Last updated on October 17, 2024
G. Chauhan, M. Farag, S.R. Cohen, R.V. Pappu. (2024). Reply to Conformations of protein chains at the interface biomolecular condensates. Nature Communications, Matters Arising, In press.
A. Holla, E.W. Martin, T. Dannenhofer-Lafage, K.M. Ruff, S.L. König, M.F. Nüesch, A. Chowdhury, J.M. Louis, A. Soranno, D. Nettels, R.V. Pappu*, R.B. Best*, T. Mittag*, B. Schuler*. (*Co-corresponding authors). (2024). Identifying sequence effects on chain dimensions of disordered proteins by integrating simulations and experiments. Journal of the American Chemical Society Au, In press.
A. E. Posey§, A. Bremer§, N. A. Erkamp§, A. Pant, Y. Dai, T. Mittag*, R.V. Pappu*. (§Equal contributions; *Co-corresponding authors). (2024). Biomolecular condensates are characterized by interphase electric potentials. Journal of the American Chemical Society. 146: 28268-28281. Access Article
S. R. Cohen, P. R. Banerjee, R.V. Pappu. (2024). Direct computations of viscoelastic moduli of biomolecular condensates. Journal of Chemical Physics. 161: 095103. Access Article
D. Qian, H. Ausserwöger, T. Sneideris, M. Farag, R.V. Pappu†, T.P.J. Knowles†. (2024). Dominance analysis to assess solute contributions in multicomponent phase equilibria. (†Corresponding authors). Proceedings of the National Academy of Sciences.121: e2407453121. Access Article
I. Alshareedah§, W.M. Borcherds§, S.R. Cohen§, A. Singh, A.E. Posey, M. Farag, A. Bremer, G. W. Strout, D.T. Tomares, R.V. Pappu†, T. Mittag†, P.R. Banerjee†. (§Co-first authors; †Co-corresponding authors). (2024). Sequence-specific interactions determine viscoelastic moduli and aging dynamics of protein condensates. Nature Physics. 20:1482-1491. Access Article
S. J. Wang*, R. Gupta, A. Benegal, R. Avula, Y-Y. Huang, M.D. Vahey, R. K. Chakrabarty, R.V. Pappu, S. Singamaneni, J. V. Putthuserry*, M. R. King*. (*Co-corresponding authors). (2024). A high-avidity, thermostable, and low-cost synthetic capture for ultrasensitive detection and quantification of viral antigens and aerosols. ACS Sensors, 9: 3096-3104. Access Article
M. Kar, L. T. Vogel†, G. Chauhan†, S. Felekyan, H. Ausserwöger, T.J. Welsh, F. Dar, A.R. Kamath, T.P.J. Knowles, A.A. Hyman§, C.A.M. Seidel§, R.V. Pappu§. (2024). Solutes unmask differences in clustering versus phase separation of FET proteins. (†Equal contributions; §Co-Corresponding authors). Nature Communications, 15: 4408. Access Article
F. Dar†, S. R. Cohen†, D. M. Mitrea, A. H. Phillips, G. Nagy, W. C. Leite, C. B. Stanley, J-M. Choi†,§, R. W. Kriwacki§, R. V. Pappu§. (†Equal contributors; §Co-corresponding authors). (2024). Biomolecular condensates form spatially inhomogeneous network fluids. Nature Communications, 15:3413. Access Article
E.A. Lemke, M.M. Babu, R.W. Kriwacki, T. Mittag, R.V. Pappu, P.E. Wright, J.D. Forman-Kay. (2024). Intrinsic Disorder: A term to define the specific characteristic of protein conformational heterogeneity. Molecular Cell, 84: 1188-1190. Access Article
M.R. King, K.M. Ruff, A.Z. Lin, A. Pant, J.M. Lalmansingh, T. Wu, M. Farag, W. Ouyang, M.J. Fossat, E. Lundberg, M.D. Lew, M.D. Vahey, R.V. Pappu. (2024). Macromolecular condensation organizes nucleolar sub-phases and sets up a pH gradient. Cell, 187: 1889-1906.E24. Access Article
M. R. King, K. M. Ruff, R.V. Pappu. (2024). Emergent microenvironments of nucleoli. Nucleus, 15: 2319957. Access Article
G. A. Pérez, R.V. Pappu, D. Milovanovic. (2024). Tear down this wall: Phosphorylation regulates the internal interfaces of postsynaptic condensates. Trends In Cell Biology, 34: 174-276. Spotlight article. Access Article
G. Chauhan, A. Bremer, F. Dar, T. Mittag, R.V. Pappu. (2024). Crowder titrations enable the quantification of driving forces for macromolecular phase separation. Biophysical Journal, 123: 1376-1392. Access Article
A.Z. Lin†, K.M. Ruff†, F. Dar†, A. Jalihal, M.R. King, J.M. Lalmansingh, A.E. Posey, N.A. Erkamp, I. Seim, A. S. Gladfelter§, R. V. Pappu§ (†Co-first authors; §Co-corresponding authors). (2023). Dynamical control enables the formation of demixed biomolecular condensates. Nature Communications, 14: 7678. Access Article
G. M. Wadsworth§, W.J. Zahurancik§, X. Zeng§, P. Pullara, L. B. Lai, V. Sidharthan, R.V. Pappu*, V. Gopalan*, P.R. Banerjee*. (§Co-first authors; *Co-corresponding authors). (2023). RNAs undergo phase transitions with lower critical solution temperatures. Nature Chemistry, 15: 1693 - 1704. Access Article
A. Patil*, A. R. Strom*, J.A. Paulo, C.K. Collings, K.M. Ruff, M-K Shinn, A.Sankar, K.S. Cervantes, T. Wauer, J.D. St. Laurent, G. Xu, S.P. Gygi, R.V. Pappu, C. P. Brangwynne†, and C. Kadoch†. (*Co-first authors; †Co-corresponding authors). (2023). A single disordered region controls cBAF chromatin remodeling through condensation and partner recruitment. Cell, 186: 4936-4955. Access article
M. Farag, W.M. Borcherds§, A. Bremer§, T. Mittag†, R.V. Pappu†. (2023). Phase separation of protein mixtures is driven by the interplay of homotypic and heterotypic interactions. (§Equal contributions; †Co-corresponding authors). Nature Communications, 14: 5527. Access Article
