A pre-existing hydrophobic collapse in the unfolded state of an ultrafast folding protein

• Published in: Nature Vol. 447; no. 7140; pp. 106 - 109
• Main Authors: HUN MOK, K, KUHN, Lars T, GOEZ, Martin, DAY, Iain J, LIN, Jasper C, ANDERSEN, Niels H, HORE, P. J
• Format: Journal Article
• Language: English
• Published: London Nature Publishing 03.05.2007; Nature Publishing Group
• Subjects: Biological and medical sciences; Chains; Collapse; Computer simulation; Conformational dynamics in molecular biology; Dynamics; Experiments; Folding; Free energy; Fundamental and applied biological sciences. Psychology; Heterogeneity; Hydrophobic and Hydrophilic Interactions; Magnetic Resonance Spectroscopy; Mathematical analysis; Models, Chemical; Models, Molecular; Molecular biophysics; Molecular structure; NMR; Nuclear magnetic resonance; Photochemistry; Protein Conformation; Protein Denaturation; Protein Engineering; Protein Folding; Proteins; Research methodology; Time Factors; Dynamic nuclear polarization; Nuclear magnetic resonance; Investigation method; Atomic structure; Refolding; Protein
• ISSN: 0028-0836; 1476-4687; 1476-4679
• DOI: 10.1038/nature05728

Insights into the conformational passage of a polypeptide chain across its free energy landscape have come from the judicious combination of experimental studies and computer simulations. Even though some unfolded and partially folded proteins are now known to possess biological function or to be involved in aggregation phenomena associated with disease states, experimentally derived atomic-level information on these structures remains sparse as a result of conformational heterogeneity and dynamics. Here we present a technique that can provide such information. Using a 'Trp-cage' miniprotein known as TC5b (ref. 5), we report photochemically induced dynamic nuclear polarization NMR pulse-labelling experiments that involve rapid in situ protein refolding. These experiments allow dipolar cross-relaxation with hyperpolarized aromatic side chain nuclei in the unfolded state to be identified and quantified in the resulting folded-state spectrum. We find that there is residual structure due to hydrophobic collapse in the unfolded state of this small protein, with strong inter-residue contacts between side chains that are relatively distant from one another in the native state. Prior structuring, even with the formation of non-native rather than native contacts, may be a feature associated with fast folding events in proteins.