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--> Search for: Home Faculty Members Departmental Information Directories Giving Webmail Home Faculty Members Departmental Information Directories Giving Webmail Search for: Alex Holehouse Assistant Professor Biochemistry and Molecular Biophysics Lab Website Publications (PubMed / NIH) Office: 223B McDonnell Sciences Building Phone: 314-273-8371 Email: [email protected]   Research We explore how intrinsically disordered protein regions confer biological function and how this goes wrong in disease. The lab integrates physics-based models (all-atom and coarse-grained simulations) with informatics and machine learning to develop sequence-specific predictions. We then test those predictions either within the lab, or with collaborators around the world. Of particular interest is understanding how disordered proteins drive self-assembly in the context of biological phase separation, with a major emphasis on understanding when, how, and why this might be important for normal cellular function. Select Publications Jasmine Cubuk, Lina Greenberg, Akiva E Greenberg, Ryan J Emenecker, Melissa D Stuchell-Brereton, Alex S Holehouse, Andrea Soranno &＃038; Michael J Greenberg (2024). &＃8220;Structural dynamics of the intrinsically disordered linker region of cardiac troponin T&＃8221; bioRxiv. [Preprint]. 2024 May 31:2024.05.30.596451. doi: 10.1101/2024.05.30.596451. (Abstract) Jasmine Cubuk, Jhullian J Alston, J Jeremías Incicco, Alex S Holehouse, Kathleen B Hall, Melissa D Stuchell-Brereton &＃038; Andrea Soranno (2024). &＃8220;The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA&＃8221; Nucleic Acids Res. 2024 Mar 21;52(5):2609-2624. doi: 10.1093/nar/gkad1215. (Abstract) Garrett M. Ginell &＃038; Alex S. Holehouse (2022). &＃8220;An Introduction to the Stickers-and-Spacers Framework as Applied to Biomolecular Condensates&＃8221; Methods Mol Biol. 2023;2563:95-116. doi: 10.1007/978-1-0716-2663-4_4. (Abstract) Nicolás S. González-Foutel, Juliana Glavina, Wade M. Borcherds, Matías Safranchik, Susana Barrera-Vilarmau, Amin Sagar, Alejandro Estaña, Amelie Barozet, Nicolás A. Garrone, Gregorio Fernandez-Ballester, Clara Blanes-Mira, Ignacio E. Sánchez, Gonzalo de Prat-Gay, Juan Cortés, Pau Bernadó, Rohit V. Pappu, Alex S. Holehouse, Gary W. Daughdrill, &＃038; Lucía B. Chemes (2022). &＃8220;Conformational buffering underlies functional selection in intrinsically disordered protein regions&＃8221; Nat Struct Mol Biol. 2022 Aug;29(8):781-790. doi: 10.1038/s41594-022-00811-w. Epub 2022 Aug 10. (Abstract) Daniel Griffith &＃038; Alex S. Holehouse (2021). &＃8220;PARROT is a flexible recurrent neural network framework for analysis of large protein datasets&＃8221; Elife. 2021 Sep 17;10:e70576. doi: 10.7554/eLife.70576. (Abstract) Ishan Taneja &＃038; Alex S. Holehouse (2021). &＃8220;Folded domain charge properties influence the conformational behavior of disordered tails&＃8221; Curr Res Struct Biol. 2021 Sep 7;3:216-228. doi: 10.1016/j.crstbi.2021.08.002. eCollection 2021. (Abstract) Ryan J. Emenecker, Daniel Griffith, &＃038; Alex S. Holehouse (2021). &＃8220;Metapredict: a fast, accurate, and easy-to-use predictor of consensus disorder and structure&＃8221; Biophys J. 2021 Sep 2;S0006-3495(21)00725-6. doi: 10.1016/j.bpj.2021.08.039. Online ahead of print. (Abstract) Yanniv Dorone, Steven Boeynaems, Eduardo Flores, Benjamin Jin, Shannon Hateley, Flavia Bossi, Elena Lazarus, Janice G. Pennington, Emiel Michiels, Mathias De Decker, Katlijn Vints, Pieter Baatsen, George W. Bassel, Marisa S. Otegui, Alex S. Holehouse, Moises Exposito-Alonso, Shahar Sukenik, Aaron D. Gitler, Seung Y. Rhee (2021). &＃8220;A prion-like protein regulator of seed germination undergoes hydration-dependent phase separation&＃8221; Cell. 2021 Aug 5;184(16):4284-4298.e27. doi: 10.1016/j.cell.2021.06.009. Epub 2021 Jul 6. (Abstract) Shubhanjali Minhas &＃038; Alex S. Holehouse (2021). &＃8220;Step on the cGAS! Viral inhibition of cGAS phase separation with cytosolic DNA&＃8221; Mol Cell. 2021 Jul 1;81(13):2688-2689. doi: 10.1016/j.molcel.2021.06.007. (Abstract) Ryan J. Emenecker, Alex S. Holehouse, &＃038; Lucia C. Strader (2021). &＃8220;Sequence determinants of in cell condensate morphology, dynamics, and oligomerization as measured by number and brightness analysis&＃8221; Cell Commun Signal. 2021 Jun 5;19(1):65. doi: 10.1186/s12964-021-00744-9. (Abstract) E. Sethe Burgie, Zachary T. K. Gannam, Katrice E. McLoughlin, Christopher D. Sherman, Alex S. Holehouse, Robert J. Stankey, &＃038; Richard D. Vierstra (2021). &＃8220;Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families&＃8221; Proc Natl Acad Sci U S A. 2021 Jun 1;118(22):e2105649118. doi: 10.1073/pnas.2105649118. (Abstract) Jasmine Cubuk, Jhullian J. Alston, J. Jeremías Incicco, Sukrit Singh, Melissa D. Stuchell-Brereton, Michael D. Ward, Maxwell I. Zimmerman, Neha Vithani, Daniel Griffith, Jason A. Wagoner, Gregory R. Bowman, Kathleen B. Hall, Andrea Soranno, &＃038; Alex S. Holehouse. (2021). &＃8220;The SARS-CoV-2 nucleocapsid protein is dynamic, disordered, and phase separates with RNA&＃8221; Nat Commun. 2021 Mar 29;12(1):1936. doi: 10.1038/s41467-021-21953-3. (Abstract) Jason D Fernandes, Sarvenaz Sarabipour, Christopher T Smith, Natalie M Niemi, Nafisa M Jadavji, Ariangela J Kozik, Alex S Holehouse, Vikas Pejaver, Orsolya Symmons, Alexandre W Bisson Filho, &＃038; Amanda Haage (2020). &＃8220;A survey-based analysis of the academic job market&＃8221; Elife. 2020 Jun 12;9:e54097. doi: 10.7554/eLife.54097. Online ahead of print. (Abstract) Holehouse A.S. &＃038; Sukenik S. (2020). &＃8220;Controlling Structural Bias in Intrinsically Disordered Proteins Using Solution Space Scanning.&＃8221; J Chem Theory Comput. 2020 Mar 10;16(3):1794-1805. doi: 10.1021/acs.jctc.9b00604. Epub 2020 Feb 17. (Abstract) Rawlings A.E., Liravi P., Corbett S., Holehouse A.S., &＃038; Staniland S.S. (2020). &＃8220;Investigating the ferric ion binding site of magnetite biomineralisation protein Mms6.&＃8221; PLoS One. 2020 Feb 25;15(2):e0228708. doi: 10.1371/journal.pone.0228708. eCollection 2020. 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