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 α-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.

Nitrile-derivatized amino acids have recently been proposed to serve as infrared (IR) probes of local environment of proteins. In this Letter, we presented results regarding the temperature dependence of the CN stretching vibration of a nitrile-derivatized phenylalanine, PheCN, in water. Two-dimensional (2D) infrared correlation analysis revealed that at least three species, corresponding to PheCN molecules with either free or hydrogen-bonded CN groups, exist. This microheterogeneity was further studied by a global curve-fitting procedure, which yielded: ΔH=−4.7kcalmol−1, ΔS=−15calK−1mol−1, and ΔCp=−79calK−1mol−1, for the transition from the free to hydrogen-bonded species.

Here, we describe the folding/unfolding kinetics of α 3 D, a small designed three-helix bundle. Both IR temperature jump and ultrafast fluorescence mixing methods reveal a single-exponential process consistent with a minimal folding time of 3.2 ± 1.2 μs (at ≈50°C), indicating that a protein can fold on the 1- to 5-μs time scale. Furthermore, the single-exponential nature of the relaxation indicates that the prefactor for transition state (TS)-folding models is probably ≥1 (μs) –1 for a protein of this size and topology. Molecular dynamics simulations and IR spectroscopy provide a molecular rationale for the rapid, single-exponential folding of this protein. α 3 D shows a significant bias toward local helical structure in the thermally denatured state. The molecular dynamics-simulated TS ensemble is highly heterogeneous and dynamic, allowing access to the TS via multiple pathways.

The helix-coil transition kinetics of an α-helical peptide were investigated by time-resolved infrared spectroscopy coupled with laser-induced temperature-jump initiation method. Specific isotope labeling of the amide carbonyl groups with 13 C at selected residues was used to obtain site-specific information. The relaxation kinetics following a temperature jump, obtained by probing the amide I′ band of the peptide backbone, exhibit nonexponential behavior and are sensitive to both initial and final temperatures. These data are consistent with a conformation diffusion process on the folding energy landscape, in accord with a recent molecular dynamics simulation study.

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTTime-Resolved Infrared Study of the Helix−Coil Transition Using 13C-Labeled Helical PeptidesCheng-Yen Huang, Zelleka Getahun, Ting Wang, William F. DeGrado, and Feng GaiView Author Information Department of Chemistry Department of Biochemistry and Biophysics University of Pennsylvania Philadelphia, Pennsylvania 19104 Cite this: J. Am. Chem. Soc. 2001, 123, 48, 12111–12112Publication Date (Web):November 7, 2001Publication History Received16 July 2001Published online7 November 2001Published inissue 1 December 2001https://pubs.acs.org/doi/10.1021/ja016631qhttps://doi.org/10.1021/ja016631qrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views594Altmetric-Citations91LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Amides,Conformation,Kinetics,Nucleation,Peptides and proteins Get e-Alerts

The helix-coil transition of a synthetic alpha-helical peptide (the D-Arg peptide), Ac-YGG(KAAAA)(3)-CO-D-Arg-CONH(2), was studied by static far-UV circular dichroism (CD) and time-resolved infrared spectroscopy coupled with the laser-induced temperature-jump technique for rapid relaxation initiation. Equilibrium thermal unfolding measurements of the D-Arg peptide monitored by CD spectroscopy reveal an apparent two-state helix-coil transition, with a thermal melting temperature around 10 degrees C. Time-resolved infrared (IR) measurements following a laser-induced temperature jump, however, reveal biphasic (or multiphasic) relaxation kinetics. The fast phase rises within the 20 ns response time of the detection system. The slow phase has a decay lifetime of approximately 140 ns at 300 K and exhibits monotonic temperature dependence with an apparent activation energy around 15.5 kcal/mol.