Thursday, July 30, 2026
No menu items!
HomeNatureRational design of disordered proteins for sequence–function investigation

Rational design of disordered proteins for sequence–function investigation

  • Holehouse, A. S. & Kragelund, B. B. The molecular basis for cellular function of intrinsically disordered protein regions. Nat. Rev. Mol. Cell Biol. 25, 187–211 (2024).

    Article 
    PubMed 

    Google Scholar
     

  • Albanese, K. I., Barbe, S., Tagami, S., Woolfson, D. N. & Schiex, T. Computational protein design. Nat. Rev. Methods Primers 5, 13 (2025).

    Article 

    Google Scholar
     

  • Tesei, G., Pesce, F. & Lindorff-Larsen, K. Computational design of intrinsically disordered proteins. Curr. Opin. Struct. Biol. 96, 103210 (2026).

    Article 
    PubMed 

    Google Scholar
     

  • Moses, D. et al. Structural biases in disordered proteins are prevalent in the cell. Nat. Struct. Mol. Biol. 31, 283–292 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Das, R. K., Ruff, K. M. & Pappu, R. V. Relating sequence encoded information to form and function of intrinsically disordered proteins. Curr. Opin. Struct. Biol. 32, 102–112 (2015).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Das, R. K. & Pappu, R. V. Conformations of intrinsically disordered proteins are influenced by linear sequence distributions of oppositely charged residues. Proc. Natl Acad. Sci. USA 110, 13392–13397 (2013).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Staller, M. V. et al. A high-throughput mutational scan of an intrinsically disordered acidic transcriptional activation domain. Cell Syst. 6, 444–455 (2018).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Pesce, F. et al. Design of intrinsically disordered protein variants with diverse structural properties. Sci. Adv. 10, eadm9926 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zarin, T., Tsai, C. N., Nguyen Ba, A. N. & Moses, A. M. Selection maintains signaling function of a highly diverged intrinsically disordered region. Proc. Natl Acad. Sci. USA 114, E1450–E1459 (2017).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Das, R. K., Huang, Y., Phillips, A. H., Kriwacki, R. W. & Pappu, R. V. Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling. Proc. Natl Acad. Sci. USA 113, 5616–5621 (2016).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Holehouse, A. S., Das, R. K., Ahad, J. N., Richardson, M. O. G. & Pappu, R. V. CIDER: resources to analyze sequence-ensemble relationships of intrinsically disordered proteins. Biophys. J. 112, 16–21 (2017).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Novak, B., Lotthammer, J. M., Emenecker, R. J. & Holehouse, A. S. Accurate predictions of disordered protein ensembles with STARLING. Nature 652, 240–250 (2026).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • González-Foutel, N. S. et al. Conformational buffering underlies functional selection in intrinsically disordered protein regions. Nat. Struct. Mol. Biol. 29, 781–790 (2022).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Zeno, W. F. et al. Molecular mechanisms of membrane curvature sensing by a disordered protein. J. Am. Chem. Soc. 141, 10361–10371 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Halladin, D. K. et al. Entropy-driven translocation of disordered proteins through the Gram-positive bacterial cell wall. Nat. Microbiol. 6, 1055–1065 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Berlow, R. B., Dyson, H. J. & Wright, P. E. Hypersensitive termination of the hypoxic response by a disordered protein switch. Nature 543, 447–451 (2017).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Schuler, B., König, I., Soranno, A. & Nettels, D. Impact of in-cell and in-vitro crowding on the conformations and dynamics of an intrinsically disordered protein. Angew. Chem. Int. Ed. https://doi.org/10.1002/anie.202016804 (2021).

  • Ruff, K. M. et al Molecular grammars of predicted intrinsically disordered regions that span the human proteome. Cell 189, 323–342 (2025).

