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Published online before print June 13, 2007, 10.1110/ps.062673207
Protein Science (2007), 16:1249-1256. Published by Cold Spring Harbor Laboratory Press. Copyright © 2007 The Protein Society
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Threading a peptide through a peptide: Protein loops, rotaxanes, and knots

John W. Blankenship1 and Philip E. Dawson

Departments of Chemistry and Cell Biology, The Scripps Research Institute, La Jolla, California 92037, USA

(RECEIVED November 20, 2006; FINAL REVISION February 27, 2007; ACCEPTED April 3, 2007)

Proteins adopt complex folds in nature that typically avoid conformations that are knotted or "threaded" through closed loops. Is this the result of fundamental barriers to folding, or have proteins simply evolved to avoid threaded conformations? Organic synthesis has been used in supramolecular chemistry to install topological links in small molecules. By following these principles, we now show that it is possible to assemble a topologically linked protein complex by threading a linear protein through a cyclic protein to form a [2]pseudo-rotaxane. Subsequent ring closure using native chemical ligation cyclizes the linear protein, forming a [2]heterocatenane. Although the kinetics of protein threading are slower than the folding kinetics of the native protein, threading appears to be a highly efficient process.

Keywords: protein structure/folding; conformational changes; circular dichroism; fluorescence; forces and stability; thermodynamics, hydrodynamics; kinetics; synthesis of peptides and proteins


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