J.M. Lalmansingh, A.T. Keeley, K.M. Ruff, R.V. Pappu, A.S. Holehouse. (2023). SOURSOP: A Python package for the analysis of simulations of intrinsically disordered proteins. Journal of Chemical Theory and Computation, 19: 5609-5620. Featured on the cover. Access Article
M-K. Shinn, R.V. Pappu. Soaping up transcriptional condensates. (2023). Developmental Cell, 58: 915-916. Access Article
M. Farag, A.S. Holehouse, X. Zeng, R.V. Pappu. (2023). FIREBALL: A tool to fit protein phase diagrams based on mean-field theories for polymer solutions. Biophysical Journal, 122: 1-8. Access Article
R.V. Pappu, S. R. Cohen, F. Dar, M. Farag, M. Kar. (2023). Phase transitions of associative biomacromolecules. Chemical Reviews, 123: 8945-8987. Access Article
Y. Dai, M. Farag, D. Lee, X. Zeng, K. Kim, H-i. Son, X. Guo, M. Ney, D.M. Shapiro, R.V. Pappu, A. Chilkoti, L. You. (2023). Programmable synthetic biomolecular condensates for cellular control. Nature Chemical Biology, 19: 518 - 528. Access Article
X. Zeng, R.V. Pappu. (2023). Developments in describing equilibrium phase transitions of multivalent associative macromolecules. Current Opinion in Structural Biology, 75: 102540. Access Article
M. J. Fossat§, A.E. Posey§, R.V. Pappu. (§Co-first authors). (2023). Uncovering the contributions of charge regulation to the stability of single alpha helices. ChemPhysChem, 24: e202200746. Access Article
M. Farag, S.R. Cohen, A. Bremer, W.M. Borcherds, T. Mittag, R.V. Pappu. (2022). Condensates formed by prion-like low-complexity domains have small-world network structures and interfaces defined by expanded conformations. Nature Communications, 13: 7722. Access Article
A. Bremer§, A.E. Posey§, M. Borgia, W.M. Borcherds, M. Farag, R.V. Pappu†, T. Mittag†. (§Co-first authors; †Co-corresponding authors). (2022). Quantifying coexistence concentrations in multi-component phase-separating systems using analytical HPLC. Biomolecules, 12: 1480. Access Article
M-K. Shinn, M.C. Cohan, J.L. Bullock, K.M. Ruff†, P. A. Levin†, R.V. Pappu†. (2022). Connecting sequence features within the disordered C-terminal linker of B. subtilis FtsZ to molecular functions and bacterial cell division. (†Co-corresponding authors). Proceedings of the National Academy of Sciences USA, 119: e2211178119. Access Article
M. Feric, A. Sarfallah, F. Dar, D. Temiakov, R.V. Pappu, T. Misteli. (2022). Mesoscale structure-function relationships in mitochondrial transcriptional condensates. Proceedings of the National Academy of Sciences USA, 119: e2207303119. Access Article
N.S. Gonzalez-Foutel, J. Glavina, W.M. Borcherds, M. Safranchik, S. Barrera-Vilarmau, A. Sagar, A. Estaña, A. Barozet, N. Garrone, G. Fernandez-Ballester, C. Blanes-Mira, I.E. Sánchez, G. de Prat-Gay, J. Cortés, P. Bernadó, R.V. Pappu*, A.S. Holehouse*, G.W. Daughdrill* L.B. Chemes*. (*Co-corresponding authors). (2022). Conformational buffering underlies functional selection in intrinsically disordered protein regions. Nature Structural and Molecular Biology, 29: 781-790. Access Article
K.M. Ruff§, Y-H. Choi§, D. Cox, A. Ormsby, Y. Myung, D. B. Ascher, S.E. Radford, R.V. Pappu†, D.M. Hatters†. (2022). Sequence grammar for phase separation of unfolded states of globular proteins. (§Co-first authors; †Co-corresponding authors). Molecular Cell, 82: 3193-3208.e8. Access Article
M. Kar, F. Dar, T. J. Welsh, L. Vogel, R. Kühnemuth, A. Majumdar, G. Krainer, T. M. Franzmann, S. Alberti, C. A. M. Seidel, T. P.J. Knowles, A. A. Hyman†, R. V. Pappu†. (2022). Phase separating RNA binding proteins form heterogeneous distributions of clusters in subsaturated solutions. (†Co-corresponding authors). Proceedings of the National Academy of Sciences USA, 119: e2202222119. Access Article
T. Mittag, R.V. Pappu. (2022). A conceptual framework for understanding phase separation and addressing open questions and challenges. Peer reviewed, commissioned perspective. Molecular Cell, 82: 2201-2214. Access Article
X. Zeng, K.M. Ruff, R.V. Pappu. (2022). Competing interactions give rise to two-state behavior and switch-like transitions in charge-rich intrinsically disordered proteins. Proceedings of the National Academy of Sciences USA, 119: e2200559119. Access Article
I. Seim, A.E. Posey, W.T. Snead, B.M. Stormo, D. Klotsa, R.V. Pappu†, A.S. Gladfelter†. (†Co-corresponding authors). (2022). Dilute phase oligomerization opposes phase separation and modulates material properties of a ribonucleoprotein condensate. Proceedings of the National Academy of Sciences USA, 119: e2120799119. Access Article
M.V. Staller, E. Ramirez, A.S. Holehouse, R.V. Pappu, B.A. Cohen. (2022). Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains. Cell Systems, 13: 334-335.e5. Access Article
M.C. Cohan†, M-K. Shinn†, J.M. Lalmansingh, R.V. Pappu. (2022). Uncovering non-random binary patterns within sequences of intrinsically disordered proteins. (†Co-first authors). Journal of Molecular Biology, 434: 167373. Access Article
A. Bremer§, M. Farag§, W.M. Borcherds§, I. Peran, E.W. Martin, R.V. Pappu†, T. Mittag†. (2022). Deciphering how naturally occurring sequence features impact the phase behaviours of disordered prion-like domains. (§Co-first authors; †Co-corresponding authors). Nature Chemistry, 14: 196-207. Access Article
