Publications

Publications & Pre-prints

2024

Biomolecular Condensates can Enhance Pathological RNA Clustering, Mahendran, T. S., Wadsworth, G. M., Singh, A., & Banerjee, P. R., bioRxiv, doi: 10.1101/2024.06.11.598371 Link to the Pre-print

Fluorogenic RNA-based Biomaterials for Imaging and Tracking the Cargo of Extracellular Vesicles, Bonacquisti, E. E., Ferguson, S. W., Wadsworth, G. M., Jasiewicz, N. E., Wang, J., Chaudhari, A. P., Kussatz, C. C., Nogueira, A. T., Keeley, D. P., Itano, M. S., Bolton, M. L., Hahn, K. M., Banerjee, P. R., Nguyen, J., Journal of Controlled Release, Volume 374, 2024, Pages 349-368, doi: 10.1016/j.jconrel.2024.07.043 Link to the Paper

Diffusiophoresis Promotes Phase Separation and Transport of Biomolecular Condensates, Doan, V. S.,  Alshareedah, I., Singh, A., Banerjee, P. R.,  Shin, S., Nature Communications, volume 15, Article number: 7686 (2024), doi: 10.1038/s41467-024-51840-6 Link to the Paper

Sequence-Specific Interactions Determine Viscoelasticity and Ageing Dynamics of Protein Condensates, Alshareedah, I., Borcherds, W. M., Cohen, S. R., Singh, A., Posey, A. E., Farag, M., Bremer, A., Strout, G. W., Tomares, D. T., Pappu, R. V., Mittag, T., & Banerjee, P. R., Nature Physics, Volume 20, Pages 1482–1491 (2024), doi: 10.1038/s41567-024-02048-y Link to the Paper

Direct Computations of Viscoelastic Moduli of Biomolecular Condensates, Cohen, S. R., Banerjee, P. R., & Pappu, R. V., Journal of Chemical Physics, 7 September 2024; 161 (9): 095103, doi: 10.1063/5.0223001 Link to the Paper

Determinants of viscoelasticity and flow activation energy in biomolecular condensates: Alshareedah, I., Singh, A., Yang, S., Ramachandran, V., Quinn, A., Potoyan, D. A., Banerjee, P. R. Science Advances, 16 Feb 2024, Vol 10, Issue 7, doi: 10.1126/sciadv.adi6539 Link to the Paper

Heterotypic interactions can drive selective co-condensation of prion-like low-complexity domains of FET proteins and mammalian SWI/SNF complex Davis, R. B., Supakar, A., Ranganath, A. K., Moosa, M. M., Banerjee, P. R. Nature Communications volume 15, Article number: 1168 (2024) Link to the Paper

2023

RNAs undergo phase transitions with lower critical solution temperatures Wadsworth, G. M., Zahurancik, W. J., Zeng, X., Pullara, P., Lai, L. B., Sidharthan, V., Pappu, R. V., Gopalan, V., Banerjee, P. R. Nature Chemistry volume 15, pages 1693–1704 (2023) Link to the paper

Dissecting the biophysics and biology of intrinsically disordered proteins. Banerjee, P. R., Holehouse, A. S., Kriwacki, R., Robustelli, P., Jiang, H., Sobolevsky, A. I., Hurley, J. M., Mendell, J. T. Trends in Biochemical Sciences. Link to the paper

Heterotypic Interactions in the Dilute Phase can Drive Co-Condensation of Prion-Like Low-Complexity Domains of FET Proteins and Mammalian SWI/SNF Complex. Davis, R. B., Ranganath, A.K., Moosa, M. M., Banerjee, P. R. Link to pre-print

Determinants of Viscoelasticity and Flow Activation Energy in Biomolecular Condensates. Alshareedah, I., Singh, A., Quinn, A., & Banerjee, P. R. bioRxiv. Link to pre-print

2022

RNAs undergo phase transitions with lower critical solution temperatures. Wadsworth, G. M., Zahurancik, W. J., Zeng, X., Pullara, P., Lai, L. B., Sidharthan, V., Pappu, R.V., Gopalan, V. & Banerjee, P. R. bioRxiv. Link to pre-print

Measurement of Protein and Nucleic Acid Diffusion Coefficients Within Biomolecular Condensates Using In-Droplet Fluorescence Correlation Spectroscopy. Alshareedah, I., & Banerjee, P. R. Phase-Separated Biomolecular Condensates (pp. 199-213). Humana, New York, NY. Link to the Chapter

Ectopic biomolecular phase transitions: fusion proteins in cancer pathologies. Davis, R. B., Moosa, M. M., & Banerjee, P. R. Trends in Cell Biology. Link to the paper

RNA chain length and stoichiometry govern surface tension and stability of protein-RNA condensates. Laghmach, R., Alshareedah, I., Pham, M., Raju, M., Banerjee, P. R., & Potoyan, D. A. iscience, 25(4), 104105. Link to the paper

Temperature-dependent Reentrant Phase Transition of RNA-polycation Mixtures. Pullara, P., Alshareedah, I., Banerjee, P. R. Soft Matter 18.7 (2022): 1342-1349. Link to the paper
From the Themed Collection: 2021 Soft Matter Emerging Investigators.

