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1

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

Holehouse, Alex S., Pappu, Rohit V.

Journal:

Annual Review of Biophysics

Year:

2018

Language:

english

File:

PDF, 1.60 MB

english, 2018

2

Tardigrades use intrinsically disordered proteins to survive desiccation

Boothby, Thomas C., Piszkiewicz, Samantha, Holehouse, Alex, Pappu, Rohit V., Pielak, Gary J.

Journal:

Year:

2018

Language:

english

File:

PDF, 68 KB

english, 2018

3

Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions

Choi, Jeong-Mo, Holehouse, Alex S., Pappu, Rohit V.

Journal:

Annual Review of Biophysics

Year:

2020

Language:

english

File:

PDF, 1.55 MB

english, 2020

4

Tardigrade Disordered Proteins Mediate Desiccation Tolerance

Boothby, Thomas C., Piszkiewicz, Samantha, Mehta, Aakash, Brozena, Alexandra, Tapia, Hugo, Koshland, Doug, Holehouse, Alex, Pappu, Rohit, Goldstein, Bob, Pielak, Gary

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 45 KB

english, 2017

5

FUS Zigzags Its Way to Cross Beta

Holehouse, Alex S., Pappu, Rohit V.

Journal:

Year:

2017

Language:

english

File:

PDF, 802 KB

english, 2017

6

Gelation and Vitrification of Tardigrade IDPs

Boothby, Thomas C., Piszkiewicz, Samantha, Mehta, Aakash, Brozena, Alexandra, Tapia, Hugo, Koshland, Doug, Holehouse, Alex, Pappu, Rohit, Goldstein, Bob, Pielak, Gary

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 62 KB

english, 2018

7

RNA-Induced Conformational Switching and Clustering of G3BP Drive Stress Granule Assembly by Condensation

GuillÃ©n-Boixet, Jordina, Kopach, Andrii, Holehouse, Alex S., Wittmann, Sina, Jahnel, Marcus, SchlÃ¼Ãler, Raimund, Kim, Kyoohyun, Trussina, Irmela R.E.A., Wang, Jie, Mateju, Daniel, Poser, Ina, Mahar

Journal:

Year:

2020

File:

PDF, 7.03 MB

2020

8

Parsing the Contributions of Polypeptide Backbones and Sidechains to Denaturation in Concentrated Aqueous Solutions of Urea and Guanidinium Chloride

Holehouse, Alex S., Lyle, Nicholas, Vitalis, Andreas, Thirumalai, Devarajan, Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 44 KB

english, 2014

9

[IEEE 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) - San Diego, CA, USA (2012.05.9-2012.05.12)] 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) - Developing a novel integrated model of p38 MAPK and glucocorticoid signalling pathways

Holehouse, Alex, Yang, Xian, Adcock, Ian, Guo, Yike

Year:

2012

Language:

english

File:

PDF, 2.97 MB

english, 2012

10

Quantitative Assessments of the Distinct Contributions of Polypeptide Backbone Amides versus Side Chain Groups to Chain Expansion via Chemical Denaturation

Holehouse, Alex S., Garai, Kanchan, Lyle, Nicholas, Vitalis, Andreas, Pappu, Rohit V.

Journal:

Journal of the American Chemical Society

Year:

2015

Language:

english

File:

PDF, 2.62 MB

english, 2015

11

Protein polymers: Encoding phase transitions

Holehouse, Alex S., Pappu, Rohit V.

Journal:

Nature Materials

Year:

2015

Language:

english

File:

PDF, 243 KB

english, 2015

12

Dynamic Sampling of Multiple Conformations in FimH Modulates Bacterial Adhesion

Kalas, Vasilios, Pinkner, Jerome S., Holehouse, Alex S., Zhang, Hao, Gross, Michael L., Pappu, Rohit V., Hultgren, Scott J.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 57 KB

english, 2016

13

Proteomic and Biophysical Analysis of Polar Tracts

Ruff, Kiersten M., Holehouse, Alex S., Richardson, Mary G.O., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 44 KB

english, 2016

14

Physical Principles that Govern the Sequence-Encoded Phase Behavior of Intrinsically Disordered Block-Copolymeric Proteins

Holehouse, Alex S., Harmon, Tyler S., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 41 KB

english, 2016

15

CIDER: Classification of Intrinsically Disordered Ensemble Regions

Holehouse, Alex S., Ahad, James, Das, Rahul K., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 36 KB

english, 2015

16

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

Pak, Chi W., Kosno, Martyna, Holehouse, Alex S., Padrick, Shae B., Mittal, Anuradha, Ali, Rustam, Yunus, Ali A., Liu, David R., Pappu, Rohit V., Rosen, Michael K.