C. D. Keating, R. V. Pappu. (2021). Liquid-liquid phase separation: A widespread and versatile way to organize aqueous solutions. Journal of Physical Chemistry B, 125: 12399-12340. Access Article
M.J. Fossat, A.E. Posey, R.V. Pappu. (2021). Quantifying charge state heterogeneity for proteins with multiple ionizable residues. Biophysical Journal, 120: 1-16. Access Article
L-P Bergeron-Sandoval, S. Kumar, H.K. Heris, C.L.A. Chang, C.E. Cornell, S. L. Keller, P. François, A.G. Hendricks, A.J. Ehrlicher, R.V. Pappu†, S. W. Michnick†. (2021). Endocytic proteins with prion-like domains form viscoelastic condensates that enable membrane remodeling. (†Co-corresponding authors). Proceedings of the National Academy of Sciences USA, 118: e2113789118. Access Article
M. Kar, A.E. Posey, F. Dar, A.A. Hyman*, R.V. Pappu*. (2021). Glycine-rich peptides from FUS have an intrinsic ability to self-assemble into fibers and networked fibrils. (*Co-corresponding authors). Biochemistry, 60: 3213-3222. Access Article
K.M. Ruff, R.V. Pappu. (2021). AlphaFold and implications for intrinsically disordered proteins. Journal of Molecular Biology, 433: 167208. Access Article
K.M. Ruff, F. Dar, R.V. Pappu. (2021). Polyphasic linkage and the impact of ligand binding on the regulation of biomolecular condensates. Biophysics Reviews, 2: 021302. Access Article
M.J. Fossat†, X. Zeng†, R.V. Pappu. (2021) Uncovering differences in hydration free energies and structures for model compound mimics of charged sidechains of amino acids. (†Co-first authors). Journal of Physical Chemistry B, 125: 4148-4161. Access Article
A.E. Posey§,†, K.M. Ruff§, J.M. Lalmansingh§, T. Kandola, R. Halfmann, R.V. Pappu†. (2021). Mechanistic inferences from analysis of measurements of protein phase transitions in live cells. (§Co-first authors; †Co-corresponding authors). Journal of Molecular Biology, 443: 166848. Access Article
X. Zeng, C. Liu, M.J. Fossat, P. Ren, A. Chilkoti, R.V. Pappu. (2021). Design of intrinsically disordered proteins that undergo phase transitions with lower critical solution temperatures. APL Materials, 9, 021119. Access Article
K.M. Ruff§,†, F. Dar§, R.V. Pappu† (2021). Ligand effects on phase separation of multivalent macromolecules. (§Co-first authors; †Co-corresponding authors). Proceedings of the National Academy of Sciences USA, 118: e2017184118. Access Article
M. Lorenzini, S. Burel, A. Lesage, E. Wagner, C. Charrière, P-M. Chevillard, M. Bérangère, D. Maloney, K.M. Ruff, R. V. Pappu, S. Wagner, J.M. Nerbonne, J. R. Silva, R.R. Townsend, L.S. Maier, C. Marrioneau. (2021). Proteomic and functional mapping of cardiac Nav1.5 channel phosphorylation reveals multisite regulation of surface expression and gating. Journal of General Physiology, 153: e202012646. Access Article
T. Lazar, E. Martínez-Pérez, F. Quaglia, A. Hatos, L. B. Chemes, J.A. Iserte, N. A. Méndez, N. A. Garrone, T. E. Saldaño, J. Marchetti, A. J. Velez Rueda, P. Bernado, M. Blackledge, T. N. Cordeiro, E. Fagerberg, Julie D. Forman-Kay, M. S. Fornasari, T. J. Gibson, G-N. W. Gomes, C. C. Gradinaru, T. Head-Gordon, M. R. Jensen, E. A. Lemke, S. Longhi, C. Marino-Buslje, G. Minervini, T. Mittag, A. M. Monzon, R.V. Pappu, G. Parisi, S. Ricard-Blum, K. M. Ruff, E. Salladini, M. Skepö, D. Svergun, S. D. Vallet, M. Varadi, P. S. Tompa*, S. C.E. Tosatto*, D. Piovesan. PED in 2021: A major update of the protein ensemble database for intrinsically disordered proteins. Nucleic Acids Research, 49: D404-D411. Access article
R.V. Pappu. (2020). Phase separation – a physical mechanism for organizing information and biochemical reactions. Developmental Cell, 55: 1-3. Access Article
C. Mathieu, R.V. Pappu, J.P. Taylor. (2020). Beyond aggregation: pathological phase transitions in neurodegenerative disease. Science, 370: 56-60. Access Article
J-M. Choi, A.A. Hyman, R.V. Pappu. (2020). Generalized models for bond percolation transitions of associative polymers. Physical Review E, 102: 042403. Access Article
F. Dar, R.V. Pappu. (2020). Restricting the size of condensates. eLife, 9:e59663. Invited and reviewed insight article. Access Article
X. Zeng, A.S. Holehouse, A. Chilkoti, T. Mittag, R.V. Pappu. (2020). Connecting coil-globule transitions to full phase diagrams for intrinsically disordered proteins. Biophysical Journal. 119: 1-17. Access Article
M.C. Cohan, R.V. Pappu. (2020). Making the case for disordered proteins and biomolecular condensates in bacteria. Trends in Biochemical Sciences, 45: 668-680. Access Article
J. Guillén-Boixet, A. Kopach, A. S. Holehouse, S. Wittmann, M. Jahnel, R. Schlüßler, I. R. E. A. Trussina, J. Wang, D. Mateju, I. Poser, S. Maharana, M. Ruer-Gruß, D. Richter, Y-T. Chang, A. Honigmann, A. A. Hyman, R.V. Pappu, S. Alberti, T. M. Franzmann. (2020). RNA induces conformational rearrangements and clustering of G3BP that drive condensation and stress granule formation. Cell, 181: 346-361. Access Article