  • Moses, D. et al. Revealing the hidden sensitivity of intrinsically disordered proteins to their chemical environment. J. Phys. Chem. Lett. 11, 10131–10136 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marsh, J. A. & Forman-Kay, J. D. Sequence determinants of compaction in intrinsically disordered proteins. Biophys. J. 98, 2383–2390 (2010).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Müller-Späth, S. et al. From the cover: charge interactions can dominate the dimensions of intrinsically disordered proteins. Proc. Natl Acad. Sci. USA 107, 14609–14614 (2010).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Mao, A. H., Crick, S. L., Vitalis, A., Chicoine, C. L. & Pappu, R. V. Net charge per residue modulates conformational ensembles of intrinsically disordered proteins. Proc. Natl Acad. Sci. USA 107, 8183–8188 (2010).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sørensen, C. S. & Kjaergaard, M. Effective concentrations enforced by intrinsically disordered linkers are governed by polymer physics. Proc. Natl Acad. Sci. USA 116, 23124–23131 (2019).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Boeynaems, S. et al. Aberrant phase separation is a common killing strategy of positively charged peptides in biology and human disease. Preprint at bioRxiv https://doi.org/10.1101/2023.03.09.531820 (2023).

  • Schmidt, H. B. & Görlich, D. Transport selectivity of nuclear pores, phase separation, and membraneless organelles. Trends Biochem. Sci. 41, 46–61 (2016).

    Article 
    PubMed 

    Google Scholar
     

  • Enriquez-Toledo, C. et al. A molecular grammar for environmental sensitivity in intrinsically disordered protein regions. Preprint at bioRxiv https://doi.org/10.64898/2026.04.20.719774 (2026).

  • Soranno, A. et al. Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. Proc. Natl Acad. Sci. USA 111, 4874–4879 (2014).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Sukenik, S., Ren, P. & Gruebele, M. Weak protein-protein interactions in live cells are quantified by cell-volume modulation. Proc. Natl Acad. Sci. USA 114, 6776–6781 (2017).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Speer, S. L., Stewart, C. J., Sapir, L., Harries, D. & Pielak, G. J. Macromolecular crowding is more than hard-core repulsions. Annu. Rev. Biophys. https://doi.org/10.1146/annurev-biophys-091321-071829 (2022).

  • Ginell, G. M. et al. Sequence-based prediction of intermolecular interactions driven by disordered regions. Science 388, eadq8381 (2025).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Martin, E. W. et al. Valence and patterning of aromatic residues determine the phase behavior of prion-like domains. Science 367, 694–699 (2020).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Wang, J. et al. A molecular grammar governing the driving forces for phase separation of prion-like RNA binding proteins. Cell 174, 688–699 (2018).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Marks, R. A. et al. Life on the dry side: a roadmap to understanding desiccation tolerance and accelerating translational applications. Nat. Commun. 16, 3284 (2025).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Olgenblum, G. I., Hutcheson, B. O., Pielak, G. J. & Harries, D. Protecting proteins from desiccation stress using molecular glasses and gels. Chem. Rev. 124, 5668–5694 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hibshman, J. D. & Goldstein, B. LEA motifs promote desiccation tolerance in vivo. BMC Biol. 19, 263 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Nguyen, K. et al. A phase transition modulates the protective function of a tardigrade disordered protein during desiccation. Protein Sci. 34, e70300 (2025).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lotthammer, J. M., Ginell, G. M., Griffith, D., Emenecker, R. J. & Holehouse, A. S. Direct prediction of intrinsically disordered protein conformational properties from sequence. Nat. Methods 21, 465–476 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tolleter, D. et al. Structure and function of a mitochondrial late embryogenesis abundant protein are revealed by desiccation. Plant Cell 19, 1580–1589 (2007).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Bremer, A., Wolff, M., Thalhammer, A. & Hincha, D. K. Folding of intrinsically disordered plant LEA proteins is driven by glycerol-induced crowding and the presence of membranes. FEBS J. 284, 919–936 (2017).

