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Constructing ensembles for intrinsically disordered proteins
Open accessAbstract
The relatively flat energy landscapes associated with intrinsically disordered proteins makes modeling these systems especially problematic. A comprehensive model for these proteins requires one to build an ensemble consisting of a finite collection of structures, and their corresponding relative stabilities, which adequately capture the range of accessible states of the protein. In this regard, methods that use computational techniques to interpret experimental data in terms of such ensembles are an essential part of the modeling process. In this review, we critically assess the advantages and limitations of current techniques and discuss new methods for the validation of these ensembles.
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Cites
Structural Polymorphism of 441-Residue Tau at Single Residue Resolution
Mukrasch, M. D., Bibow, S., Korukottu, J., Jeganathan, S., Biernat, J., Griesinger, C., Mandelkow, E., & Zweckstetter, M. (2009) · PLoS Biology · doi:10.1371/journal.pbio.1000034 · Cited by 652
Fischer, D., Mukrasch, M. D., Biernat, J., Bibow, S., Blackledge, M., Griesinger, C., Mandelkow, E., & Zweckstetter, M. (2009) · Biochemistry · doi:10.1021/bi901090m · Cited by 149
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The ensemble nature of allostery
Motlagh, H. N., Wrabl, J. O., Li, J., & Hilser, V. J. (2014) · Nature · doi:10.1038/nature13001 · Cited by 1,247
AlphaFold2: A Role for Disordered Protein/Region Prediction?
Wilson, C. J., Choy, W.-Y., & Karttunen, M. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23094591 · Cited by 173
Finding Our Way in the Dark Proteome
Bhowmick, A., Brookes, D. H., Yost, S. R., Dyson, H. J., Forman-Kay, J. D., Gunter, D., Head-Gordon, M., Hura, G. L., Pande, V. S., Wemmer, D. E., et al. (2016) · Journal of the American Chemical Society · doi:10.1021/jacs.6b06543 · Cited by 128
From a structural average to the conformational ensemble of a DNA bulge
Shi, X., Beauchamp, K. A., Harbury, P. B., & Herschlag, D. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1317032111 · Cited by 38
Terakawa, T., Higo, J., & Takada, S. (2014) · Biophysical Journal · doi:10.1016/j.bpj.2014.06.026 · Cited by 32
Networks of Networks: An Essay on Multi-Level Biological Organization
Uversky, V. N., & Giuliani, A. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.706260 · Cited by 28
Brown, A. H., Rodger, P. M., Evans, J. S., & Walsh, T. R. (2014) · Biomacromolecules · doi:10.1021/bm501263s · Cited by 28
AlphaFold2 modeling and molecular dynamics simulations of an intrinsically disordered protein
Guo, H.-B., Huntington, B., Perminov, A., Smith, K., Hastings, N., Dennis, P., Kelley-Loughnane, N., & Berry, R. (2024) · PLOS ONE · doi:10.1371/journal.pone.0301866 · Cited by 13
Conformational Characterization of Intrinsically Disordered Proteins and Its Biological Significance
Delaforge, E., Cordeiro, T. N., Bernadó, P., & Sibille, N. (2018) · Modern Magnetic Resonance · doi:10.1007/978-3-319-28388-3_52 · Cited by 7
Sandelin, A. E., Nencini, R., Yasar, E., Fudo, S., Stratoulias, V., Kajander, T., & Ollila, O. H. S. (2025) · Communications Chemistry · doi:10.1038/s42004-025-01623-x · Cited by 5
Metadata
- Authors
- Fisher, C. K., & Stultz, C. M.
- Venue
- Current Opinion in Structural Biology
- Publisher
- Elsevier BV
- Published
- 2011-06
- Volume
- 21
- Issue
- 3
- Pages
- 426-431
- ISSN
- 0959-440X (ISSN-L)
- OpenAlex
- W1972013995
- Cited by
- 275
- References
- 2
- FWCI
- 1.61
- Type
- journal article
- Language
- en
- Open access
- green
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