M.C. Cohan, A.M.P. Eddelbuettel, P.A. Levin, R.V. Pappu. Dissecting the functional contributions of the intrinsically disordered C-terminal tail of B. subtilis FtsZ. (2020). Journal of Molecular Biology, 432: 3205-3221. Access Article
J. A. Greig, T. A. Nguyen, M. Lee, A. S. Holehouse, A. E. Posey, R. V. Pappu, G. J. Jedd. (2020). Arginine-enriched mixed-charge domains provide cohesion for nuclear speckle condensates. Molecular Cell, 77: 1-14. Access Article
E.W. Martin†, A. S. Holehouse†, I. Peran†, M. Farag, J.J. Incicco, A. Bremer, C.R. Grace, A. Soranno, R.V. Pappu§, T. Mittag§ (†Co-first authors and §co-corresponding authors). (2020). Valence and patterning of aromatic residues determine the phase behavior of prion-like domains. Science, 367: 694-699. Access Article
J-M. Choi, A.S. Holehouse, R.V. Pappu. (2020). Physical principles underlying the complex biology of intracellular phase transitions. Annual Review of Biophysics, 49: 107-133. Access Article
J-M. Choi§, F. Dar§, R.V. Pappu. (2019). LASSI: A lattice model for simulating phase transitions of multivalent proteins. (§Co-first authors). PLoS Computational Biology, 15: e1007028. Access Article
M. J. Fossat, R.V. Pappu. (2019). q-Canonical Monte Carlo sampling for modeling the linkage between charge regulation and conformational equilibria of peptides. Journal of Physical Chemistry B, 123: 6952 – 6967. Access Article
W. Bai, C. Sargent, J-M. Choi, R.V. Pappu, F. Zhang. (2019). Covalently assembled single chain protein nanostructures with ultrahigh stability. Nature Communications. 10: 3317. Access Article
J. Cable, C. Brangwynne, G. Seydoux, D. Cowburn, R.V. Pappu, C.A. Castãneda, L.E. Berchowitz, Z. Chen, M. Jonikas, A. Dernburg, T. Mittag, N.L. Fawzi. (2019). Phase separation in Biology and Disease – a symposium report. Annals of the New York Academy of Sciences, 1452: 3-11. Access Article
M.C. Cohan, K.M. Ruff, R.V. Pappu. (2019). Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins. Protein Engineering, Design and Selection. 32(4): 191-202. Access Article
S.K. Powers, A.S. Holehouse, D.A. Korasick, K.H. Schreiber, E. Tycksen, J.M. Jez, R.V. Pappu, L.C. Strader. (2019). Nucleo-cytoplasmic partitioning of ARF proteins control auxin responses in Arabidopsis thaliana. Molecular Cell, 76: 177-190.e5. Access Article
I. Peran†, A.S. Holehouse†, I.S. Caricco, R.V. Pappu§, O. Bilsel§, D.P. Raleigh§. (2019). Unfolded states under folding conditions accommodate sequence-specific conformational preferences alongside ensemble-averaged features of random coils. (2019). Proceedings of the National Academy of Sciences USA. 116(25): 12301 – 12310. (†Co-first authors; §Co-corresponding authors). Access Article
S. Boeynaems†, A.S. Holehouse, V. Weinhardt, D. Kovacs, J. Van Lindt, C. Larabell, L. Van Den Bosch, R. Das, P. Tompa, R.V. Pappu†, A. Gitler†. (2019) Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties. Proceedings of the National Academy of Sciences USA, 116: 7889-7898. (†Co-corresponding authors). Access Article
R. Beveridge†, L G. Migas†, R. K. Das, R. V. Pappu, R. W. Kriwacki, P. E. Barran. (2019) Ion mobility mass spectrometry helps uncover the impact of charge patterning on the conformational distributions of intrinsically disordered proteins. Journal of the American Chemical Society, 141: 4908-4918. (†Co-first authors). Access Article
J-M. Choi, R.V. Pappu (2019) Improvements to the ABSINTH forcefield for proteins based on experimentally derived amino-acid specific backbone conformational statistics.
Journal of Chemical Theory and Computation, 15: 1367-1382, Access Article
J-M. Choi, R.V. Pappu (2019) Experimentally derived and computationally optimized conformational statistics for blocked amino acids.
Journal of Chemical Theory and Computation, 15: 1355-1366, Access Article
K.M. Ruff✝, R.V. Pappu✝, A.S. Holehouse✝ (✝Co-corresponding authors) (2019) Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: Insights from multiscale simulations.
Current Opinions in Structural Biology, 56:1-10, Access Article
A.E. Posey*, A.S. Holehouse*, R.V. Pappu (*co-first authors) (2018) Phase separation of intrinsically disordered proteins.
Methods in Enzymology, 611: 1-30 Access Article
E. Ortega, S. Rengachari, Z. Ibrahim, N. Hoghoughi, J. Gaucher, A.S. Holehouse, S. Khochbin, D. Panne (2018) Transcription factor dimerization activates the p300 acetyltransferase.
Nature, 562: 538-544 Access Article
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S. Roberts, T. S. Harmon, J. L. Schaal, K. Li, A. Hunt, V. Miao, Y. Wen, T. G. Oas, J. Collier, R. V. Pappu, A. Chilkoti (2018) Injectable tissue integrating networks from recombinant polypeptides with tunable order.
Nature Materials, 17: 1154-1163 Access Article
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T.Y. Yoo, J-M. Choi, W. Conway C-H. Yu, R.V. Pappu, D.J. Needleman (2018). Measuring NDC80 binding reveals molecular basis of tension-dependent kinetochore-microtubule attachments.
eLife, 7: e36392 Access Article
G. Fuertes*, N. Banterle*, K.M. Ruff*, A. Chowdhury*, R.V. Pappu✝, D. I. Svergun✝, E.A. Lemke✝ (*Co-first authors, ✝Co-corresponding authors) (2018). Comment on “Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water.”
