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Protein Science (2004), 13:177-189. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Helix formation and the unfolded state of a 52-residue helical protein

Wei Cao1, Clay Bracken1, Neville R. Kallenbach2 and Min Lu1

1 Department of Biochemistry, Weill Medical College of Cornell University, New York, New York 10021, USA
2 Department of Chemistry, New York University, New York, New York 10003, USA

Reprint requests to: Min Lu or Clay Bracken, Department of Biochemistry, Weill Medical College of Cornell University, New York, NY 10021, USA; e-mail: mlu{at}med.cornell.edu or wcb2001{at}med.cornell.edu; fax: (212) 746-8875.

A growing class of proteins in biological processes has been found to be unfolded on isolation under normal solution conditions. We have used NMR spectroscopy to characterize the structural and dynamic properties of the unfolded and partially folded states of a 52-residue alanine-rich protein (Ala-14) at temperatures from -5°C to 40°C. At 40°C, alanine residues in Ala-14 adopt {phi} and {psi} angles, consistent with a significant ensemble population of polyproline II conformation. Analysis of relaxation rates in the protein reveals that a series of residues, Gln 35–Ala 36–Ala 37–Lys 38–Asp 39–Asp 40–Ala 41–Ala 42, displays slow motional dynamics at both -5°C and 40°C. Temperature-dependent chemical shift changes indicate that this region is the site of helix initiation. The remaining N-terminal residues become increasingly dynamic as they extend from the nucleation site. The C terminus remains dynamic and changes less with temperature, indicating it is relatively unstructured. Ala-14 provides a high-resolution portrait of the unfolded state and the process of helix nucleation and propagation in the absence of tertiary contacts, information that bears on early events in protein folding.

Keywords: unstructured proteins; helix formation; protein folding; protein structure; NMR


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