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  • 1.
    Orellana, Laura
    et al.
    Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, S-10691 Stockholm, Sweden..
    Gustavsson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Bergh, Cathrine
    KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. KTH, Centres, SeRC - Swedish e-Science Research Centre.
    Yoluk, Ozge
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. Univ Maryland, Sch Pharm, Dept Pharmaceut Sci, Baltimore, MD 21201 USA..
    Lindahl, Erik
    KTH, Centres, SeRC - Swedish e-Science Research Centre. KTH, School of Engineering Sciences (SCI), Applied Physics, Biophysics. Stockholm Univ, Dept Biochem & Biophys, Sci Life Lab, S-10691 Stockholm, Sweden..
    eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces2019In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 35, no 18, p. 3505-3507Article in journal (Refereed)
    Abstract [en]

    A Summary: Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Brownian Dynamics Importance Sampling, a coarse-grained simulation algorithm, which spontaneously predicts transition intermediates trapped experimentally. In addition to path-generation, the server provides an interactive 2D-motion landscape graphical representation of the transitions or any additional conformers to explore their structural relationships.

  • 2.
    Orellana, Laura
    et al.
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, S-11419 Stockholm, Sweden..
    Thorne, Amy H.
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA..
    Lema, Rafael
    Barcelona Inst Sci & Technol, Inst Res Biomed IRB Barcelona, Barcelona 08028, Catalonia, Spain..
    Gustavsson, Johan
    KTH, School of Electrical Engineering and Computer Science (EECS), Computational Science and Technology (CST).
    Parisian, Alison D.
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA..
    Hospital, Adam
    Barcelona Inst Sci & Technol, Inst Res Biomed IRB Barcelona, Barcelona 08028, Catalonia, Spain..
    Cordeiro, Tiago N.
    Univ Nova Lisboa, Inst Tecnol Quim & Biol Antonio Xavier, P-2780157 Oeiras, Portugal..
    Bernado, Pau
    Univ Montpellier, CNRS, INSERM, CBS, F-34090 Montpellier, France..
    Scott, Andrew M.
    Austin Hosp, Olivia Newton John Canc Res Inst, Heidelberg, Vic 3084, Australia.;La Trobe Univ, Sch Canc Med, Bundoora, Vic 3086, Australia..
    Brun-Heath, Isabelle
    Barcelona Inst Sci & Technol, Inst Res Biomed IRB Barcelona, Barcelona 08028, Catalonia, Spain..
    Lindahl, Erik
    KTH, Centres, Science for Life Laboratory, SciLifeLab. Stockholm Univ, Dept Biochem & Biophys, S-11419 Stockholm, Sweden..
    Cavenee, Webster K.
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA..
    Furnari, Frank B.
    Univ Calif San Diego, Ludwig Inst Canc Res, La Jolla, CA 92093 USA..
    Orozco, Modesto
    Barcelona Inst Sci & Technol, Inst Res Biomed IRB Barcelona, Barcelona 08028, Catalonia, Spain.;Univ Barcelona, Dept Biochem & Biomed, E-08028 Barcelona, Catalonia, Spain..
    Oncogenic mutations at the EGFR ectodomain structurally converge to remove a steric hindrance on a kinase-coupled cryptic epitope2019In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 116, no 20, p. 10009-10018Article in journal (Refereed)
    Abstract [en]

    Epidermal growth factor receptor (EGFR) signaling is initiated by a large ligand-favored conformational change of the extracellular domain (ECD) from a closed, self-inhibited tethered monomer, to an open untethered state, which exposes a loop required for strong dimerization and activation. In glioblastomas (GBMs), structurally heterogeneous missense and deletion mutations concentrate at the ECD for unclear reasons. We explore the conformational impact of GBM missense mutations, combining elastic network models (ENMs) with multiple molecular dynamics (MD) trajectories. Our simulations reveal that the main missense class, located at the I-II interface away from the self-inhibitory tether, can unexpectedly favor spontaneous untethering to a compact intermediate state, here validated by small-angle X-ray scattering (SAXS). Significantly, such intermediate is characterized by the rotation of a large ECD fragment (N-TR1), deleted in the most common GBM mutation, EGFRvIII, and that makes accessible a cryptic epitope characteristic of cancer cells. This observation suggested potential structural equivalence of missense and deletion ECD changes in GBMs. Corroborating this hypothesis, our FACS, in vitro, and in vivo data demonstrate that entirely different ECD variants all converge to remove N-TR1 steric hindrance from the 806-epitope, which we show is allosterically coupled to an intermediate kinase and hallmarks increased oncogenicity. Finally, the detected extraintracellular coupling allows for synergistic cotargeting of the intermediate with mAb806 and inhibitors, which is proved herein.

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