Science, 361: eaau8230, Access Article
H. Mirbaha, O.A. Morozova, K.M. Ruff, A. Sharma, X. Liu, M. Goodarzi, R.V. Pappu, D.W. Colby, H. Mirzaei, L.A. Joachimiak, M.I. Diamond (2018) Inert and seed-competent tau monomers elucidate the structural origins of aggregation.
eLife, 7: e36584, Access Article
A.E. Posey, R.V. Pappu (2018) A first glimpse of nucleation of phase transitions in living cells.
Molecular Cell (invited preview) 71: 1-3 Access Article
J. Wang, J.M. Choi, A.S. Holehouse, X. Zhang, M. Jahnel, R. Lemaitre, S. Maharana, A. Pozniakovsky, D. Drechsel, I. Poser, R.V. Pappu, S. Alberti, A.A. Hyman (2018) A molecular grammar underlying the driving forces for phase separation of prion-like RNA binding proteins.
Cell, 174: 688-699, Access Article
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K.M. Ruff, S. Roberts, A. Chilkoti✝, R.V. Pappu✝ (✝Co-corresponding authors) (2018) Advances in understanding stimulus responsive phase behavior of intrinsically disordered protein polymers.
Journal of Molecular Biology, 430: 4619-4635 (invited review for special issue on phase separation), Access Article
A. Mittal, A.S. Holehouse, M.C. Cohan, R.V. Pappu (2018) Sequence-to-conformation relationships of disordered regions tethered to folded domains of proteins
Journal of Molecular Biology, 430:2403-2421 Access Article
E. A. Newcombe*, K. M. Ruff*, Y. M. Ramdzan, A. Sethi, A. R. Ormsby, O. Kleifeld, A. W. Purcell, P. R. Gooley, R. V. Pappu✝, D. M. Hatters✝ (✝Co-corresponding authors) (2018) Tadpole-like conformations of huntingtin exon 1 are characterized by conformational heterogeneity that persists for wild type and pathogenic polyglutamine lengths
Journal of Molecular Biology, 430:10 1442 - 1458, Access Article
T.S. Harmon, A.S. Holehouse, R.V. Pappu (2018) Differential solvation of intrinsically disordered linkers drives the formation of spatially organized droplets in ternary systems of linear multivalent proteins
New Journal of Physics, 20: 045002, Access Article
M.V. Staller, A.S. Holehouse, D. Swain-Lenz, R. Das, R.V. Pappu, B.A. Cohen (2018) A high-throughput mutational scan of an intrinsically disordered acidic transcriptional activation domain
Cell Systems, 6: 444-455.e6, Access Article
K. Garai, A.E. Posey, X. Li, E.M. Powers, J. Buxbaum, R.V. Pappu (2018) Inhibition of amyloid beta fibril formation by monomeric human Transthyretin
Protein Science, 27: 1252-1261, Access Article
A.E. Posey, K.M. Ruff, T.S. Harmon, S.L. Crick, A. Li, M.I. Diamond, R.V. Pappu (2018) Profilin reduces aggregation and phase separation of huntingtin N-terminal fragments by preferentially binding to soluble monomers and oligomers
Journal of Biological Chemistry, 293: 3734-3746, Access Article
A.S. Holehouse, R.V. Pappu (2018) Collapse transitions of proteins and the interplay amongst polypeptide backbone, sidechain, and solvent interactions.
Annual Review of Biophysics, 47: 19-39, Access Article
A.S. Holehouse✝, R.V. Pappu✝ (✝Co-corresponding authors) (2018) Functional implications of intracellular phase transitions. (invited perspective)
Biochemistry, 57:(17), 2415-2423. Acess Article
T. M. Franzmann, M. Jahnel, A. Pozniakovsky, J. Mahamid, A.S. Holehouse, E. Nüske, D. Richter, W. Baumeister, S.W. Grill, R.V. Pappu, A.A. Hyman, S. Alberti (2018) Phase separation by a yeast prion protein promotes cellular fitness.
Science, 359: eaao5654. Acess Article
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J. Fei*✝, M. Jadaliha*, T.S. Harmon$, I.T.S. Li$, B. Hua, Q. Hao, A.S. Holehouse, M. Reyer, Q. Sun, S.M. Freier, R.V. Pappu, K.V. Prasanth✝, and T. Ha (*Co-first authors, $ Equal contribution, ✝Co-corresponding authors) (2017) Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution.
Journal of Cell Science, 130: 4180 - 4192. Access Article
T.S. Harmon, A.S. Holehouse, M.K. Rosen, R.V. Pappu (2017) Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins.
eLife, 6: 30294. Access Article
** News coverage (Washington University)
A.S. Holehouse, R.V. Pappu (2017) FUS zigzags its way to cross beta. (Invited Preview)
Cell, 171: 499-500. Access Article
J.B. Warner IV*, K.M. Ruff*, P.S. Tan, E.A. Lemke, R.V. Pappu✝, H.A. Lashuel✝ (*Co-first authors, ✝Co-corresponding authors) (2017) Monomeric huntingtin exon 1 has similar overall structural features for wild type and pathological polyglutamine lengths.
Journal of the American Chemical Society, 139: 14456-14469. Access Article
** News coverage (C&E news)
** News coverage (Washington University)
K. Sherry, R.K. Das, R.V. Pappu✝, D. Barrick✝ [✝Co-corresponding authors] (2017) Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch receptor.
K.M. Ruff✝, A.S. Holehouse [✝Corresponding author] (2017) SAXS versus FRET: A matter of heterogeneity? (Invited New & Notable Piece),
G. Fuertes*, N. Banterle*, K.M. Ruff*, A. Chowdhury, D. Mercadante, C. Koehler, M. Kachala, G.E. Girona, S. Milles, A. Mishra, P.R. Onck, F. Gräter, S. Esteban-Martin, R.V. Pappu✝, D.I. Svergun✝, E.A. Lemke✝ [*Co-first authors, ✝Co-corresponding authors] (2017) Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS versus FRET measurements.