    Article 
    PubMed 

    Google Scholar
     

  • Shraddha, K. C. et al. Disordered proteins interact with the chemical environment to tune their protective function during drying. eLife 13, RP97231 (2024).

    Article 

    Google Scholar
     

  • Nicholson, V., Maharjan, S., Sukenik, S. & Boothby, T. C. OsmoFold: a high-throughput tool for predicting the impact of osmolytes on protein structure. Biophys. J. https://doi.org/10.1016/j.bpj.2025.08.034 (2025).

  • Malki, A. et al. Fibril structure of desiccation-protective tardigrade protein CAHS-8. Angew. Chem. Int. Ed. 65, e19912 (2026).

    Article 

    Google Scholar
     

  • Sanchez-Martinez, S. et al. Labile assembly of a tardigrade protein induces biostasis. Protein Sci. 33, e4941 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Romero-Perez, P. S., Dorone, Y., Flores, E., Sukenik, S. & Boeynaems, S. When phased without water: biophysics of cellular desiccation, from biomolecules to condensates. Chem. Rev. 123, 9010–9035 (2023).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Langstein-Skora, I. et al. Sequence and chemical specificity define the functional landscape of intrinsically disordered regions. Nat. Cell Biol. 28, 323–337 (2026).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Greig, J. A. et al. Arginine-enriched mixed-charge domains provide cohesion for nuclear speckle condensation. Mol. Cell 77, 1237–1250 (2020).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Romero-Pérez, P. S. et al. Protein surface chemistry encodes an adaptive tolerance to desiccation. Cell Syst. 16, 101407 (2025).

    Article 
    PubMed 

    Google Scholar
     

  • Solomon, D. A. et al. C9ORF72-derived polyGR polypeptides disrupt passive nucleocytoplasmic transport by tuning protein affinity for the nuclear pore barrier. Preprint at bioRxiv https://doi.org/10.64898/2026.03.16.711670 (2026).

  • Alshareedah, I. et al. Sequence-specific interactions determine viscoelasticity and aging dynamics of protein condensates. Nat. Phys. 20, 1482–1491 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Battaglia, M., Olvera-Carrillo, Y., Garciarrubio, A., Campos, F. & Covarrubias, A. A. The enigmatic LEA proteins and other hydrophilins. Plant Physiol. 148, 6–24 (2008).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tesei, G. et al. Conformational ensembles of the human intrinsically disordered proteome. Nature 626, 897–904 (2024).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Pritišanac, I. et al. A functional map of the human intrinsically disordered proteome. Proc. Natl Acad. Sci. USA 123, e2604562123 (2026).

  • Alamdari, S. et al. Protein generation with evolutionary diffusion: sequence is all you need. Preprint at bioRxiv https://doi.org/10.1101/2023.09.11.556673 (2023).

  • Strome, B., Elemam, K., Pritisanac, I., Forman-Kay, J. D. & Moses, A. M. Computational design of intrinsically disordered protein regions by matching bulk molecular properties. Preprint at bioRxiv https://doi.org/10.1101/2023.04.28.538739 (2023).

  • Krueger, R. K., Brenner, M. P. & Shrinivas, K. Generalized design of sequence–ensemble–function relationships for intrinsically disordered proteins. Nat. Comput. Sci. 6, 512–523 (2025).

  • Bhat, S. et al. De novo design of peptide binders to conformationally diverse targets with contrastive language modeling. Sci. Adv. 11, eadr8638 (2025).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Chen, L. T. et al. Target sequence-conditioned design of peptide binders using masked language modeling. Nat. Biotechnol. 44, 1002–1010 (2025).

  • An, Y., Webb, M. A. & Jacobs, W. M. Active learning of the thermodynamics-dynamics trade-off in protein condensates. Sci. Adv. 10, eadj2448 (2024).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Brown, C. J., Johnson, A. K., Dunker, A. K. & Daughdrill, G. W. Evolution and disorder. Curr. Opin. Struct. Biol. 21, 441–446 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lin, Z. et al. Evolutionary-scale prediction of atomic-level protein structure with a language model. Science 379, 1123–1130 (2023).

