Link to full page (citation export, more details):

Alpha-Helix folding in the presence of structural constraints

Full Text PDF:

PDF icon pnas08.pdf


PDF icon ps08_s.pdf

J.A. Ihalainen; B. Paoli; S. Muff; E.H.G. Backus; J. Bredenbeck; G.A. Woolley; A. Caflisch; P. Hamm

Journal: Proc. Natl. Acad. Sci. U.S.A.
Year: 2008
Volume: 105
Issue: 28
Pages: 9588-9593
DOI: 10.1073/pnas.0712099105
Type of Publication: Journal Article

Amino Acid Sequence; Isotopes; Kinetics; Peptides; Photochemistry; Protein Folding; Protein Structure, Secondary; Spectroscopy, Fourier Transform Infrared; Thermodynamics


We have investigated the site-specific folding kinetics of a photoswitchable cross-linked α-helical peptide by using single 13C=18O isotope labeling together with time-resolved IR spectroscopy. We observe that the folding times differ from site to site by a factor of eight at low temperatures (6 °C), whereas at high temperatures (45 °C), the spread is considerably smaller. The trivial sum of the site signals coincides with the overall folding signal of the unlabeled peptide, and different sites fold in a noncooperative manner. Moreover, one of the sites exhibits a decrease of hydrogen bonding upon folding, implying that the unfolded state at low temperature is not unstructured. Molecular dynamics simulations at low temperature reveal a stretched-exponential behavior which originates from parallel folding routes that start from a kinetically partitioned unfolded ensemble. Different metastable structures (i.e., traps) in the unfolded ensemble have a different ratio of loop and helical content. Control simulations of the peptide at high temperature, as well as without the cross-linker at low temperature, show faster and simpler (i.e., single-exponential) folding kinetics. The experimental and simulation results together provide strong evidence that the rate-limiting step in formation of a structurally constrained α-helix is the escape from heterogeneous traps rather than the nucleation rate. This conclusion has important implications for an α-helical segment within a protein, rather than an isolated α-helix, because the cross-linker is a structural constraint similar to those present during the folding of a globular protein.