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Biophysical studies of phase separation integrating experimental and computational methods
Affiliation:1. Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, United States;2. Department of Biomedical Engineering, University of Texas at Austin, Austin, TX 78712, United States;3. Department of Chemical and Biomolecular Engineering, Lehigh University, 111 Research Drive, Bethlehem, PA, 18015, United States;1. Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Worcester, Massachusetts;1. Neuroscience Graduate Program, Brown University, Providence, RI 02912, USA;2. Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA;3. Graduate Program in Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI 02912, USA;4. Department of Chemical and Biomolecular Engineering, Lehigh University, Bethlehem, PA 18015, USA;1. Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI 02912, USA;2. Graduate Program in Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02912, USA;1. Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany;2. Department of Biomedical Engineering and Center for Biological Systems Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA;3. Research Institute of Molecular Pathology, Campus-Vienna-Biocenter 1, 1030 Vienna, Austria;1. Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA;2. KU Leuven, Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), Leuven, Belgium;3. VIB, Center for Brain and Disease Research, Laboratory of Neurobiology, Leuven, Belgium;4. Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany;5. Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI, USA;6. Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN, USA;7. Institute of Molecular Life Sciences, University of Zürich, Zürich, Switzerland;8. Switch Laboratory, VIB, Leuven, Belgium;9. KU Leuven, Department for Cellular and Molecular Medicine, Leuven, Belgium;10. Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA;11. Department of Pharmacology, Boston University School of Medicine, Boston, MA, USA;12. Department of Neurology, Boston University School of Medicine, Boston, MA, USA;13. VIB, Center for Structural Biology (CSB), Vrije Universiteit Brussel (VUB), Brussels, Belgium;14. Institute of Enzymology, Research Centre for Natural Sciences of the Hungarian Academy of Sciences, Budapest, Hungary;15. MTA-DE Laboratory of Protein Dynamics, Department of Biochemistry and Molecular Biology, University of Debrecen, Debrecen, Hungary
Abstract:Biomolecular phase separation that contributes to the formation of membraneless organelles and biomolecular condensates has recently gained tremendous attention because of the importance of these assemblies in physiology, disease, and engineering applications. Understanding and directing biomolecular phase separation requires a multiscale view of the biophysical properties of these phases. Yet, many classic tools to characterize biomolecular properties do not apply in these condensed phases. Here, we discuss insights obtained from spectroscopic methods, in particular nuclear magnetic resonance and optical spectroscopy, in understanding the molecular and atomic interactions that underlie the formation of protein-rich condensates. We also review approaches closely coupling nuclear magnetic resonance data with computational methods especially coarse-grained and all-atom molecular simulations, which provide insight into molecular features of phase separation. Finally, we point to future methodolical developments, particularly visualizing biophysical properties of condensates in cells.
Keywords:Protein nuclear magnetic resonance spectroscopy (NMR)  Phase separation  Biomolecular condensates  Membraneless organelles  Molecular dynamics simulations  Advanced sampling techniques  Hyperspectral imaging  Raman spectroscopy  Förster resonance energy transfer (FRET)  Fluorescence lifetime imaging  Magic angle spinning solid state NMR spectroscopy
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