Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) are important components in the cellular function and their biological role has been the focus of a growing number of publications. “Liquid-like" granules rich in intrinsically disordered proteins and RNA play key roles in critical cellular functions such as RNA processing and translation. These complexes or RNA and RNA-binding proteins, known as Ribonucleoproteins (RNP), are commonly involved in processing RNA transcripts and mediate cell function in response to stress and other environmental perturbations. The malfunction of these granules has been implicated in numerous diseases, however the mechanistic underpinnings of these disease states is not well understood. Elastin-like polypeptides (ELPs) are a family of lab-designed IDPs which, while not normally found in nature, share many of the same characteristics as natural IDPs including temperature responsiveness and salt/pH sensitivity. Since ELPs are genetically encoded as a sequence of amino acids, they can be fused to various RNA binding proteins and form synthetic IDP-RNA-rich granules. These synthetic granules can be engineered for a variety of synthetic biology applications. For example, one can recreate natural IDP-RNA granules using synthetic IDP-RNA granules to study the mechanistic underpinnings of natural systems and their disease states. From a genetic engineering standpoint, one can use ELPs fused to a protein targeting specific mRNAs to modulate gene expression by sequestering target mRNA using ELPs' temperature-responsive phase separation activity.

An Ode to IDP's, by Daniel Shapiro:

IDP intrinsically disordered
IDP sway
IDP protein
IDP binds RNA

IDP clump
IDP sequester
IDP hides RNA
Ribosome can’t get ‘er

IDP wiggle
IDP repeat
IDP jiggle
IDP VPGVGeet

IDP turn gene off
IDP inhibit
IDP doesn’t work as expected
IDP a whole clown exhibit

IDP at 20 degrees
IDP soluble
IDP at 37 degrees?
IDP insoluble

IDP is love
IDP is life
IDP doesn’t purify
IDP causes me strife

IDP I love you
IDP is for me
IDP controls gene expression
IDP makes my PhD

Publications

Strader, Rachel L., Yulia Shmidov, and Ashutosh Chilkoti. “Encoding Structure in Intrinsically Disordered Protein Biomaterials.” Accounts of Chemical Research 57, no. 3 (February 2024): 302–11. https://doi.org/10.1021/acs.accounts.3c00624.

Sethi, Vaishali, Dana Cohen-Gerassi, Sagi Meir, Max Ney, Yulia Shmidov, Gil Koren, Lihi Adler-Abramovich, Ashutosh Chilkoti, and Roy Beck. “Modulating hierarchical self-assembly in thermoresponsive intrinsically disordered proteins through high-temperature incubation time.” Scientific Reports 13, no. 1 (December 2023): 21688. https://doi.org/10.1038/s41598-023-48483-w.

Dai, Yifan, Christian F. Chamberlayne, Marco S. Messina, Christopher J. Chang, Richard N. Zare, Lingchong You, and Ashutosh Chilkoti. “Interface of biomolecular condensates modulates redox reactions.” Chem 9, no. 6 (June 2023): 1594–1609. https://doi.org/10.1016/j.chempr.2023.04.001.

Dai, Yifan, Mina Farag, Dongheon Lee, Xiangze Zeng, Kyeri Kim, Hye-In Son, Xiao Guo, et al. “Programmable synthetic biomolecular condensates for cellular control.” Nature Chemical Biology 19, no. 4 (April 2023): 518–28. https://doi.org/10.1038/s41589-022-01252-8.

Y. Dai, You, L. , and Chilkoti, A. , “Engineering synthetic biomolecular condensates”, Nature Reviews Bioengineering, 2023.

Roden, Christine A., Yifan Dai, Catherine A. Giannetti, Ian Seim, Myungwoon Lee, Rachel Sealfon, Grace A. McLaughlin, et al. “Double-stranded RNA drives SARS-CoV-2 nucleocapsid protein to undergo phase separation at specific temperatures.” Nucleic Acids Res 50, no. 14 (August 12, 2022): 8168–92. https://doi.org/10.1093/nar/gkac596.

Shapiro, Daniel Mark, Max Ney, Seyed Ali Eghtesadi, and Ashutosh Chilkoti. “Protein Phase Separation Arising from Intrinsic Disorder: First-Principles to Bespoke Applications.” The Journal of Physical Chemistry. B 125, no. 25 (July 2021): 6740–59. https://doi.org/10.1021/acs.jpcb.1c01146.

Dzuricky, Michael, Bradley A. Rogers, Abdulla Shahid, Paul S. Cremer, and Ashutosh Chilkoti. “De novo engineering of intracellular condensates using artificial disordered proteins.” Nature Chemistry 12, no. 9 (September 2020): 814–25. https://doi.org/10.1038/s41557-020-0511-7.

Roberts, Stefan, Vincent Miao, Simone Costa, Joseph Simon, Garrett Kelly, Tejank Shah, Stefan Zauscher, and Ashutosh Chilkoti. “Complex microparticle architectures from stimuli-responsive intrinsically disordered proteins.” Nature Communications 11, no. 1 (March 2020): 1342. https://doi.org/10.1038/s41467-020-15128-9.

Simon, Joseph R., Seyed Ali Eghtesadi, Michael Dzuricky, Lingchong You, and Ashutosh Chilkoti. “Engineered Ribonucleoprotein Granules Inhibit Translation in Protocells.” Molecular Cell 75, no. 1 (July 2019): 66-75.e5. https://doi.org/10.1016/j.molcel.2019.05.010.

Banskota, Samagya, Parisa Yousefpour, Nadia Kirmani, Xinghai Li, and Ashutosh Chilkoti. “Long circulating genetically encoded intrinsically disordered zwitterionic polypeptides for drug delivery.” Biomaterials 192 (February 2019): 475–85. https://doi.org/10.1016/j.biomaterials.2018.11.012.