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Items: 1 to 50 of 112

1.

LASSI: A lattice model for simulating phase transitions of multivalent proteins.

Choi JM, Dar F, Pappu RV.

PLoS Comput Biol. 2019 Oct 21;15(10):e1007028. doi: 10.1371/journal.pcbi.1007028. [Epub ahead of print]

2.

Nucleo-cytoplasmic Partitioning of ARF Proteins Controls Auxin Responses in Arabidopsis thaliana.

Powers SK, Holehouse AS, Korasick DA, Schreiber KH, Clark NM, Jing H, Emenecker R, Han S, Tycksen E, Hwang I, Sozzani R, Jez JM, Pappu RV, Strader LC.

Mol Cell. 2019 Oct 3;76(1):177-190.e5. doi: 10.1016/j.molcel.2019.06.044. Epub 2019 Aug 14.

PMID:
31421981
3.

Information theoretic measures for quantifying sequence-ensemble relationships of intrinsically disordered proteins.

Cohan MC, Ruff KM, Pappu RV.

Protein Eng Des Sel. 2019 Aug 3. pii: gzz014. doi: 10.1093/protein/gzz014. [Epub ahead of print]

PMID:
31375817
4.

q-Canonical Monte Carlo Sampling for Modeling the Linkage between Charge Regulation and Conformational Equilibria of Peptides.

Fossat MJ, Pappu RV.

J Phys Chem B. 2019 Aug 15;123(32):6952-6967. doi: 10.1021/acs.jpcb.9b05206. Epub 2019 Aug 7.

PMID:
31362509
5.

Covalently-assembled single-chain protein nanostructures with ultra-high stability.

Bai W, Sargent CJ, Choi JM, Pappu RV, Zhang F.

Nat Commun. 2019 Jul 25;10(1):3317. doi: 10.1038/s41467-019-11285-8.

6.

Phase separation in biology and disease-a symposium report.

Cable J, Brangwynne C, Seydoux G, Cowburn D, Pappu RV, Castañeda CA, Berchowitz LE, Chen Z, Jonikas M, Dernburg A, Mittag T, Fawzi NL.

Ann N Y Acad Sci. 2019 Sep;1452(1):3-11. doi: 10.1111/nyas.14126. Epub 2019 Jun 14.

PMID:
31199001
7.

Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions.

Peran I, Holehouse AS, Carrico IS, Pappu RV, Bilsel O, Raleigh DP.

Proc Natl Acad Sci U S A. 2019 Jun 18;116(25):12301-12310. doi: 10.1073/pnas.1818206116. Epub 2019 Jun 5.

8.

Spontaneous driving forces give rise to protein-RNA condensates with coexisting phases and complex material properties.

Boeynaems S, Holehouse AS, Weinhardt V, Kovacs D, Van Lindt J, Larabell C, Van Den Bosch L, Das R, Tompa PS, Pappu RV, Gitler AD.

Proc Natl Acad Sci U S A. 2019 Apr 16;116(16):7889-7898. doi: 10.1073/pnas.1821038116. Epub 2019 Mar 29.

9.

Ion Mobility Mass Spectrometry Uncovers the Impact of the Patterning of Oppositely Charged Residues on the Conformational Distributions of Intrinsically Disordered Proteins.

Beveridge R, Migas LG, Das RK, Pappu RV, Kriwacki RW, Barran PE.

J Am Chem Soc. 2019 Mar 27;141(12):4908-4918. doi: 10.1021/jacs.8b13483. Epub 2019 Mar 12.

10.

Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.

Choi JM, Pappu RV.

J Chem Theory Comput. 2019 Feb 12;15(2):1367-1382. doi: 10.1021/acs.jctc.8b00573. Epub 2019 Jan 22.

PMID:
30633502
11.

Experimentally Derived and Computationally Optimized Backbone Conformational Statistics for Blocked Amino Acids.

Choi JM, Pappu RV.

J Chem Theory Comput. 2019 Feb 12;15(2):1355-1366. doi: 10.1021/acs.jctc.8b00572. Epub 2019 Jan 22.

PMID:
30516982
12.

Phase Separation of Intrinsically Disordered Proteins.

Posey AE, Holehouse AS, Pappu RV.

Methods Enzymol. 2018;611:1-30. doi: 10.1016/bs.mie.2018.09.035. Epub 2018 Oct 31.

PMID:
30471685
13.

Conformational preferences and phase behavior of intrinsically disordered low complexity sequences: insights from multiscale simulations.

