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Recent Publications

Lee, E., Rauscher, S. (2024) The conformational space of the SARS-CoV-2 main protease active site loops is determined by ligand binding and interprotomer allostery. Biochemistry. doi: 10.1021/acs.biochem.4c00575

Klyshko, E., Kim, J. S., McGough, L., Valeeva, V., Lee, E., Ranganathan, R., Rauscher, S. (2024) Functional Protein Dynamics in a Crystal. Nature Communications 15, 3244. doi: 10.1038/s41467-024-47473-4

O’Mara, M. L., Rauscher, S., Wetmore, S. D. (2024) Introduction to the RSC Advances themed collection on “New insights into biomolecular systems from large-scale simulations” RSC Advances 14, 6985-6986. doi:10.1039/D4RA90012J

Joron, K., Oliveira Viegas, J., Haas-Neill, L., Bier, S., Drori, P., Dvir, S., Lin Lim, P. S., Rauscher, S., Meshorer, E., and Lerner E. (2023) Fluorescent protein lifetimes report increased local densities and phases of nuclear condensates during embryonic stem cell differentiation. Nature Communications 14, 4885. doi:10.1038/s41467-023-40647-6

Klyshko, E., Kim, J. S., and Rauscher, S. (2023) LAWS: Local alignment for water sites — Tracking ordered water in simulations. Biophysical Journal 122, 2871-2883. doi:10.1016/j.bpj.2022.09.012

Armstrong, H. K., Bording-Jorgensen, M., Santer, D. M., Zhang, Z., Valcheva, R., Rieger, A. M., Kim, J. S., Dijk, S. I., Mahmood, R., Ogungbola, O., Jovel, J., Moreau, F., Gorman, H., Dickner, R., Jerasi, J., Mander,I. K., Lafleur, D., Cheng, C., Petrova, A., Jeanson, T. L., Mason, A., Sergi, C. M., Levine, A., Chadee, K., Armstrong, D., Rauscher, S., Bernstein, C. N., Carroll, M. W., Huynh, H. Q., Walter, J., Madsen, K. L., Dieleman, L. A., Wine, E. (2022) Unfermented β-fructan fibers fuel inflammation in select inflammatory bowel disease patients. Gastroenterology (in press). doi:10.1053/j.gastro.2022.09.034

Jang, J., Reed, P. M. M., Rauscher, S., Woolley, G. A. (2022) Point (S-to-G) Mutations in the W (S/G) GE Motif in Red/Green Cyanobacteriochrome GAF Domains Enhance Thermal Reversion Rates. Biochemistry 61, 1444-1455. doi:10.1021/acs.biochem.2c00060

Lazar, T., Guharoy, M., Vranken, W., Rauscher, S., Wodak, S. J., Tompa, P. (2020) Distance-based metrics for comparing conformational ensembles of intrinsically disordered proteins. Biophysical Journal 118, 2952-2965. doi:10.1101/2020.04.06.027979

de Araujo, E. D., Erdogan, F., Neubauer, H., Meneksedag-Erol, D., Manaswiyoungkul, P., Eram, M., Qadree, A., Israelian, J., Orlova, A., Seo, H. S., Suske, T., Pham, H. T. T., Boersma, A., Tangermann, S., Kenner, L., Rulicke, T., Dong, A., Ravichandran, M., Brown, P., Audette, G., Rauscher, S., Dhe- Paganon, S., Moriggl, R., Gunning, P. T. (2019) Structural and Functional Consequences of the STAT5B N642H Driver Mutation. Nature Communications 10, 1-15. doi:10.1038/s41467-019-10422-7

Meneksedag-Erol D., Rauscher S. (2019) Atomistic Simulation Tools to Study Protein Self-Aggregation. In Protein Self-Assembly. Methods in Molecular Biology, vol 2039. edited by Jennifer McManus, Springer/Humana, New York, NY, p. 243-262. doi:10.1007/978-1-4939-9678-0_17

Bandyopadhyay A., Van Eps N., Eger B., Rauscher S., Yedidi R., Moroni T., West G., Robinson K., Griffin P., Mitchell J. and Ernst O. (2018) A Novel Polar Core and Weakly Fixed C-Tail in Squid Arrestin Provide New Insight into Interaction with Rhodopsin. Journal of Molecular Biology 430, 4102-4118. doi: 10.1016/j.jmb.2018.08.009

Rauscher, S. and Pomès, R. (2017) The Liquid Structure of Elastin. eLife 6, e26526. doi:10.7554/eLife.26526

Huang, J., Rauscher, S., Nawrocki, G., Ran,T., Feig, M., de Groot, B. L., Grubmüller, H., and MacKerell Jr., A. D. (2017) CHARMM36m: An Improved Force Field for Folded and Intrinsically Disordered Proteins. Nature Methods 14, 71-73 doi:10.1038/ NMETH.4067

Rauscher, S., Gapsys, V., Gajda, M. J., Zweckstetter, M., de Groot, B. L., and Grubmüller, H. (2015) Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment. Journal of Chemical theory and Computation 11, 5513−5524. doi: 10.1021/acs.jctc.5b00736

Naqvi, A., Rauscher, S., Rousseau, D. and Pomès, R. (2014) e Conformational Ensemble of the β‐Casein Phosphopeptide Reveals Two Independent Intrinsically Disordered Segments. Biochemistry 53, 6402−6408. doi: 10.1021/bi500107u

Neale, C., Madill, C. Rauscher, S., and Pomès, R. (2013) Accelerating Convergence in Molecular Dynamics Simulations of Solutes in Lipid Membranes by Conducting a Random Walk along the Bilayer Normal. Journal of Chemical theory and Computation 9, 3686–3703. doi: 10.1021/ct301005b

Rauscher, S. and Pomès, R. Structural Disorder and Protein Elasticity. In Fuzziness: Structural Disorder in Protein Complexes, edited by Peter Tompa and Monika Fuxreiter. Austin/New York: Landes Bioscience/Springer Science & Business Media, 2012:159-183. doi: 10.1007/978-1-4614-0659-4_10.

Seo, M., Rauscher, S., Pomès, R., and Tieleman, D. P. (2012) Improving Internal Peptide Dynamics in the Coarse-Grained MARTINI Model: Toward Large-Scale Simulations of Amyloid- and Elastin-like Peptides. Journal of Chemical theory and Computation 8, 1774–1785. doi: 10.1021/ct200876v

Li, G., Rauscher, S., Baud, S., and Pomès, R. (2012) Binding of Inositol Stereoisomers to Model Amyloidogenic Peptides. Journal of Physical Chemistry B 116, 1111-1119. doi: 10.1021/jp208567n

Nikolic, A., Baud, S., Rauscher, S. and Pomès, R. (2011) Molecular mechanism of β- sheet self-organization at water-hydrophobic interfaces. Proteins 79, 1-22. doi: 10.1002/prot.22854

Rauscher, S. and Pomès, R. (2010) Molecular Simulations of Protein Disorder. Biochemistry and Cell Biology 88, 269-290. doi: 10.1139/o09-169