Computational Drug Discovery and Design

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  1. Lo ̈hr T, Jussupow A, Camilloni C (2017)
    Metadynamic metainference: convergence
    towards force field independent structural
    ensembles of a disordered peptide. J Chem
    Phys 146:165102

  2. Drinkwater N, Cossins BP, Keeble AH et al
    (2014) Human immunoglobulin E flexes
    between acutely bent and extended confor-
    mations. Nat Struct Mol Biol 21:397–404

  3. Davies AM, Allan EG, Keeble AH et al (2017)
    Allosteric mechanism of action of the thera-
    peutic anti-IgE antibody omalizumab. J Biol
    Chem 292:9975–9987

  4. Sutto L, Marsili S, Valencia A et al (2015)
    From residue coevolution to protein confor-
    mational ensembles and functional dynamics.
    Proc Natl Acad Sci U S A 112:13567–13572

  5. Stetz G, Verkhivker GM (2017) Computa-
    tional analysis of residue interaction networks
    and coevolutionary relationships in the
    Hsp70 chaperones: a community-hopping
    model of allosteric regulation and communi-
    cation. PLoS Comput Biol 13:e1005299

  6. Lakhani B, Thayer KM, Hingorani MM et al
    (2017) Evolutionary covariance combined
    with molecular dynamics predicts a frame-
    work for allostery in the MutS DNA mis-
    match repair protein. J Phys Chem B
    121:2049–2061

  7. Morcos F, Jana B, Hwa T et al (2013) Coevo-
    lutionary signals across protein lineages help
    capture multiple protein conformations. Proc
    Natl Acad Sci U S A 110:20533–20538

  8. Sfriso P, Duran-Frigola M, Mosca R et al
    (2016) Residues coevolution guides the sys-
    tematic identification of alternative functional
    conformations in proteins. Structure
    24:116–126

  9. Morrone JA, Perez A, MacCallum J et al
    (2017) Computed binding of peptides to
    proteins with MELD-accelerated molecular
    dynamics. J Chem Theory Comput
    13:870–876

  10. Miao Y, Feher VA, McCammon JA (2015)
    Gaussian accelerated molecular dynamics:
    unconstrained enhanced sampling and free
    energy calculation. J Chem Theory Comput
    11:3584–3595

  11. Grant BJ, Gorfe AA, McCammon JA (2009)
    Ras conformational switching: simulating
    nucleotide-dependent conformational transi-
    tions with accelerated molecular dynamics.
    PLoS Comput Biol 5:e1000325

  12. Bucher D, Grant BJ, Markwick PR et al
    (2011) Accessing a hidden conformation of
    the maltose binding protein using accelerated


molecular dynamics. PLoS Comput Biol 7:
e1002034


  1. Roe DR, Bergonzo C, Cheatham TE (2014)
    Evaluation of enhanced sampling provided by
    accelerated molecular dynamics with Hamil-
    tonian replica exchange methods. J Phys
    Chem B 118:3543–3552

  2. Kubitzki MB, de Groot BL (2008) The atom-
    istic mechanism of conformational transition
    in adenylate kinase: a TEE-REX molecular
    dynamics study. Structure 16:1175–1182

  3. Shao Q (2016) Enhanced conformational
    sampling technique provides an energy land-
    scape view of large-scale protein conforma-
    tional transitions. Phys Chem Chem Phys
    18:29170–29182

  4. Shao Q, Xu Z, Wang J et al (2017) Energetics
    and structural characterization of the “DFG-
    flip” conformational transition of B-RAF
    kinase: a SITS molecular dynamics study.
    Phys Chem Chem Phys 19:1257–1267

  5. Dror R, Arlow D, Borhani D et al (2009)
    Identification of two distinct inactive confor-
    mations of the beta 2-adrenergic receptor
    reconciles structural and biochemical obser-
    vations. Proc Natl Acad Sci U S A
    106:4689–4694

  6. Shan Y, Arkhipov A, Kim ET et al (2013)
    Transitions to catalytically inactive conforma-
    tions in EGFR kinase. Proc Natl Acad Sci U S
    A 110:7270–7275

  7. Cooper A, Dryden DT (1984) Allostery with-
    out conformational change. A plausible
    model. Eur Biophys J 11:103–109

  8. Palazzesi F, Barducci A, Tollinger M et al
    (2013) The allosteric communication path-
    ways in KIX domain of CBP. Proc Natl Acad
    Sci U S A 110:14237–14242

  9. Gasper PM, Fuglestad B, Komives EA et al
    (2012) Allosteric networks in thrombin dis-
    tinguish procoagulant vs. anticoagulant activ-
    ities. Proc Natl Acad Sci U S A
    109:21216–21222

  10. Fuglestad B, Gasper PM, McCammon JA et al
    (2013) correlated motions and residual frus-
    tration in thrombin. J Phys Chem B
    117:12857–12863

  11. Clarke D, Sethi A, Li S et al (2016) Identify-
    ing allosteric hotspots with dynamics: applica-
    tion to inter- and intra-species conservation.
    Structure 24:826–837

  12. Greener JG, Sternberg MJ (2015) AlloPred:
    prediction of allosteric pockets on proteins
    using normal mode perturbation analysis.
    BMC Bioinformatics 16:335

  13. Gur M, Zomot E, Bahar I (2013) Global
    motions exhibited by proteins in micro- to


Computational Study of Protein Conformational Transitions 363
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