Untying Knots in Proteins
Abstract
A shoelace can be readily untied by pulling its ends rather than its loops. Attempting to untie a native knot in a protein can also succeed or fail depending on where one pulls. However, thermal fluctuations induced by the surrounding water affect conformations stochastically and may add to the uncertainty of the outcome. When the protein is pulled by the termini, the knot can only get tightened, and any attempt at untying results in failure. We show that, by pulling specific amino acids, one may easily retract a terminal segment of the backbone from the knotting loop and untangle the knot. At still other amino acids, the outcome of pulling can go either way. We study the dependence of the untying probability on the way the protein is grasped, the pulling speed, and the temperature. Elucidation of the mechanisms underlying this dependence is critical for a successful experimental realization of protein knot untying.
Additional Information
© 2010 American Chemical Society. Received: April 1, 2010. Publication Date (Web): September 21, 2010. This work was supported by the EC FUNMOL FP7-NMP-2007-SMALL-1 project, grant agreement 213382, and the EU Innovative Economy grant POIG.01.02. J.S. was funded by NSF-PHY-0822283 and NSF-MCB-0543906 and P. Sułkowski by a Marie Curie IOF Fellowship and Foundation for Polish Science.Attached Files
Supplemental Material - ja102441z_si_001.pdf
Files
Name | Size | Download all |
---|---|---|
md5:4c91f65920467bba35a61fb4bba259ff
|
503.8 kB | Preview Download |
Additional details
- Eprint ID
- 20631
- Resolver ID
- CaltechAUTHORS:20101102-090247649
- 213382
- EC FUNMOL FP7-NMP-2007-SMALL-1 project
- POIG.01.02
- EU Innovative Economy
- NSF-PHY-0822283
- NSF
- NSF-MCB-0543906
- NSF
- Marie Curie IOF Fellowship
- Foundation for Polish Science
- Created
-
2010-11-02Created from EPrint's datestamp field
- Updated
-
2021-11-09Created from EPrint's last_modified field