M.T. Wei*, S. Elbaum-Garfinkle*, A.S. Holehouse*, C.C.H. Chen, M. Feric, C.B. Arnold, R.D. Priestley, R.V. Pappu✝, C.P. Brangwynne✝ [*Co-first authors, ✝Co-corresponding authors] (2017) Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles.
** News coverage (EurekaAlert)
** News coverage (Princeton University)
** IDP State Letter Summary
S. Chatterjee, P. Luthra, E. Esaulova, E. Agapov, B. Yen, D. Borek, M. Edwards, A. Mittal, D. Jordan, P. Ramanan, M. Moore, R.V. Pappu, M. Holtzman, M.N. Artyomov, C. Basler, G. Amarasinghe, and D. Leung (2017) Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses.
** News coverage (EurekAlert)
J. Clarke & R.V. Pappu (2017) Protein Folding and Binding, Complexity Comes of Age.
P. Sormanni, D. Piovesan, G. Heller, M. Bonomi, P. Kukic, C. Camilloni, M. Fuxreiter, Z. Dosztanyi, R.V. Pappu, M.M. Babu, S. Longhi, P.S. Tompa, A.K. Dunker, V.N. Uversky, S. Tosatto, M. Vendruscolo (2017) Simultaneous quantification of protein order and disorder. (Commentary).
T.S. Harmon, A.S. Holehouse, R.V. Pappu (2017) To mix, or to demix, that is the question (Invited New & Notable Piece),
V. Kalas, J.S. Pinkner, T.J. Hannan, M.E. Hibbing, K.W. Dodson, A.S. Holehouse, H. Zhang, N.H. Tolia, M.L. Gross, R.V. Pappu, J. Janetka, S.J. Hultgren (2017) Evolutionary fine-tuning of conformational ensembles in FimH during host-pathogen interactions.
A.S. Holehouse✝, R.K. Das, J.N. Ahad, M.O.G. Richardson, R.V. Pappu✝ [✝Co-corresponding authors] (2017) CIDER: Resources to analyze sequence-ensemble relationships of intrinsically disordered proteins.
- Selected and evaluated by Faculty of 1000
- Selected as one of the "Best of 2017" by the Biophysical Journal
E.W. Martin*, A.S. Holehouse*, C.R. Grace, A. Hughs, R.V. Pappu✝, T. Mittag✝ [*Co-first authors, ✝Co-corresponding authors] (2016) Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and Upon Multisite Phosphorylation.
T.S. Harmon, M.D. Crabtree, S.L. Shammas, A.E. Posey, J. Clarke, R.V. Pappu (2016) GADIS: Algorithm for Designing Sequences to Achieve Target Secondary Structure Profiles of Intrinsically Disordered Proteins.
C.W. Pak, M. Kosno, A.S. Holehouse, S.B. Padrick, A. Mittal, R. Ali, A.A. Yunus, D.R. Liu, R.V. Pappu✝, M.K. Rosen✝ [✝Co-corresponding authors] (2016) Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein.
M. Feric, N. Vaidya, T.S. Harmon, D.M. Mitrea, L. Zhu, T.M. Richardson, R.W. Kriwacki, R.V. Pappu, C.P. Brangwynne (2016) Coexisting Liquid Phases Underlie Nucleolar Subcompartments.
** News coverage (EurekAlert)
** News coverage (Princeton University)
R.K. Das, Y. Huang, A. H. Phillips, R.W. Kriwacki, R.V. Pappu (2016) Cryptic Sequence Features Within the Disordered Protein p27Kip1 Regulate Cell Cycle Signaling.
** News coverage (Phys.org)
** IDP State Letter Summary
S. Banjade, Q. Wu, A. Mittal, W.B. Peeples, R.V. Pappu, M.K. Rosen (2015) A Conserved Interdomain Linker Promotes Phase Separation of the Multivalent Adaptor Protein Nck.
K.M. Ruff, T.S. Harmon, R.V. Pappu (2015) CAMELOT: A Machine Learning Approach for Coarse-grained Simulations of Aggregation of Block-copolymeric Protein Sequences.
C.P. Brangwynne, P.S. Tompa, R.V. Pappu (2015) Polymer Physics of Intracellular Phase Transitions.
A.S. Holehouse, R.V. Pappu (2015) Encoding phase transitions. (Invited News & Views Piece),
R.K. Das, K.M. Ruff, R.V. Pappu (2015) Relating Sequence Encoded Information to Form and Function of Intrinsically Disordered Proteins.
M.I. Diamond, S. Cai, A. Boudreau, C.J. Carey Jr., N. Lyle, R.V. Pappu, S.J. Swamidass, M. Bissell, H. Piwnica-Worms, J. Shao (2015) Subcellular Localization and Ser-137 Phosphorylation Regulate Tumor-Suppressive Activity of Profilin-1.
A.S. Holehouse, K. Garai, N. Lyle, A. Vitalis, R.V. Pappu (2015) Quantitative Assessments of the Distinct Contributions of Polypeptide Backbone Amides versus Sidechain Groups to Chain Expansion via Chemical Denaturation.
A.G. Kozlov, E. Weiland, A. Mittal, V. Waldman, E. Antony, N. Fazio, R.V. Pappu, T.M. Lohman (2015) Intrinsically Disordered C-terminal Tails of E.coli Single Stranded DNA Binding Protein Regulate Cooperative Binding to Single Stranded DNA.
A. Mittal, R.K. Das, A. Vitalis, R.V. Pappu (2015) ABSINTH Implicit Solvation Model and Force Field Paradigm for Use in Simulations of Intrinsically Disordered Proteins. Book chapter in Computational Approaches to Protein Dynamics: From Quantum to Coarse-Grained Methods, pp. 181-201. Ed. Monika Fuxreiter. CRC Press, Boca Raton, FL. Link to book (Amazon)
R.V. Pappu (2015) Cell Signaling, Division, and Organization Mediated by Intrinsically Disordered Proteins.