Ruff KM, Pappu RV, Holehouse AS.

Curr Opin Struct Biol. 2019 Jun;56:1-10. doi: 10.1016/j.sbi.2018.10.003. Epub 2018 Nov 12. Review.

PMID:
30439585
14.

Author Correction: Injectable tissue integrating networks from recombinant polypeptides with tunable order.

Roberts S, Harmon TS, Schaal JL, Miao V, Li KJ, Hunt A, Wen Y, Oas TG, Collier JH, Pappu RV, Chilkoti A.

Nat Mater. 2018 Dec;17(12):1164. doi: 10.1038/s41563-018-0233-z.

15.

Injectable tissue integrating networks from recombinant polypeptides with tunable order.

Roberts S, Harmon TS, Schaal JL, Miao V, Li KJ, Hunt A, Wen Y, Oas TG, Collier JH, Pappu RV, Chilkoti A.

Nat Mater. 2018 Dec;17(12):1154-1163. doi: 10.1038/s41563-018-0182-6. Epub 2018 Oct 15. Erratum in: Nat Mater. 2018 Oct 31;:.

PMID:
30323334
16.

Comment on "Innovative scattering analysis shows that hydrophobic disordered proteins are expanded in water".

Fuertes G, Banterle N, Ruff KM, Chowdhury A, Pappu RV, Svergun DI, Lemke EA.

Science. 2018 Aug 31;361(6405). pii: eaau8230. doi: 10.1126/science.aau8230.

PMID:
30166461
17.

Measuring NDC80 binding reveals the molecular basis of tension-dependent kinetochore-microtubule attachments.

Yoo TY, Choi JM, Conway W, Yu CH, Pappu RV, Needleman DJ.

Elife. 2018 Jul 25;7. pii: e36392. doi: 10.7554/eLife.36392.

18.

Inert and seed-competent tau monomers suggest structural origins of aggregation.

Mirbaha H, Chen D, Morazova OA, Ruff KM, Sharma AM, Liu X, Goodarzi M, Pappu RV, Colby DW, Mirzaei H, Joachimiak LA, Diamond MI.

Elife. 2018 Jul 10;7. pii: e36584. doi: 10.7554/eLife.36584.

19.

A First Glimpse of Nucleation of Phase Transitions in Living Cells.

Posey AE, Pappu RV.

Mol Cell. 2018 Jul 5;71(1):1-3. doi: 10.1016/j.molcel.2018.06.028.

20.

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins.

Wang J, Choi JM, Holehouse AS, Lee HO, Zhang X, Jahnel M, Maharana S, Lemaitre R, Pozniakovsky A, Drechsel D, Poser I, Pappu RV, Alberti S, Hyman AA.

Cell. 2018 Jul 26;174(3):688-699.e16. doi: 10.1016/j.cell.2018.06.006. Epub 2018 Jun 28.

21.

Advances in Understanding Stimulus-Responsive Phase Behavior of Intrinsically Disordered Protein Polymers.

Ruff KM, Roberts S, Chilkoti A, Pappu RV.

J Mol Biol. 2018 Nov 2;430(23):4619-4635. doi: 10.1016/j.jmb.2018.06.031. Epub 2018 Jun 24. Review.

22.

Sequence-to-Conformation Relationships of Disordered Regions Tethered to Folded Domains of Proteins.

Mittal A, Holehouse AS, Cohan MC, Pappu RV.

J Mol Biol. 2018 Aug 3;430(16):2403-2421. doi: 10.1016/j.jmb.2018.05.012. Epub 2018 May 12.

23.

Tadpole-like Conformations of Huntingtin Exon 1 Are Characterized by Conformational Heterogeneity that Persists regardless of Polyglutamine Length.

Newcombe EA, Ruff KM, Sethi A, Ormsby AR, Ramdzan YM, Fox A, Purcell AW, Gooley PR, Pappu RV, Hatters DM.

J Mol Biol. 2018 May 11;430(10):1442-1458. doi: 10.1016/j.jmb.2018.03.031. Epub 2018 Apr 5.

24.

A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain.

Staller MV, Holehouse AS, Swain-Lenz D, Das RK, Pappu RV, Cohen BA.

Cell Syst. 2018 Apr 25;6(4):444-455.e6. doi: 10.1016/j.cels.2018.01.015. Epub 2018 Mar 7.

25.

Inhibition of amyloid beta fibril formation by monomeric human transthyretin.

Garai K, Posey AE, Li X, Buxbaum JN, Pappu RV.