2021

Programmable Viscoelasticity in Protein-RNA Condensates with Disordered Sticker-Spacer Polypeptides. Alshareedah, I., Moosa, M. M., Pham, M., Potoyan, D. A., Banerjee, P. R. Nature Communications. 12, Article number: 6620 (2021) Link to the paper

Read the UB press release on our article Here

FUS Oncofusion Protein Condensates Recruit mSWI/SNF Chromatin Remodelers via Heterotypic Interactions Between Prion-like Domains. Davis, R. B., Kaur, T., Moosa, M. M., Banerjee, P. R. Protein Science: Special Issue on Biophysics of Biomolecular Condensates. 30(7):1454-1466. Link to the paper

Access to freely available preprint version at bioRxiv. Link to pre-print.

Programmable Viscoelasticity in Protein-RNA Condensates with Disordered Sticker-Spacer Polypeptides. Alshareedah, I., Moosa, M. M., Banerjee, P. R. bioRxiv. Link to pre-print.

Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Morphologies. Kaur, T., Raju, M., Alshareedah, I., Davis, R. B., Potoyan, D. A., Banerjee, P. R. Nature Communications. 12, Article number: 872 (2021). Link to the paper.

Quantifying Viscosity and Surface Tension of Multi-Component Protein-Nucleic Acid Condensates. Alshareedah, I., Thurston, G. M. & Banerjee, P. R. Biophysical Journal. 120(7):1161-1169. Link to the paper.

Read the New and Notable highlight of our Biophysical Journal paper by Yu and Lemke.

2020

Sequence-encoded and Composition-dependent Protein-RNA Interactions Control Multiphasic Condensate Topologies. Kaur, T., Raju, M., Alshareedah, I., Davis, R. B., Potoyan, D. A., Banerjee, P. R. bioRxiv. 2020.08.30.273748. Link to the preprint.

Methods for Characterizing the Material Properties of Biomolecular Condensates. Alshareedah, I., Kaur, T., Banerjee, P. R. 2020. Methods in Enzymology. Volume 646, 2021, Pages 143-183. Free access to this chapter until March 05, 2021. Link.

Subversion of Host Stress Granules by Coronaviruses: Potential Roles of π-rich Disordered Domains of Viral Nucleocapsids. Moosa, M. M., Banerjee, P. R. 2020. J Med Virol. 10.1002/jmv.26195. DOI: 10.1002/jmv.26195. Link to the paper.

Phase Transition of RNA-protein Complexes into Ordered Hollow Condensates.Alshareedah, I., Moosa, M. M., Raju, M., Potoyan, D. A., Banerjee, P. R. 2020. Proceedings of the National Academy of Sciences. DOI: 10.1073/pnas.1922365117. Link to the paper.

Protein-RNA vesicles

Protein-RNA vesicles

News Highlight in UB News and Views

2019

Interplay Between Short-range Attraction and Long-range Repulsion Controls Reentrant Liquid Condensation of Ribonucleoprotein-RNA Complexes.Alshareedah, I., Kaur, T., Ngo, J., Seppala, H., Djomnang Kounatse, L.-A., Wang, W., Moosa, M. M., Banerjee, P. R. 2019. J. Am. Chem. Soc. 141, 37, 14593-14602. Link: https://doi.org/10.1021/jacs.9b03689

Molecular Crowding Tunes Material States of Ribonucleoprotein Condensates.Kaur, T., Alshareedah, I., Wang, W., Ngo, J., Moosa, M. M., Banerjee, P. R. 2019. Biomolecules, 9(2), 71; Link: https://doi.org/10.3390/biom9020071.

