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Useful Articles

Macromolecular Crowding

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  1. Weak Chemical Interactions That Drive Protein Evolution: Crowding, Sticking, and Quinary Structure in Folding and Function. Guin D, Gruebele M. Chem. Rev. 2019, 119, 10691-10717. doi: 10.1021/acs.chemrev.8b00753.

  2. Modeling Crowded Environment in Molecular Simulations. Ostrowska N, Feig M, Trylska J. Front. Mol. Biosci. 2019, 6, 86. doi: 10.3389/fmolb.2019.00086. Review

  3. Understanding biochemical processes in the presence of sub-diffusive behavior of biomolecules in solution and living cells. Basak S, Sengupta S, Chattopadhyay K. Biophys. Rev. 2019, 6, 851-872. doi: 10.1007/s12551-019-00580-9. Review

  4. Toward an understanding of biochemical equilibria within living cells. Rivas G, Minton AP. Biophys Rev. 2018, 10, 241-253. doi: 10.1007/s12551-017-0347-6. Review

  5. Towards developing principles of protein folding and dynamics in the cell. Cheung MS, Gasic AG. Phys Biol. 2018, 15, 063001. doi: 10.1088/1478-3975/aaced2. Review.

  6. What macromolecular crystallogenesis tells us - what is needed in the future. Giegé R. IUCrJ. 2017 May 24;4, 340-349. doi: 10.1107/S2052252517006595. eCollection 2017 Jul 1. Review

  7. Microorganisms maintain crowding homeostasis. van den Berg J, Boersma AJ, Poolman B. Nat Rev Microbiol. 2017, 5, 309-318. doi: 10.1038/nrmicro.2017.17.  Review

  8. The macromolecular crowding effect--from in vitro into the cell. Gnutt D, Ebbinghaus S. Biol Chem. 2016, 397, 37-44. doi: 10.1515/hsz-2015-0161. Review

  9. Emergence of life: Physical chemistry changes the paradigm. Spitzer J, Pielak GJ, Poolman B. Biol Direct. 2015, 10, 33. doi: 10.1186/s13062-015-0060-y. Review.

Protein Aggregation

  1. Targeting α-synuclein for PD Therapeutics: A Pursuit on All Fronts. Teil M, Arotcarena ML, Faggiani E, Laferriere F, Bezard E, Dehay B. Biomolecules 2020, 10, pii: E391. doi: 10.3390/biom10030391. Review

  2. How and Why to Build a Mathematical Model: A Case Study Using Prion Aggregation. Banwarth-Kuhn M, Sindi SS. J Biol Chem. 2020, pii: jbc.REV119.009851. doi: 10.1074/jbc.REV119.009851. [Epub ahead of print] Review

  3. The Hydrophobic Effect Characterises the Thermodynamic Signature of Amyloid Fibril Growth. van Gils JHM, van Dijk E, Peduzzo A, Hofmann A, Vettore N, Schützmann MP, Groth G, Mouhib H, Otzen DE, Buell AK, Abeln S. PLoS Comput Biol.  2020, 16, e1007767. doi: 10.1371/journal.pcbi.1007767

  4. Effects of in Vivo Conditions on Amyloid Aggregation. Owen MC, Gnutt D, Gao M, Wärmländer SKTS, Jarvet J, Gräslund A, Winter R, Ebbinghaus S, Strodel B. Chem Soc Rev. 2019, 48, 3946-3996.  doi: 10.1039/c8cs00034d.

  5. Could Heat Therapy Be an Effective Treatment for Alzheimer's and Parkinson's Diseases? A Narrative Review. Hunt AP, Minett GM, Gibson OR, Kerr GK, Stewart IB. Front Physiol. 2020, 10, 1556. doi: 10.3389/fphys.2019.01556. Review

  6. The catalytic nature of protein aggregation. Dear AJ, Meisl G, Michaels TCT, Zimmermann MR, Linse S, Knowles TPJ. J Chem Phys. 2020,152, 045101. doi: 10.1063/1.5133635

  7. Differences in nucleation behavior underlie the contrasting aggregation kinetics of the Aβ40 and Aβ42 peptides. Meisl G, Yang X, Hellstrand E, Frohm B, Kirkegaard JB, Cohen SI, Dobson CM, Linse S, Knowles TP. Proc Natl Acad Sci U S A. 2014, 11, 9384-9. doi: 10.1073/pnas.1401564111.

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Microscopy

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  1. About samples, giving examples: optimized procedures for Single Molecule Localization Microscopy. Jimenez A, Friedl K, Leterrier C. Methods  2020, 174, 100-114.  https://doi.org/10.1016/j.ymeth.2019.05.008

  2. MINFLUX nanoscopy delivers 3D multicolor nanometer resolution in cells. Hell SW. Nature Methods 2020, 17, 217-224.

  3. Super-resolution microscopy demystified. Schermelleh  L, Ferrand L, Huser  T, Eggeling C, Sauer M, Biehlmaier O, Drummen GPC. Nat. Rev. Cell Biol. 2019, 21, 72-84.

  4. Microscopy and cell biology: New methods and new questions. Morris JD, Payne CK. Annu. Rev. Phys. Chem. 2019, 70, 199–218.

  5. An introduction to optical super-resolution microscopy for the adventurous biologist. Vangindertael J, Camacho R, Sempels W, Mizuno H, Dedecker P, Janssen KPF. Methods Appl. Fluoresc. 2018, 6, 022003. https://doi.org/10.1088/2050-6120/aaae0c

  6. Super-Resolution Microscopy: From Single Molecules to Supramolecular Assemblies. Mennella V. Trends Cell Biol. 2015, 12, 730. http://dx.doi.org/10.1016/j.tcb.2015.10.004

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Single Molecule Fluorescence Studies of Biomolecules

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  1. In-cell single-molecule FRET measurements reveal three conformational state changes in RAF protein. Okamotoa K, Hibino K, Sako Y. BBA Gen Subjects 2020, 1864, 129358.

  2. Single-molecule insights into the temperature and pressure dependent conformational dynamics of nucleic acids in the presence of crowders and osmolytes. Arns L, Knop JM, Patra S, Anders C, Winter R.  Biophys. Chem. 2019, 251, 106190. doi: 10.1016/j.bpc.2019.106190. Review 

  3. Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World. Ray S, Widom JR, Walter NG. Chem. Rev. 2018, 118, 4120-4155. doi: 10.1021/acs.chemrev.7b00519. Review

  4. Single-Molecule FRET Spectroscopy and the Polymer Physics of Unfolded and Intrinsically Disordered Proteins. Schuler B, Soranno A, Hofmann H, Nettels D. Annu. Rev. Biophys. 2016, 45, 207-31. doi: 10.1146/annurev-biophys-062215-010915. Review

  5. Single-molecule studies of intrinsically disordered proteins. Brucale M, Schuler B, Samorì B. Chem. Rev. 2014, 114, 3281-317. doi: 10.1021/cr400297g. Epub 2014 Jan 17. Review

  6. Protein folding studied by single-molecule FRET. Schuler B, Eaton WA. Curr Opin Struct Biol. 2008, 18, 16-26. doi: 10.1016/j.sbi.2007.12.003. Review

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