Journal:

Year:

2016

Language:

english

File:

PDF, 3.50 MB

english, 2016

17

Profilin Binding Modulates the Aggregation and Phase Separation of Huntingtin N-Terminal Fragments via Polyphasic Linkage

Posey, Ammon E., Ruff, Kiersten M., Harmon, Tyler S., Holehouse, Alex S., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 39 KB

english, 2016

18

Sequence determinants of the conformational properties of an intrinsically disordered protein prior to and upon multisite phosphorylation

Martin, Erik W, Holehouse, Alex S, Grace, Christy R., Hughes, Alex, Pappu, Rohit V, Mittag, Tanja

Journal:

Journal of the American Chemical Society

Year:

2016

Language:

english

File:

PDF, 2.86 MB

english, 2016

19

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

Holehouse, Alex S., Das, Rahul K., Ahad, James N., Richardson, Mary O.G., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 997 KB

english, 2017

20

Simulations and Experiments Provide a Convergent View of Protein Unfolded States under Folding Conditions

Holehouse, Alex S., Perana, Ivan, Carrico, Isaac S., Bilsel, Osman, Raleigh, Daniel P., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 43 KB

english, 2017

21

The Intrinsically Disordered Tail of FtsZ Impacts Polymerization and Bacterial Cell Division Through Sequence-Encoded Charge Patterning

Cohan, Megan C., Posey, Ammon, Grigsby, Steven, Holehouse, Alex S., Mittal, Anuradha, Buske, Paul J., Levin, Petra, Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 60 KB

english, 2017

22

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

Kalas, Vasilios, Pinkner, Jerome S., Hannan, Thomas J., Hibbing, Michael E., Dodson, Karen W., Holehouse, Alex S., Zhang, Hao, Tolia, Niraj H., Gross, Michael L., Pappu, Rohit V., Janetka, James, Hult

Journal:

Science Advances

Year:

2017

Language:

english

File:

PDF, 1.43 MB

english, 2017

23

To Mix, or To Demix, That Is the Question

Harmon, Tyler S., Holehouse, Alex S., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 536 KB

english, 2017

24

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

Martin, Erik W., Holehouse, Alex S., Pappu, Rohit V., Mittag, Tanja

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 40 KB

english, 2017

25

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

Wei, Ming-Tzo, Elbaum-Garfinkle, Shana, Holehouse, Alex S., Chen, Carlos Chih-Hsiung, Feric, Marina, Arnold, Craig B., Priestley, Rodney D., Pappu, Rohit V., Brangwynne, Clifford P.

Journal:

Nature Chemistry

Year:

2017

Language:

english

File:

PDF, 4.57 MB

english, 2017

26

SAXS versus FRET: A Matter of Heterogeneity?

Ruff, Kiersten M., Holehouse, Alex S.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 293 KB

english, 2017

27

Functional Implications of Intracellular Phase Transitions

Holehouse, Alex S, Pappu, Rohit V

Journal:

Year:

2018

Language:

english

File:

PDF, 1.16 MB

english, 2018

28

A General Framework for Predicting and Understanding Sequence-Encoded Phase Diagrams of Intrinsically Disordered Proteins

Holehouse, Alex S., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 39 KB

english, 2018

29

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

Staller, Max V., Holehouse, Alex S., Swain-Lenz, Devjanee, Das, Rahul K., Pappu, Rohit V., Cohen, Barak A.

Journal:

Year:

2018

Language:

english

File:

PDF, 13.17 MB

english, 2018

30

Differential solvation of intrinsically disordered linkers drives the formation of spatially organized droplets in ternary systems of linear multivalent proteins

Harmon, Tyler Scott, Holehouse, Alex S, Pappu, Rohit V

Journal:

New Journal of Physics

Year:

2018

Language:

english

File:

PDF, 2.77 MB

english, 2018

31

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

Mittal, Anuradha, Holehouse, Alex S., Cohan, Megan C., Pappu, Rohit V.

Journal:

Journal of Molecular Biology

Year:

2018

Language:

english

File:

PDF, 2.27 MB

english, 2018

32

Molecular Grammar Governing Phase Behavior of Intrinsically Disordered Proteins with Prion-like Domains

Choi, Jeong-Mo, Wang, Jie, Holehouse, Alex S., Alberti, Simon, Hyman, Anthony A., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 39 KB

english, 2018

33

Reproducible Analysis of Post-Translational Modifications in Proteomes—Application to Human Mutations

Holehouse, Alex S., Naegle, Kristen M., Lisacek, Frederique

Journal:

Year:

2015

Language:

english

File:

PDF, 2.12 MB

english, 2015

34

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

Wang, Jie, Choi, Jeong-Mo, Holehouse, Alex S., Lee, Hyun O., Zhang, Xiaojie, Jahnel, Marcus, Maharana, Shovamayee, Lemaitre, Régis, Pozniakovsky, Andrei, Drechsel, David, Poser, Ina, Pappu, Rohit V.,

Journal:

Year:

2018

Language:

english

File:

PDF, 8.47 MB

english, 2018

35

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

Harmon, Tyler S, Holehouse, Alex S, Rosen, Michael K, Pappu, Rohit V

Journal:

Year:

2017

Language:

english

File:

