Computational Drug Discovery and Design

(backadmin) #1
592:2439–2441. https://doi.org/10.1113/
jphysiol.2014.272252


  1. Lambert NA, Javitch JA (2014) CrossTalk
    opposing view: weighing the evidence for class
    A GPCR dimers, the jury is still out. J Physiol
    592:2443–2445. https://doi.org/10.1113/
    jphysiol.2014.272997

  2. James JR, Oliveira MI, Carmo AM et al (2006)
    A rigorous experimental framework for detect-
    ing protein oligomerization using biolumines-
    cence resonance energy transfer. Nat Methods
    3:1001–1006. https://doi.org/10.1038/
    nmeth978

  3. Meyer BH, Segura J-M, Martinez KL et al
    (2006) FRET imaging reveals that functional
    neurokinin-1 receptors are monomeric and
    reside in membrane microdomains of live
    cells. Proc Natl Acad Sci U S A
    103:2138–2143. https://doi.org/10.1073/
    pnas.0507686103

  4. Gaitonde SA, Gonza ́Lez-Maeso J (2017) Con-
    tribution of heteromerization to G protein-
    coupled receptor function. Curr Opin Pharma-
    col 32:23–31. https://doi.org/10.1016/j.
    coph.2016.10.006

  5. Guidolin D, Agnati LF, Marcoli M et al (2014)
    G-protein-coupled receptor type A heteromers
    as an emerging therapeutic target. Expert Opin
    Ther Targets 8222:1–19.https://doi.org/10.
    1517/14728222.2014.981155

  6. Shonberg J, Scammells PJ, Capuano B (2011)
    Design strategies for bivalent ligands targeting
    GPCRs. ChemMedChem 6:963–974.https://
    doi.org/10.1002/cmdc.201100101

  7. Vin ̃als X, Moreno E, Lanfumey L et al (2015)
    Cognitive impairment induced by delta9-
    tetrahydrocannabinol occurs through hetero-
    mers between cannabinoid CB 1 and serotonin
    5-HT2A receptors. PLoS Biol. https://doi.
    org/10.1371/journal.pbio.1002194

  8. Jastrzebska B, Chen Y, Orban T et al (2015)
    Disruption of rhodopsin dimerization with
    synthetic peptides targeting an interaction
    interface. J Biol Chem 290:25728–25744.
    https://doi.org/10.1074/jbc.M115.662684

  9. Wang J, He L, Combs C et al (2006) Dimer-
    ization of CXCR4 in living malignant cells:
    control of cell migration by a synthetic peptide
    that reduces homologous CXCR4 interactions.
    Mol Cancer Ther 5:2474–2483.https://doi.
    org/10.1158/1535-7163.MCT-05-0261

  10. Hebert TE, Moffett S, Morello JP et al (1996)
    A peptide derived from a beta2-adrenergic
    receptor transmembrane domain inhibits both
    receptor dimerization and activation. J Biol
    Chem 271:16384–16392. https://doi.org/
    10.1074/jbc.271.27.16384
    75. Khelashvili G, Dorff K, Shan J et al (2010)
    GPCR-OKB: the G protein coupled receptor
    oligomer knowledge base. Bioinformatics
    26:1804–1805.https://doi.org/10.1093/bio
    informatics/btq264
    76. Kufareva I, Katritch V, Participants of GPCR
    Dock 2013, Stevens RC, Abagyan R (2014)
    Advances in GPCR modeling evaluated by the
    GPCR Dock 2013 assessment: meeting new
    challenges. Structure 22:1120–1139.https://
    doi.org/10.1016/j.str.2014.06.012
    77. Casciari D, Seeber M, Fanelli F (2006) Quater-
    nary structure predictions of transmembrane
    proteins starting from the monomer: a
    docking-based approach. BMC Bioinformatics
    7:340.https://doi.org/10.1186/1471-2105-
    7-340
    78. Dell’Orco D, Casciari D, Fanelli F (2008)
    Quaternary structure predictions and estima-
    tion of mutational effects on the free energy
    of dimerization of the OMPLA protein. J
    Struct Biol 163:155–162. https://doi.org/
    10.1016/j.jsb.2008.05.006
    79. Kaczor AA, Guixa`-Gonza ́lez R, Carrio ̃Petal
    (2015) Multi-component protein – protein
    docking based protocol with external scoring
    for modeling dimers of g protein-coupled
    receptors. Mol Inform 34:246–255.https://
    doi.org/10.1002/minf.201400088
    80. Chaudhury S, Berrondo M, Weitzner BD et al
    (2011) Benchmarking and analysis of protein
    docking performance in Rosetta v3.2. PLoS
    One 6:e22477. https://doi.org/10.1371/
    journal.pone.0022477
    81. Jo ̈rg M, Kaczor AA, Mak FS et al (2014) Inves-
    tigation of novel ropinirole analogues: synthe-
    sis, pharmacological evaluation and
    computational analysis of dopamine D2 recep-
    tor functionalized congeners and homobiva-
    lent ligands. MedChemComm 5:891–898.
    https://doi.org/10.1039/C4MD00066H
    82. Kaczor AA, Jo ̈rg M, Capuano B (2016) The
    dopamine D2 receptor dimer and its interac-
    tion with homobivalent antagonists: homology
    modeling, docking and molecular dynamics. J
    Mol Model 22:203. https://doi.org/10.
    1007/s00894-016-3065-2
    83. Viswanath S, Dominguez L, Foster LS et al
    (2015) Extension of a protein docking algo-
    rithm to membranes and applications to amy-
    loid precursor protein dimerization. Proteins
    83:2170–2185. https://doi.org/10.1002/
    prot.24934
    84. MacCallum JL, Bennett WFD, Tieleman DP
    (2007) Partitioning of amino acid side chains
    into lipid bilayers: results from computer simu-
    lations and comparison to experiment. J Gen


304 Agnieszka A. Kaczor et al.

Free download pdf