Protein Sci. 2018 Jul;27(7):1252-1261. doi: 10.1002/pro.3396. Epub 2018 Mar 14.

26.

Profilin reduces aggregation and phase separation of huntingtin N-terminal fragments by preferentially binding to soluble monomers and oligomers.

Posey AE, Ruff KM, Harmon TS, Crick SL, Li A, Diamond MI, Pappu RV.

J Biol Chem. 2018 Mar 9;293(10):3734-3746. doi: 10.1074/jbc.RA117.000357. Epub 2018 Jan 22.

27.

Collapse Transitions of Proteins and the Interplay Among Backbone, Sidechain, and Solvent Interactions.

Holehouse AS, Pappu RV.

Annu Rev Biophys. 2018 Jan 18. doi: 10.1146/annurev-biophys-070317-032838. [Epub ahead of print]

PMID:
29345991
28.

Functional Implications of Intracellular Phase Transitions.

Holehouse AS, Pappu RV.

Biochemistry. 2018 May 1;57(17):2415-2423. doi: 10.1021/acs.biochem.7b01136. Epub 2018 Jan 24.

29.

Phase separation of a yeast prion protein promotes cellular fitness.

Franzmann TM, Jahnel M, Pozniakovsky A, Mahamid J, Holehouse AS, Nüske E, Richter D, Baumeister W, Grill SW, Pappu RV, Hyman AA, Alberti S.

Science. 2018 Jan 5;359(6371). pii: eaao5654. doi: 10.1126/science.aao5654.

PMID:
29301985
30.

Quantitative analysis of multilayer organization of proteins and RNA in nuclear speckles at super resolution.

Fei J, Jadaliha M, Harmon TS, Li ITS, Hua B, Hao Q, Holehouse AS, Reyer M, Sun Q, Freier SM, Pappu RV, Prasanth KV, Ha T.

J Cell Sci. 2017 Dec 15;130(24):4180-4192. doi: 10.1242/jcs.206854. Epub 2017 Nov 13.

31.

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins.

Harmon TS, Holehouse AS, Rosen MK, Pappu RV.

Elife. 2017 Nov 1;6. pii: e30294. doi: 10.7554/eLife.30294.

32.

Control of transcriptional activity by design of charge patterning in the intrinsically disordered RAM region of the Notch receptor.

Sherry KP, Das RK, Pappu RV, Barrick D.

Proc Natl Acad Sci U S A. 2017 Oct 31;114(44):E9243-E9252. doi: 10.1073/pnas.1706083114. Epub 2017 Oct 12.

33.

Phase behaviour of disordered proteins underlying low density and high permeability of liquid organelles.

Wei MT, Elbaum-Garfinkle S, Holehouse AS, Chen CC, Feric M, Arnold CB, Priestley RD, Pappu RV, Brangwynne CP.

Nat Chem. 2017 Nov;9(11):1118-1125. doi: 10.1038/nchem.2803. Epub 2017 Jun 26.

PMID:
29064502
34.

FUS Zigzags Its Way to Cross Beta.

Holehouse AS, Pappu RV.

Cell. 2017 Oct 19;171(3):499-500. doi: 10.1016/j.cell.2017.10.007.

35.

Monomeric Huntingtin Exon 1 Has Similar Overall Structural Features for Wild-Type and Pathological Polyglutamine Lengths.

Warner JB 4th, Ruff KM, Tan PS, Lemke EA, Pappu RV, Lashuel HA.

J Am Chem Soc. 2017 Oct 18;139(41):14456-14469. doi: 10.1021/jacs.7b06659. Epub 2017 Oct 9.

36.

Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.

Fuertes G, Banterle N, Ruff KM, Chowdhury A, Mercadante D, Koehler C, Kachala M, Estrada Girona G, Milles S, Mishra A, Onck PR, Gräter F, Esteban-Martín S, Pappu RV, Svergun DI, Lemke EA.

Proc Natl Acad Sci U S A. 2017 Aug 1;114(31):E6342-E6351. doi: 10.1073/pnas.1704692114. Epub 2017 Jul 17.

37.

Structural basis for human respiratory syncytial virus NS1-mediated modulation of host responses.

Chatterjee S, Luthra P, Esaulova E, Agapov E, Yen BC, Borek DM, Edwards MR, Mittal A, Jordan DS, Ramanan P, Moore ML, Pappu RV, Holtzman MJ, Artyomov MN, Basler CF, Amarasinghe GK, Leung DW.

