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PEDS Advance Access originally published online on April 27, 2005
Protein Engineering Design and Selection 2005 18(5):229-237; doi:10.1093/protein/gzi025
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oupjournals.org

Ubiquitin folds through a highly polarized transition state

Heather M. Went and Sophie E. Jackson1

Chemistry Department and Centre for Protein Engineering, Lensfield Road, Cambridge CB2 1EW, UK

1 To whom correspondence should be addressed. E-mail: sej13{at}cam.ac.uk

The small {alpha}/ß protein ubiquitin has been used as a model system for experimental and computational studies on protein folding for many years. Here, we present a comprehensive {phi}-value analysis and characterize the structure and energetics of the transition state ensemble (TSE). Twenty-seven non-disruptive mutations are made throughout the structure and a range of {phi}-values from zero to one are observed. The values cluster such that medium and high values and found only in the N-terminal region of the protein, whilst the C-terminal region has consistently low {phi}-values. In the TSE, the main {alpha}-helix appears to be fully formed (two {phi}-values which specifically probe helical structure are one) and the helix is stabilized by packing against the first ß-turn, which is partially structured. In striking comparison, the {phi}-values in the C-terminal region are all very low, suggesting that this region of the protein is largely unstructured in the TSE. Data are consistent with a nucleation–condensation mechanism in which there is a highly polarized folding nucleus comprising the first ß-hairpin and the {alpha}-helix. Data presented from the protein engineering study and {phi}-value analysis are compared with results from other experimental studies and also computational studies.

Keywords: folding nucleus/nucleation–condensation/transition-state ensemble/two-state

Received February 11, 2005; accepted March 22, 2005.

Edited by Elizabeth Meiering


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[Abstract] [Full Text] [PDF]


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