Length Dependent Helix−Coil Transition Kinetics of Nine Alanine-Based Peptides

Abstract

It is well-known that end caps and the peptide length can dramatically influence the thermodynamics of the helix-coil transition. However, their roles in determining the kinetics of the helix-coil transition have not been studied extensively and are less well understood. Kinetic Ising models and sequential kinetic models involving barrier crossing via diffusion all predict that the helix formation time depends monotonically on the peptide length with the relaxation time increasing with respect to increasing chain length. Here, we have studied the helix-coil transition kinetics of a series of Ala-based -helical peptides of different length (19-39 residues), with and without end caps, using time-resolved infrared spectroscopy coupled with laser-induced temperature jump (T-jump) initiation method. The helical content of these peptides was kinetically monitored by probing the amide carbonyl stretching frequencies (i.e., the amide I band) of the peptide backbone. We found that the relaxation rates for peptides with efficient end caps are more rapid than those of the corresponding peptides without good end caps. These results indicate that efficient end-capping sequences can not only stabilize preexisting helices but also promote helix formation through initiation. Furthermore, we found that the relaxation times of these peptides, following a T-jump of 1-11 °C, show rather complex behaviors as a function of the peptide length, in disagreement with theoretical predications. Theses results are not readily explained by theories in which Ala is taken to have a single helical propensity (s). However, recent studies have suggested that s depends on chain length; when this factor is considered, the mean first-passage times of the coil-to-helix transition show similar dependence on the peptide length as those observed experimentally.

Testing the diffusing boundary model for the helix–coil transition in peptides

“…1). A T-jump study on helix unfolding found that different s-values are required to describe the stability of helical peptides with varying lengths (18). In our study, in contrast, the same s-value describes the behavior of the different length peptides, which is in agreement with previous results by Rohl et al (15) and with the Lifson-Roig model.…”

α-Helix formation in a photoswitchable peptide tracked from picoseconds to microseconds by time-resolved IR spectroscopy

“…This conclusion has been confirmed by simple lattice dynamics models (44,45) that revealed stretching factors ␤ Ͻ 1 with decreasing temperature. The kinetic effect of helix stabilization was investigated by Wang et al (30). For 19-mer peptides (length comparable with FK11X), the use of stabilizing capping residues resulted in acceleration and stretching of the kinetics.…”

“…In FK11X, Lys has been replaced by Arg to further increase helicity (28), and a Gln residue is used for C-terminal capping (29). Capping has been observed not only to stabilize the helix but also to speed up folding (30). Two alanines at positions 3 and 14 have been replaced by cysteine to allow for the attachment of the photoswitchable linker.…”

Vibrational−Exciton Couplings for the Amide I, II, III, and A Modes of Peptides

“…43 The fluctuating Hamiltonian is constructed for 100 snapshots obtained from a 2 ns MD trajectory generated earlier. 44 Figure 9 shows the 3D structure of SPE 3 from one MD snapshot and the distribution of Ramachandran angles.…”