Nat Microbiol. 2017 Jun 30;2:17101. doi: 10.1038/nmicrobiol.2017.101.

38.

Editorial overview: Protein Folding and Binding, Complexity Comes of Age.

Clarke J, Pappu RV.

Curr Opin Struct Biol. 2017 Feb;42:v-vii. doi: 10.1016/j.sbi.2017.03.004. No abstract available.

PMID:
28351535
39.

Simultaneous quantification of protein order and disorder.

Sormanni P, Piovesan D, Heller GT, Bonomi M, Kukic P, Camilloni C, Fuxreiter M, Dosztanyi Z, Pappu RV, Babu MM, Longhi S, Tompa P, Dunker AK, Uversky VN, Tosatto SC, Vendruscolo M.

Nat Chem Biol. 2017 Mar 22;13(4):339-342. doi: 10.1038/nchembio.2331. No abstract available.

PMID:
28328918
40.

To Mix, or To Demix, That Is the Question.

Harmon TS, Holehouse AS, Pappu RV.

Biophys J. 2017 Feb 28;112(4):565-567. doi: 10.1016/j.bpj.2016.12.031. No abstract available.

41.

Evolutionary fine-tuning of conformational ensembles in FimH during host-pathogen interactions.

Kalas V, Pinkner JS, Hannan TJ, Hibbing ME, Dodson KW, Holehouse AS, Zhang H, Tolia NH, Gross ML, Pappu RV, Janetka J, Hultgren SJ.

Sci Adv. 2017 Feb 10;3(2):e1601944. doi: 10.1126/sciadv.1601944. eCollection 2017 Feb.

42.

CIDER: Resources to Analyze Sequence-Ensemble Relationships of Intrinsically Disordered Proteins.

Holehouse AS, Das RK, Ahad JN, Richardson MO, Pappu RV.

Biophys J. 2017 Jan 10;112(1):16-21. doi: 10.1016/j.bpj.2016.11.3200.

43.

Sequence Determinants of the Conformational Properties of an Intrinsically Disordered Protein Prior to and upon Multisite Phosphorylation.

Martin EW, Holehouse AS, Grace CR, Hughes A, Pappu RV, Mittag T.

J Am Chem Soc. 2016 Nov 30;138(47):15323-15335. Epub 2016 Nov 17.

44.

GADIS: Algorithm for designing sequences to achieve target secondary structure profiles of intrinsically disordered proteins.

Harmon TS, Crabtree MD, Shammas SL, Posey AE, Clarke J, Pappu RV.

Protein Eng Des Sel. 2016 Sep;29(9):339-46. doi: 10.1093/protein/gzw034. Epub 2016 Aug 8.

45.

Sequence Determinants of Intracellular Phase Separation by Complex Coacervation of a Disordered Protein.

Pak CW, Kosno M, Holehouse AS, Padrick SB, Mittal A, Ali R, Yunus AA, Liu DR, Pappu RV, Rosen MK.

Mol Cell. 2016 Jul 7;63(1):72-85. doi: 10.1016/j.molcel.2016.05.042.

46.

Coexisting Liquid Phases Underlie Nucleolar Subcompartments.

Feric M, Vaidya N, Harmon TS, Mitrea DM, Zhu L, Richardson TM, Kriwacki RW, Pappu RV, Brangwynne CP.

Cell. 2016 Jun 16;165(7):1686-1697. doi: 10.1016/j.cell.2016.04.047. Epub 2016 May 19.

47.

Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling.

Das RK, Huang Y, Phillips AH, Kriwacki RW, Pappu RV.

Proc Natl Acad Sci U S A. 2016 May 17;113(20):5616-21. doi: 10.1073/pnas.1516277113. Epub 2016 May 2.

48.

CAMELOT: A machine learning approach for coarse-grained simulations of aggregation of block-copolymeric protein sequences.

Ruff KM, Harmon TS, Pappu RV.

J Chem Phys. 2015 Dec 28;143(24):243123. doi: 10.1063/1.4935066.

49.

Conserved interdomain linker promotes phase separation of the multivalent adaptor protein Nck.

Banjade S, Wu Q, Mittal A, Peeples WB, Pappu RV, Rosen MK.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):E6426-35. doi: 10.1073/pnas.1508778112. Epub 2015 Nov 9.

50.

Protein polymers: Encoding phase transitions.

Holehouse AS, Pappu RV.

Nat Mater. 2015 Nov;14(11):1083-4. doi: 10.1038/nmat4459. No abstract available.

PMID:
26490213

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