The DOI matches its Crossref record; 39 of the 39 references it cites were found in a registry or an index.
Protein topology determines binding mechanism
Open accessAbstract
Protein recognition and binding, which result in either transient or long-lived complexes, play a fundamental role in many biological functions, but sometimes also result in pathologic aggregates. We use a simplified simulation model to survey a range of systems where two highly flexible protein chains form a homodimer. In all cases, this model, which corresponds to a perfectly funneled energy landscape for folding and binding, reproduces the macroscopic experimental observations on whether folding and binding are coupled in one step or whether intermediates occur. Owing to the minimal frustration principle, we find that, as in the case of protein folding, the native topology is the major factor that governs the choice of binding mechanism. Even when the monomer is stable on its own, binding sometimes occurs fastest through unfolded intermediates, thus showing the speedup envisioned in the fly-casting scenario for molecular recognition.
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Citations
Cites
Principles of protein-protein interactions
Jones, S., & Thornton, J. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.1.13 · Cited by 2,684
Optimized Monte Carlo data analysis
Ferrenberg, A. M., & Swendsen, R. H. (1989) · Physical Review Letters · doi:10.1103/physrevlett.63.1195 · Cited by 2,590
Application of a Theory of Enzyme Specificity to Protein Synthesis
Koshland, D. E. (1958) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.44.2.98 · Cited by 2,396
Intrinsically disordered protein
Dunker, A. K., Lawson, J. D., Brown, C. J., Williams, R. M., Romero, P., Oh, J. S., Oldfield, C. J., Campen, A. M., Ratliff, C. M., Hipps, K. W., et al. (2001) · Journal of Molecular Graphics and Modelling · doi:10.1016/s1093-3263(00)00138-8 · Cited by 2,272
Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding
Fersht, A. (2017) · Series in Structural Biology · doi:10.1142/10574 · Cited by 2,039
Natively unfolded proteins: A point where biology waits for physics
Uversky, V. N. (2002) · Protein Science · doi:10.1110/ps.4210102 · Cited by 1,813
Intrinsically Disordered Proteins
Uversky, V. N. (2013) · Brenner's Encyclopedia of Genetics · doi:10.1016/b978-0-12-374984-0.01698-3 · Cited by 1,637
Coupling of Local Folding to Site-Specific Binding of Proteins to DNA
Spolar, R. S., & Record, M. T. (1994) · Science · doi:10.1126/science.8303294 · Cited by 1,401
Coupling of folding and binding for unstructured proteins
Dyson, H. J., & Wright, P. E. (2002) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(02)00289-0 · Cited by 1,327
Clementi, C., Nymeyer, H., & Onuchic, J. N. (2000) · Journal of Molecular Biology · doi:10.1006/jmbi.2000.3693 · Cited by 1,240
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Cited by
Onuchic, J. N., & Wolynes, P. G. (2004) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2004.01.009 · Cited by 1,301
Self-citationWATER MEDIATION IN PROTEIN FOLDING AND MOLECULAR RECOGNITION
Levy, Y., & Onuchic, J. N. (2006) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.35.040405.102134 · Cited by 1,048
Self-citationPerspective: Coarse-grained models for biomolecular systems
Noid, W. G. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4818908 · Cited by 893
Clore, G. M., & Iwahara, J. (2009) · Chemical Reviews · doi:10.1021/cr900033p · Cited by 782
The power of coarse graining in biomolecular simulations
Ingólfsson, H. I., Lopez, C. A., Uusitalo, J. J., de Jong, D. H., Gopal, S. M., Periole, X., & Marrink, S. J. (2014) · WIREs Computational Molecular Science · doi:10.1002/wcms.1169 · Cited by 572
Metadata
- Authors
- Levy, Y., Wolynes, P. G., & Onuchic, J. N.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2003-12-23
- Volume
- 101
- Issue
- 2
- Pages
- 511-516
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2053960740
- Cited by
- 324
- References
- 39
- FWCI
- 6.00
- Type
- journal article
- Language
- en
- Open access
- green
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