Detailed Microscopic Unfolding Pathways of an α‑Helix and a β‑Hairpin: Direct Observation and Molecular Dynamics

• Published in: The journal of physical chemistry. B 2014-07, Vol.118 (26), p.7233-7246
• Main Authors: Jas, Gouri S, Hegefeld, Wendy A, Middaugh, C. Russell, Johnson, Carey K, Kuczera, Krzysztof
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Circular Dichroism; Cluster Analysis; Computation; Computer simulation; Formations; Helical; Hydrogen Bonding; Hydrogen bonds; Molecular dynamics; Molecular Dynamics Simulation; Molecular Sequence Data; Pathways; Peptides; Peptides - chemistry; Peptides - metabolism; Protein Denaturation; Protein Structure, Secondary; Spectroscopy, Fourier Transform Infrared; Temperature; Thermodynamics
• ISSN: 1520-6106; 1520-5207
• DOI: 10.1021/jp500955z

We present a combined experimental and computational study of unfolding pathways of a model 21-residue α-helical heteropeptide (W1H5-21) and a 16-residue β-hairpin (GB41–56). Experimentally, we measured fluorescence energy transfer efficiency as a function of temperature, employing natural tryptophans as donors and dansylated lysines as acceptors. Secondary structural analysis was performed with circular dichroism and Fourier transform infrared spectroscopy. Our studies present markedly different unfolding pathways of the two elementary secondary structural elements. During thermal denaturation, the helical peptide exhibits an initial decrease in length, followed by an increase, while the hairpin undergoes a systematic increase in length. In the complementary computational part of the project, we performed microsecond length replica-exchange molecular dynamics simulations of the peptides in explicit solvent, yielding a detailed microscopic picture of the unfolding processes. For the α-helical peptide, we found a large heterogeneous population of intermediates that are primarily frayed single helices or helix-turn-helix motifs. Unfolding starts at the termini and proceeds through a stable helical region in the interior of the peptide but shifted off-center toward the C-terminus. The simulations explain the experimentally observed non-monotonic variation of helix length with temperature as due primarily to the presence of frayed-end single-helix intermediate structures. For the β-hairpin peptide, our simulations indicate that folding is initiated at the turn, followed by formation of the hairpin in zipper-like fashion, with Cα···Cα contacts propagating from the turn to termini and hairpin hydrogen bonds forming in parallel with these contacts. In the early stages of hairpin formation, the hydrophobic side-chain contacts are only partly populated. Intermediate structures with low numbers of β-hairpin hydrogen bonds have very low populations. This is in accord with the “broken zipper” model of Scheraga. The monotonic increase in length with temperature may be explained by the zipper-like breaking of the hairpin hydrogen bonds and backbone contacts.