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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

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

3

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

4

FUS Zigzags Its Way to Cross Beta

Holehouse, Alex S., Pappu, Rohit V.

Journal:

Year:

2017

Language:

english

File:

PDF, 802 KB

english, 2017

5

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

6

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

7

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

8

The Cold-Unfolded State is Expanded but Contains Long- and Medium-range Contacts and Is Poorly Described by Homopolymer Models

Stenzoski, Natalie E, Zou, Junjie, Piserchio, Andrea, Ghose, Ranajeet, Holehouse, Alex S, Raleigh, Daniel P.

Journal:

Year:

2020

File:

PDF, 1.17 MB

2020

9

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

10

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

11

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

12

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

13

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

14

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

15

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

16

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

Powers, Samantha K., Holehouse, Alex S., Korasick, David A., Schreiber, Katherine H., Clark, Natalie M., Jing, Hongwei, Emenecker, Ryan, Han, Soeun, Tycksen, Eric, Hwang, Ildoo, Sozzani, Rosangela, Je

Journal:

Year:

2019

File:

PDF, 4.59 MB

2019

17

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

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

Journal:

Biophysical Journal

Year:

2018

File:

PDF, 48 KB

2018

18

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

19

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

20

Evolutionarily Conserved Amino Acid Organization in Protein Low Complexity Regions Encodes Conformation, Dynamics and Assembly

Martin, Erik W., Holehouse, Alex S., Peran, Ivan, Incicco, Jeremias, Soranno, Andrea, Pappu, Rohit V., Mittag, Tanja

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 42 KB

2020

21

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

22

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

23

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

24

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

25

Investigating the ferric ion binding site of magnetite biomineralisation protein Mms6

Rawlings, Andrea E., Liravi, Panah, Corbett, Sybilla, Holehouse, Alex S., Staniland, Sarah S., Permyakov, Eugene A.

Journal:

Year:

2020

File:

PDF, 1.05 MB

2020

26

Integrative Sequence-Based Classification of Intrinsically Disordered Regions

Ginell, Garrett M., Lalmansingh, Jared, Cohan, Megan C., Holehouse, Alex S.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 48 KB

2020

27

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

28

Functional Implications of Intracellular Phase Transitions

Holehouse, Alex S, Pappu, Rohit V

Journal:

Year:

2018

Language:

english

File:

PDF, 1.16 MB

english, 2018

29

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

30

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

31

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

32

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

33

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

34

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

35

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

36

Arginine-Enriched Mixed-Charge Domains Provide Cohesion for Nuclear Speckle Condensation

Greig, Jamie A., Nguyen, Tu Anh, Lee, Michelle, Holehouse, Alex S., Posey, Ammon E., Pappu, Rohit V., Jedd, Gregory

Journal:

Year:

2020

File:

PDF, 5.27 MB

2020

37

Tuning the Activity of Disordered Proteins by Changing Solution Conditions

Moses, David, Yu, Feng, Holehouse, Alex S., Sukenik, Shahar

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 44 KB

2020

38

Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment

Moses, David, Yu, Feng, Ginell, Garrett M., Shamoon, Nora M., Koenig, Patrick S., Holehouse, Alex S., Sukenik, Shahar

Journal:

The Journal of Physical Chemistry Letters

Year:

2020

File:

PDF, 3.84 MB

2020

39

[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

40

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

41

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

42

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

43

Changes to the Intracellular Milieu Control the Population and Residual Structure of Unfolded Proteins

Wang, Yuhang, Davis, Caitlin, Holehouse, Alex S., Gruebele, Martin, Sukenik, Shahar

Journal:

Biophysical Journal

Year:

2019

Language:

english

File:

PDF, 43 KB

english, 2019

44

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

45

Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning

Holehouse, Alex S, Sukenik, Shahar

Journal:

Journal of Chemical Theory and Computation

Year:

2020

File:

PDF, 1.27 MB

2020

46

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

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

File:

PDF, 1.95 MB

2019

48

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

49

Connecting Coil-to-Globule Transitions to Full Phase Diagrams for Intrinsically Disordered Proteins

Zeng, Xiangze, Holehouse, Alex S., Chilkoti, Ashutosh, Mittag, Tanja, Pappu, Rohit V.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 2.21 MB

2020

50

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

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