    Article 
    ADS 
    MathSciNet 
    PubMed 

    Google Scholar
     

  • Liu, J. X. et al. Generative design of intrinsically disordered protein regions with IDiom. Preprint at bioRxiv https://doi.org/10.64898/2026.04.10.717777 (2026).

  • Joseph, J. A. et al. Physics-driven coarse-grained model for biomolecular phase separation with near-quantitative accuracy. Nat. Comput. Sci. 1, 732–743 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Tesei, G. & Lindorff-Larsen, K. Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range. Open Res. Eur. 2, 94 (2022).

    Article 
    PubMed 

    Google Scholar
     

  • Lotthammer, J. M. et al Metapredict enables accurate disorder prediction across the Tree of Life. Preprint at bioRxiv https://doi.org/10.1101/2024.11.05.622168 (2024).

  • Stringer, C., Wang, T., Michaelos, M. & Pachitariu, M. Cellpose: a generalist algorithm for cellular segmentation. Nat. Methods 18, 100–106 (2021).

    Article 
    PubMed 

    Google Scholar
     

  • Thevenaz, P., Ruttimann, U. E. & Unser, M. A pyramid approach to subpixel registration based on intensity. IEEE Trans. Image Process. 7, 27–41 (1998).

    Article 
    ADS 
    PubMed 

    Google Scholar
     

  • Abraham, M. J. et al. GROMACS: high performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX 1–2, 19–25 (2015).

    Article 
    ADS 

    Google Scholar
     

  • Wang, L., Brasnett, C., Borges-Araújo, L., Souza, P. C. T. & Marrink, S. J. Martini3-IDP: improved Martini 3 force field for disordered proteins. Nat. Commun. 16, 2874 (2025).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Grünewald, F. et al. Polyply; a Python suite for facilitating simulations of macromolecules and nanomaterials. Nat. Commun. 13, 68 (2022).

    Article 
    ADS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Lambert, T. J. FPbase: a community-editable fluorescent protein database. Nat. Methods 16, 277–278 (2019).

    Article 
    PubMed 

    Google Scholar
     

  • Joska, T. M., Mashruwala, A., Boyd, J. M. & Belden, W. J. A universal cloning method based on yeast homologous recombination that is simple, efficient, and versatile. J. Microbiol. Methods 100, 46–51 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hood, S. & Lewis, J. A. High-efficiency yeast electroporation v.2. Protocols.io https://doi.org/10.17504/protocols.io.5qpvorr69v4o/v2 (2022).

  • Calahan, D., Dunham, M., DeSevo, C. & Koshland, D. E. Genetic analysis of desiccation tolerance in Saccharomyces cerevisiae. Genetics 189, 507–519 (2011).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Stokes, R. H. & Robinson, R. A. Standard solutions for humidity control at 25 °C. Ind. Eng. Chem. 41, 2013–2013 (1949).

    Article 

    Google Scholar
     

  • Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Dunham, M., Gartenberg, M. & Brown, G. W. Methods in Yeast Genetics and Genomics: A Cold Spring Harbor Laboratory Course Manual, 2015 Edition (Cold Spring Harbor Laboratory Press, 2015)

  • Li, C. H. & Lee, C. K. Minimum cross entropy thresholding. Pattern Recognit. 26, 617–625 (1993).

    Article 
    ADS 

    Google Scholar
     

  • Virtanen, P. et al. SciPy 1.0: fundamental algorithms for scientific computing in Python. Nat. Methods 17, 261–272 (2020).

    Article 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Hunter, K. et al. Data for ‘Rational design of disordered proteins for sequence–function investigation’. Zenodo https://doi.org/10.5281/zenodo.18717144 (2026).

  • RELATED ARTICLES

    Most Popular

    Recent Comments