. 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

  3. 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

  4. 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

  5. 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

  6. 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

  7. 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

  8. Humphrey W, Dalke A, Schulten K (1996)
    VMD: visual molecular dynamics. J Mol
    Graph 14(1):33–38. 27–38

  9. 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

  10. 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
Free download pdf