Phase Separation of Ligand-Activated Enhancers Licenses Cooperative Chromosomal Enhancer Assembly. Nair, S. J., Yang, L., Meluzzi, D., Oh, S., Yang, F., Friedman, M., Wang, S., Suter, T., Alshareedah, I., Gamliel, A., Ma, Q., Zhang, J., Hu, Y., Tan, Y., Ohgi, K., Jayani, R., Banerjee, P. R., Aggarwal, A. K., Rosenfeld, M. G. 2019. Nature Structural & Molecular Biology. 26, 193–203; Link: https://doi.org/10.1038/s41594-019-0190-5

Divalent cations can control a   switch-like   behavior   in   heterotypic    and    homotypic    RNA    coacervates. Onuchic, P. L., Milin, A. N., Alshareedah, A., Deniz, A. A., Banerjee,P.R. 2018. Scientific Reports, Vol 9, Article number: 12161. Link: https://doi.org/10.1038/s41598-019-48457-x.

2018

Self-interaction of NPM1 modulates multiple mechanisms of liquid- liquid phase separation. Mitrea, D. M., Cika, J. A., Stanley, C. B., Nourse, A., Onuchic, P. L., Banerjee,P.R., Phillips, A. H., Park, C. G., Deniz, A. A., Kriwacki, R. W. 2018. , Nature Communications. 2018 Feb 26;9(1):842. Link to the paper.

2012-2017: Postdoctoral Work

Reentrant phase transition drives dynamic substructure formation in ribonucleoprotein droplets. Banerjee, P. R.*, Milin, A. N., Moosa M. M., Onuchic, P. L., Deniz, A. A.* 2017. Angew Chem Int Ed Engl. 2017 Sep 11;56(38):11354-11359. PMCID: PMC5647147 (*Corresponding Authors). Link to the paper.

  • Highlighted as a Very Important Paper by  Angew Chem Int Ed Engl

  • Featured in TSRI News & Views, June 2017

  • Featured in The Scientist Magazine, June 2017

NPM1 integrates into the nucleolar fraction through multi-modal interactions with R- rich linear motifs and ribosomal RNA. Mitrea, D. M., Cika, J. A., Guy, C. S., Ban, D., Banerjee, P. R., Stanley, C. B., Nourse, A., Deniz, A. A., Kriwacki, R. W. 2016. eLife;10.7554/eLife.13571. Link to the paper

Two-dimensional crowding uncovers a hidden conformation of α-synuclein.Banerjee, P. R.*, Moosa M. M., Deniz, A. A.* 2016.  Angew Chem Int Ed Engl. 55(41):12789-92. (*Corresponding Authors). Link to the paper.

Asymmetric Modulation of Protein Order-Disorder Transitions by Phosphorylation and Partner Binding. Banerjee, P. R., Mitrea, D. M., Kriwacki, R. W.,Deniz, A. A., 2015. Angew Chem Int Ed Engl. 55(5):1675-9. Link to the paper.

Shedding light on protein folding landscapes by single-molecule fluorescence. Banerjee, P. R., Deniz, A. A. 2014. Chem. Soc. Rev. 43, 1172-1188. Link to the paper.

Ultrafast cooling reveals microsecond-scale biomolecular dynamics. Polinkovsky, M. E.*, Gambin, Y.*, Banerjee, P. R.*, Erickstad, M. J., Groisman, A., Deniz, A. A. 2014. Nat Commun. 2014 Dec 17; 5:5737 (*Equal contributions first authors). Link to the paper.

Doctoral Work

Cataract-associated mutant E107A of human gamma D-crystallin shows increased attraction to alpha-crystallin and enhanced light scattering. Banerjee, P. R., Pande, A., Patrosz, J., Thruston, G. M., Pande, J. 2011. Proc. Natl. Acad. Sci. (U.S.A) 108, 574-579. Link to the paper.

  • Commentary published in PNAS (Link)

Increase in surface hydrophobicity of the cataract-associated P23T mutant of human γD-crystallin is responsible for its dramatically lower, retrograde solubility A Pande, K S Ghosh, P R Banerjee, J Pande. Biochemistry 49 (29), 6122-6129352010. Link to the paper.

NMR study of the cataract-linked P23T mutant of human γD-crystallin shows minor changes in hydrophobic patches that reflect its retrograde solubility. A Pande, J Zhang, P R Banerjee, S S Puttamadappa, A Shekhtman, J Pande. Biochemical and biophysical research communications 382 (1), 196-199242009. Link to the paper.

Molecular mechanism of the chaperone function of mini-α-crystallin, a 19-residue peptide of human α-crystallin. P R Banerjee, A Pande, A Shekhtman, J Pande. Biochemistry 54 (2), 505-515152014. Link to the paper.

Increased hydrophobicity and decreased backbone flexibility explain the lower solubility of a cataract-linked mutant of γD-crystallin. P R Banerjee, S S Puttamadappa, A Pande, A Shekhtman, J Pande. Journal of molecular biology 412 (4), 647-659152011. Link to the paper.