Gain of local structure in an amphipathic peptide does not require a specific tertiary framework

Area of Science:

• Biophysics
• Protein Chemistry
• Molecular Biology

Background:

• The globular protein thioredoxin contains a surface peptide (TRX94-108) with low intrinsic helical propensity.
• Understanding how such peptides acquire native-like structures is crucial for protein folding studies.

Purpose of the Study:

• To investigate the structural stabilization of the TRX94-108 peptide within an apolar interaction network.
• To explore the role of sodium dodecyl sulfate (SDS) binding in inducing and stabilizing alpha-helical conformation.
• To analyze the peptide's interaction with a C18 RP-HPLC matrix.

Main Methods:

• Design and synthesis of peptide variants with modulated helical propensity.
• Structural analysis using circular dichroism (CD) and capillary zone electrophoresis (CZE).
• Nuclear magnetic resonance (NMR) spectroscopy (DOSY-NMR) and molecular dynamics simulations (MDS).
• Chromatographic analysis of peptide-matrix interactions.

Main Results:

• Specific sequence elements in TRX94-108 stabilize SDS/peptide supramolecular clusters.
• Hydrophobic interactions with SDS constrain peptide conformations, promoting secondary structure.
• Molecular dynamics simulations revealed an SDS-mediated structural scaffold preserving helical conformation.
• Nonspecific apolar surfaces are sufficient for stabilizing peptide secondary structure.

Conclusions:

• Apolar interactions, like those with SDS, can induce and stabilize helical structures in peptides with low intrinsic propensity.
• This SDS-mediated mechanism provides a structural scaffold, potentially serving as a general model for peptide folding.
• Protein folding may involve initial rounds of nonspecific structure stabilization, with tertiary interactions forming as a consequence rather than a prerequisite.