The DOI matches its Crossref record; 6 of the 6 references it cites were found in a registry or an index.
Speeding molecular recognition by using the folding funnel: The fly-casting mechanism
Open accessAbstract
Protein folding and binding are kindred processes. Many proteins in the cell are unfolded, so folding and function are coupled. This paper investigates how binding kinetics is influenced by the folding of a protein. We find that a relatively unstructured protein molecule can have a greater capture radius for a specific binding site than the folded state with its restricted conformational freedom. In this scenario of binding, the unfolded state binds weakly at a relatively large distance followed by folding as the protein approaches the binding site: the “fly-casting mechanism.” We illustrate this scenario with the hypothetical kinetics of binding a single repressor molecule to a DNA site and find that the binding rate can be significantly enhanced over the rate of binding of a fully folded protein.
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Cites
Funnels, pathways, and the energy landscape of protein folding: A synthesis
Bryngelson, J. D., Onuchic, J. N., Socci, N. D., & Wolynes, P. G. (1995) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.340210302 · Cited by 2,648
Self-citationFrom Levinthal to pathways to funnels
Dill, K. A., & Chan, H. S. (1997) · Nature Structural & Molecular Biology · doi:10.1038/nsb0197-10 · Cited by 2,293
THEORY OF PROTEIN FOLDING: The Energy Landscape Perspective
Onuchic, J. N., Luthey-Schulten, Z., & Wolynes, P. G. (1997) · Annual Review of Physical Chemistry · doi:10.1146/annurev.physchem.48.1.545 · Cited by 2,210
Self-citationRadhakrishnan, I., Pérez-Alvarado, G. C., Parker, D., Dyson, H. J., Montminy, M. R., & Wright, P. E. (1997) · Cell · doi:10.1016/s0092-8674(00)80463-8 · Cited by 728
Toward an outline of the topography of a realistic protein-folding funnel.
Onuchic, J. N., Wolynes, P. G., Luthey-Schulten, Z., & Socci, N. D. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.8.3626 · Cited by 523
Self-citationThe nature of folded states of globular proteins
Honeycutt, J. D., & Thirumalai, D. (1992) · Biopolymers · doi:10.1002/bip.360320610 · Cited by 360
Cited by
Intrinsically unstructured proteins and their functions
Dyson, H. J., & Wright, P. E. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1589 · Cited by 3,871
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
Principles of docking: An overview of search algorithms and a guide to scoring functions
Halperin, I., Ma, B., Wolfson, H., & Nussinov, R. (2002) · Proteins: Structure, Function, and Bioinformatics · doi:10.1002/prot.10115 · Cited by 1,294
Intrinsically Disordered Proteins and Intrinsically Disordered Protein Regions
Oldfield, C. J., & Dunker, A. K. (2014) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-072711-164947 · Cited by 1,057
Identification of slow molecular order parameters for Markov model construction
Pérez-Hernández, G., Paul, F., Giorgino, T., De Fabritiis, G., & Noé, F. (2013) · The Journal of Chemical Physics · doi:10.1063/1.4811489 · Cited by 990
“…much interest (e.g. for the druggability of protein-protein interactions) to investigate whether the presence of pre-formed elements causes folded conformations to be selected from the ensemble (conformational selection) [54], or whether the binding rather occurs through induced-fit mechanics [85].”
Background
Metadata
- Authors
- Shoemaker, B. A., Portman, J. J., & Wolynes, P. G.
- Venue
- Proceedings of the National Academy of Sciences
- Published
- 2000-07-25
- Volume
- 97
- Issue
- 16
- Pages
- 8868-8873
- ISSN
- 0027-8424 (ISSN-L)
- 1091-6490
- OpenAlex
- W2034299708
- Cited by
- 975
- References
- 6
- FWCI
- 4.06
- Type
- journal article
- Language
- en
- Open access
- green
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- Shoemaker, B. A., Portman, J. J., & Wolynes, P. G. (2000). Speeding molecular recognition by using the folding funnel: The fly-casting mechanism. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.160259697
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
