title: Protein unfolding rates correlate as strongly as folding rates with native structure.
abstract: Although the folding rates of proteins have been studied extensively, both experimentally and theoretically, and many native state topological parameters have been proposed to correlate with or predict these rates, unfolding rates have received much less attention. Moreover, unfolding rates have generally been thought either to not relate to native topology in the same manner as folding rates, perhaps depending on different topological parameters, or to be more difficult to predict. Using a dataset of 108 proteins including two-state and multistate folders, we find that both unfolding and folding rates correlate strongly, and comparably well, with well-established measures of native topology, the absolute contact order and the long range order, with correlation coefficient values of 0.75 or higher. In addition, compared to folding rates, the absolute values of unfolding rates vary more strongly with native topology, have a larger range of values, and correlate better with thermodynamic stability. Similar trends are observed for subsets of different protein structural classes. Taken together, these results suggest that choosing a scaffold for protein engineering may require a compromise between a simple topology that will fold sufficiently quickly but also unfold quickly, and a complex topology that will unfold slowly and hence have kinetic stability, but fold slowly. These observations, together with the established role of kinetic stability in determining resistance to thermal and chemical denaturation as well as proteases, have important implications for understanding fundamental aspects of protein unfolding and folding and for protein engineering and design.
authors.affiliation: Department of Chemistry, Guelph-Waterloo Centre for Graduate Studies in Chemistry and Biochemistry, University of Waterloo, Waterloo, Ontario, Canada, N2L 1W2.
authors.forename: Aron
authors.initials: A
authors.lastname: Broom
authors.forename: Shachi
authors.initials: S
authors.lastname: Gosavi
authors.forename: Elizabeth M
authors.initials: EM
authors.lastname: Meiering
mesh_terms: D030562:Databases, Protein; D007700:Kinetics; D015202:Protein Engineering; D017510:Protein Folding; D055550:Protein Stability; D058767:Protein Unfolding; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D013816:Thermodynamics
chemical_list: D011506:Proteins
keywords: contact order; folding rate; kinetic stability; long range order; protein design; protein engineering; scaffold selection; structural complexity; topology; unfolding rate