P.J. Buske, A. Mittal, R.V. Pappu, P.A. Levin (2015) An Intrinsically Disordered Linker Plays a Critical Role in Bacterial Cell Division.
L. Ripaud, V. Chumakova, M. Antonin, A. Hastie, S. Pinkert, R. Koerner, K.M. Ruff, R.V. Pappu, D. Hornburg, M. Mann, F. U. Hartl, M. S. Hipp (2014) Overexpression of Q-rich prion-like Proteins Suppresses PolyQ Cytotoxicity and Alters the PolyQ Interactome.
K. M. Ruff, S.J. Khan, R.V. Pappu (2014) A Coarse-Grained Model for Polyglutamine Aggregation Modulated by Amphipathic Flanking Sequences.
R.V. Pappu (2014) Frozen In Beta (Invited New & Notable Piece),
W. Xu, M.R. Edwards, D.M. Borek, A.R. Feagins, A. Mittal, J.B. Alinger, K.N. Berry, B.Yen, J. Hamilton, T.J. Brett, R.V. Pappu, D.W. Leung, C.F. Basler, G.K. Amarasinghe (2014) Ebola Virus VP24 Targets a Unique NLS Binding Site on Karyopherin Alpha 5 to Selectively Compete with Nuclear Import of Phosphorylated STAT1.
A. Vitalis, R.V. Pappu (2014) A Simple Molecular Mechanics Integrator in Mixed Rigid Body and Dihedral Angle Space.
A. Mittal, N. Lyle, T. S. Harmon, R. V. Pappu (2014) Hamiltonian Switch Metropolis Monte Carlo Simulations for Improved Conformational Sampling of Intrinsically Disordered Regions Tethered to Ordered Domains of Proteins.
A. T. Tubbs, Y. Dorsett, E. Chan, B. Helmink, B. Lee, P. Hung, R. George, A. L. Bredemeyer, A. Mittal, R. V. Pappu, D. Chowdhury, N. Mosammaparast, M. S. Krangel, B. P. Sleckman (2014) KAP-1 Promotes Resection of Broken DNA Ends Not Protected by γ-H2AX and 53BP1 in G1-Phase Lymphocytes.
R. van der Lee, M. Buljan, B. Lang, R. J. Weatheritt, G.W. Daughdrill, A. K. Dunker, M.Fuxreiter, J. Gough, J. Gsponer, D. T. Jones, P. M. Kim, R. W. Kriwacki, C. J. Oldfield, R. V. Pappu, P. Tompa, V. N. Uversky, P. E. Wright, M. M. Babu (2014) Classification of Intrinsically Disordered Regions and Proteins.
B. Luan, N. Lyle, R.V. Pappu, D.P. Raleigh (2014) Denatured State Ensembles with the Same Radius of Gyration Can Form Significantly Different Long-Range Contacts.
S.L. Crick, K.M. Ruff, K. Garai, C. Frieden, R.V. Pappu (2013) Unmasking the Roles of N- and C-terminal Flanking Sequences From Exon 1 of Huntingtin as Modulators of Polyglutamine Aggregation.
R.K. Das, R.V. Pappu (2013) Conformations of Intrinsically Disordered Proteins are Influenced by Linear Sequence Distributions of Oppositely Charged Residues.
N. Lyle, R.K. Das, R.V. Pappu. (2013) A Quantitative Measure for Protein Conformational Heterogeneity.
W. Meng, B. Luan, N. Lyle, R.V. Pappu, D.P. Raleigh (2013) The Denatured State Ensemble Contains Significant Local and Long-range Structure Under Native Condition: Analysis of the N-terminal Domain of the Ribosomal Protein L9.
W. Meng*, N. Lyle*, B. Luan, D.P. Raleigh, R.V. Pappu [*Co-first-authors] (2013) Experiments and Simulations Show How Long-Range Contacts Can Form in Expanded Unfolded Proteins with Negligible Secondary Structure.
A.H. Mao, N. Lyle, R.V. Pappu (2013) Describing Sequence-Ensemble Relationships for Intrinsically Disordered Proteins.
R.K. Das, A. Mittal, R.V. Pappu (2013) How is Functional Specificity Achieved Through Disordered Regions of Proteins?
M.M. Babu, R.W. Kriwacki, R.V. Pappu (2012) Versatility from Protein Disorder.
A.H. Mao, R.V. Pappu (2012) Crystal Lattice Properties Fully Determine Short-Range Interaction Parameters for Alkali and Halide Ions.
R.K. Das, A.H. Mao, R.V. Pappu (2012) Unmasking Functional Motifs within Disordered Regions of Proteins.
A. Radhakrishnan, A. Vitalis, A.H. Mao, A.T. Steffen, R.V. Pappu (2012) Improved Atomistic Monte Carlo Simulations Demonstrate that Poly-L-Proline Adopts Heterogeneous Ensembles of Conformations of Semi-Rigid Segments Interrupted by Kinks.
S.L. Crick, R.V. Pappu (March 27, 2012) Thermodynamic and Kinetic Models for Aggregation of Intrinsically Disordered Proteins. Book chapter in Peptide Folding, Misfolding, and Nonfolding, pp. 413-440. Ed. Reinhard Schweitzer-Stenner, Vladimir Uversky. John Wiley & Sons, Hoboken, NJ. Access Article or Download Copy
R.K. Das, S.L. Crick, R.V. Pappu (2012) N-terminal Segments Modulate the α-Helical Propensities of the Intrinsically Disordered Basic Regions of bZIP Proteins.
A. Vitalis, R.V. Pappu (2011) Assessing the Contribution of Heterogeneous Distributions of Oligomers to Aggregation Mechanisms of Polyglutamine Peptides.
R. Halfmann, S. Alberti, R. Krishnan, N. Lyle, C.W. O'Donnell, O.D. King, B. Berger, R.V. Pappu, S. Lindquist (2011) Opposing Effects of Glutamine and Asparagine Govern Prion Formation by Intrinsically Disordered Proteins.