PDF, 2.42 MB

english, 2017

36

The Unfolded State of the C-Terminal Domain of L9 Expands at Low but Not at Elevated Temperatures

Stenzoski, Natalie E., Luan, Bowu, Holehouse, Alex S., Raleigh, Daniel P.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 936 KB

english, 2018

37

Transcription factor dimerization activates the p300 acetyltransferase

Ortega, Esther, Rengachari, Srinivasan, Ibrahim, Ziad, Hoghoughi, Naghmeh, Gaucher, Jonathan, Holehouse, Alex S., Khochbin, Saadi, Panne, Daniel

Journal:

Year:

2018

Language:

english

File:

PDF, 14.86 MB

english, 2018

38

Large-Scale Analysis of the Evolution of Functions Mediated by Intrinsically Disordered Regions

Richardson, Mary O.G., Holehouse, Alex S., Langstein, Iris, Korber, Philipp, Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 38 KB

english, 2018

39

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

Ruff, Kiersten M, Pappu, Rohit V, Holehouse, Alex S

Journal:

Current Opinion in Structural Biology

Year:

2019

Language:

english

File:

PDF, 636 KB

english, 2019

40

Measures Adapted from Information Theory and Energy Landscape Theory for Quantifying Sequence-To-Conformation Relationships of Intrinsically Disordered Regions

Cohan, Megan, Holehouse, Alex S., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 41 KB

2019

41

Protein Unfolded States are Characterized by the Duality of Sequence-Specific Conformational Preferences and Ensemble-Averaged Features of Canonical Random Coils

Holehouse, Alex S., Peran, Ivan, Stenzoski, Natalie E., Zou, Junjie, Piserchio, Andrea, Ghose, Ranajeet, Carrico, Isaac S., Bilsel, Osman, Raleigh, Daniel P., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 65 KB

2019

42

Experimental and Theoretical Methods for Mapping Coexistence Curves of Phase-Separating Biological Macromolecules

Posey, Ammon E., Holehouse, Alex S., Ruff, Kiersten M., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 43 KB

2019

43

Experimental and Theoretical Methods for Mapping Coexistence Curves of Phase-Separating Biological Macromolecules

Posey, Ammon E., Holehouse, Alex S., Ruff, Kiersten M., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 43 KB

english, 2019

44

Protein Unfolded States are Characterized by the Duality of Sequence-Specific Conformational Preferences and Ensemble-Averaged Features of Canonical Random Coils

Holehouse, Alex S., Peran, Ivan, Stenzoski, Natalie E., Zou, Junjie, Piserchio, Andrea, Ghose, Ranajeet, Carrico, Isaac S., Bilsel, Osman, Raleigh, Daniel P., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 65 KB

english, 2019

45

Design and characterization of mutant and wild-type huntingtin proteins produced from a toolkit of scalable eukaryotic expression systems

Harding, Rachel J., Loppnau, Peter, Ackloo, Suzanne, Lemak, Alexander, Hutchinson, Ashley, Hunt, Brittany, Holehouse, Alex S., Ho, Jolene C., Fan, Lixin, Toledo-Sherman, Leticia, Seitova, Alma, Arrows

Journal:

Journal of Biological Chemistry

Year:

2019

Language:

english

File:

PDF, 1.72 MB

english, 2019

46

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

Boeynaems, Steven, Holehouse, Alex S., Weinhardt, Venera, Kovacs, Denes, Van Lindt, Joris, Larabell, Carolyn, Van Den Bosch, Ludo, Das, Rhiju, Tompa, Peter S., Pappu, Rohit V., Gitler, Aaron D.

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

File:

PDF, 1.95 MB

2019

47

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

Boeynaems, Steven, Holehouse, Alex S., Weinhardt, Venera, Kovacs, Denes, Van Lindt, Joris, Larabell, Carolyn, Van Den Bosch, Ludo, Das, Rhiju, Tompa, Peter S., Pappu, Rohit V., Gitler, Aaron D.

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

Language:

english

File:

PDF, 1.95 MB

english, 2019

48

Internal Structure of Network Fluid Condensates Formed by Liquid-Liquid Phase Separation of a Multivalent Oligomeric Protein and a Disordered Linear Peptide

Choi, Jeong-Mo, Mitrea, Diana M., Stanley, Christopher B., Ruff, Kiersten M., Holehouse, Alex S., Kriwacki, Richard W., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 44 KB

english, 2019

49

Internal Structure of Network Fluid Condensates Formed by Liquid-Liquid Phase Separation of a Multivalent Oligomeric Protein and a Disordered Linear Peptide

Choi, Jeong-Mo, Mitrea, Diana M., Stanley, Christopher B., Ruff, Kiersten M., Holehouse, Alex S., Kriwacki, Richard W., Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2019

File:

PDF, 44 KB

2019

50

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

Peran, Ivan, Holehouse, Alex S., Carrico, Isaac S., Pappu, Rohit V., Bilsel, Osman, Raleigh, Daniel P.

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

Language:

english

File:

PDF, 1.65 MB

english, 2019