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      Molecular interactions underlying liquid-liquid phase separation of the FUS low complexity domain

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          Abstract

          The low complexity domain of the RNA-binding protein FUS (FUS LC) mediates liquid-liquid phase separation (LLPS), but interactions between the repetitive SYGQ-rich sequence of FUS LC that stabilize the liquid phase are not known in detail. By combining NMR and Raman spectroscopy, mutagenesis, and molecular simulation, we demonstrate that heterogeneous interactions involving all residue types underlie LLPS of human FUS LC. We find no evidence that FUS LC adopts conformations with traditional secondary structure elements in the condensed phase, rather it maintains conformational heterogeneity. We show that hydrogen bonding, π/sp 2 and hydrophobic interactions all contribute to stabilizing LLPS of FUS LC. In addition to contributions from tyrosine residues, we find that glutamine residues participate in contacts leading to LLPS of FUS LC. These results support a model in which FUS LC forms dynamic, multivalent interactions via multiple residue types and remains disordered in the densely packed liquid phase.

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          Is Open Access

          NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

          Summary: SPARKY (Goddard and Kneller, SPARKY 3) remains the most popular software program for NMR data analysis, despite the fact that development of the package by its originators ceased in 2001. We have taken over the development of this package and describe NMRFAM-SPARKY, which implements new functions reflecting advances in the biomolecular NMR field. NMRFAM-SPARKY has been repackaged with current versions of Python and Tcl/Tk, which support new tools for NMR peak simulation and graphical assignment determination. These tools, along with chemical shift predictions from the PACSY database, greatly accelerate protein side chain assignments. NMRFAM-SPARKY supports automated data format interconversion for interfacing with a variety of web servers including, PECAN , PINE, TALOS-N, CS-Rosetta, SHIFTX2 and PONDEROSA-C/S. Availability and implementation: The software package, along with binary and source codes, if desired, can be downloaded freely from http://pine.nmrfam.wisc.edu/download_packages.html. Instruction manuals and video tutorials can be found at http://www.nmrfam.wisc.edu/nmrfam-sparky-distribution.htm. Contact: whlee@nmrfam.wisc.edu or markley@nmrfam.wisc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
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            General purpose molecular dynamics simulations fully implemented on graphics processing units

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              Zur Lehre von der Wirkung der Salze

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                Author and article information

                Journal
                101186374
                31761
                Nat Struct Mol Biol
                Nat. Struct. Mol. Biol.
                Nature structural & molecular biology
                1545-9993
                1545-9985
                29 May 2019
                01 July 2019
                July 2019
                01 January 2020
                : 26
                : 7
                : 637-648
                Affiliations
                [1 ]Graduate Program in Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, Rhode Island, USA
                [2 ]Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, Pennsylvania, USA
                [3 ]Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey, USA
                [4 ]LUT School of Engineering Science, LUT University, Lappeenranta, Finland
                [5 ]Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Mainz, Germany
                [6 ]Department of Biomedical Engineering, University of Texas at Austin, Austin, Texas, USA
                [7 ]Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, Rhode Island, USA
                Author notes

                Author contributions

                A.C.M and N.L.F designed, performed, and analyzed data for NMR spectroscopy, phase separation assays, and microscopy. Y.K. and S.H.P. designed, performed, and analyzed data for CARS. G.L.D, G.H.Z, and J.M. designed and performed simulation experiments and analyzed the resulting data. A.C.M and N.L.F. wrote the manuscript with comments from all authors.

                Article
                NIHMS1529306
                10.1038/s41594-019-0250-x
                6613800
                31270472
                1681a344-ae33-438e-95d5-14065c65e52b

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                Molecular biology
                Molecular biology

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