A.H. Mao, R.V. Pappu (2011) Exact Recording of Metropolis-Hastings-Class Monte Carlo Simulations Using One Bit Per Sample.
D.G. Thomas, R.V. Pappu, N.A. Baker (2011) NanoParticle Ontology for Cancer Nanotechnology Research.
M.A. Wyczalkowski, A. Vitalis, R.V. Pappu (2010) New Estimators for Calculating Solvation Entropy and Enthalpy and Comparative Assessments of their Accuracy and Precision.
A.H. Mao, S.L. Crick, A. Vitalis, C. Chicoine, R.V. Pappu (2010) Net Charge Per Residue Modulates Conformational Ensembles of Intrinsically Disordered Proteins.
T.E. Williamson, A. Vitalis, S.L. Crick, R.V. Pappu (2010) Modulation of Polyglutamine Conformations and Dimer Formation by the N-terminus of Huntingtin.
X. Hu, S.L. Crick, G. Bu, C. Frieden, R.V. Pappu, J-M. Lee (2009) Amyloid Seeds Formed by Cellular Uptake, Concentration, and Aggregation of the Amyloid-Beta Peptide.
A.A. Chen, M. Marucho, N.A. Baker, R.V. Pappu (2009) Simulations of RNA Interactions with Monovalent Ions.
D.G. Thomas, R.V. Pappu, N.A. Baker (2009) NPO: Ontology for Cancer Nanotechnology Research.
H.A. Lashuel, R.V. Pappu (2009) Amyloids Go Genomic: Insights Regarding the Sequence Determinants of Prion Formation from Genome-Wide Studies.
A. Vitalis, N. Lyle, R.V. Pappu (2009) Thermodynamics of beta sheet formation in polyglutamine.
A.A. Chen, D.E. Draper, R.V. Pappu (2009) Molecular simulation studies of monovalent counterion-mediated interactions in a model RNA kissing loop.
A. Vitalis, R.V. Pappu (2009) Methods for Monte Carlo Simulations of Biomacromolecules.
R.V. Pappu, R. Nussinov (2009) Protein folding: Lessons Learned and New Frontiers.
A. Vitalis, R.V. Pappu(2009) ABSINTH: A New Continuum Solvation Model for Simulations of Polypeptides in Aqueous Solutions.
A. Vitalis, X. Wang, R.V. Pappu (2008) Atomistic Simulations of the Effects of Polyglutamine Chain Length and Solvent Quality on Conformational Equilibria and Spontaneous Homodimerization.
H.T. Tran, A. Mao, R.V. Pappu (2008) Role of Backbone-Solvent Interactions in Determining Conformational Equilibria of Intrinsically Disordered Polypeptides.
M. A. Wyczalkowski, R.V. Pappu (2008) Satisfying the Fluctuation Theorem in Free Energy Calculations with Hamiltonian Replica Exchange.
R.V. Pappu, X. Wang, A. Vitalis, S.L. Crick (2008) A Polymer Physics Perspective on Driving Forces and Mechanisms for Protein Aggregation.
A.A. Chen, R.V. Pappu (2007) Parameters of Monovalent Ions in the AMBER-99 Forcefield: Assessment of Inaccuracies and Proposed Improvements.
A. Vitalis, X. Wang, R.V. Pappu (2007) Quantitative Characterization of Intrinsic Disorder in Polyglutamine: Insights from Analysis Based on Polymer Theories.
A.A. Chen, R.V. Pappu (2007) Quantitative Characterization of Ion Pairing and Cluster Formation in Strong 1:1 Electrolytes.
S.L. Crick, M. Jayaraman, C. Frieden, R. Wetzel, R.V. Pappu (2006) Fluorescence Correlation Spectroscopy Shows That Monomeric Polyglutamine Molecules Form Collapsed Structures in Aqueous Solutions.
H.T. Tran, R.V. Pappu (2006) Toward an Accurate Theoretical Framework for Describing Ensembles for Proteins Under Strongly Denaturing Conditions.
X. Wang, A. Vitalis, M.A. Wyczalkowski, R.V. Pappu (2006) Characterizing the Conformational Ensemble of Monomeric Polyglutamine.
H.T. Tran, X. Wang, R.V. Pappu (2005) Reconciling Observations of Sequence-Specific Conformational Preferences with the Generic Behavior of Denatured Proteins.
A. Patriciu, G.S. Chirikjian, R.V. Pappu (2004) Analysis of the Conformational Dependence of Mass-metric Tensor Determinants in Serial polymers with Constraints.
A.N. Drozdov, A. Grossfield, R.V. Pappu (2004) The Role of Solvent in Determining Conformational Preferences of Alanine Dipeptide in Water.
R.V. Pappu, G.D.Rose (2002) A Simple Model for Polyproline II Structure in Unfolded States of Alanine-Based Peptides.
R.V. Pappu, R. Srinivasan, G.D. Rose (2000) The Flory Isolated Pair Hypothesis is not Valid for Polypeptide Chains: Implications for Protein Folding.
R.K. Hart, R.V. Pappu, J.W. Ponder (2000) Exploring the Similarities Between Potential Smoothing and Simulated Annealing.
R.V. Pappu (1999) Review of the Fourth Johns Hopkins Protein Folding Meeting.
R.V. Pappu, G.R. Marshall, J.W. Ponder (1999) A Potential Smoothing Algorithm Accurately Predicts Transmembrane Helix Packing.
R.V. Pappu, R.K. Hart, J.W. Ponder (1998) Analysis and Application of Potential Energy Smoothing and Search Methods for Global Optimization.
E.S. Huang, P. Koehl, M. Levitt, R.V. Pappu, J.W. Ponder (1998) Accuracy of Side-Chain Prediction Upon Near-Native Protein Backbones Generated by Ab Initio Folding Methods.
R.V. Pappu, D.L. Weaver (1998) The Early Folding Kinetics of Apomyoglobin.
R.V. Pappu, W.J. Schneller, D.L. Weaver (1996) Electrostatic Multipole Representation of a Polypeptide Chain: An Algorithm for Simulation of Polypeptide Properties.
