Refining Disordered Peptide Ensembles with Computational Amide I Spectroscopy: Application to Elastin-Like Peptides

Area of Science:

• Biophysics
• Structural Biology
• Spectroscopy

Background:

• Intrinsically disordered proteins (IDPs) present unique challenges for structural characterization due to inherent heterogeneity.
• Conventional experimental techniques often perform poorly with IDPs, necessitating alternative structural probing tools.

Purpose of the Study:

• To develop and apply novel experimental and computational tools for characterizing IDP ensembles.
• To investigate the structural properties of elastin-like peptides (ELPs) using Amide I vibrational spectroscopy.

Main Methods:

• Utilized Amide I (backbone carbonyl stretch) vibrational spectroscopy to probe local electrostatic environments and structures.
• Employed empirical frequency maps to correlate spectroscopic data with atomistic structural models.
• Applied maximum entropy analysis to molecular dynamics (MD) ensembles, constrained by experimental spectra.

Main Results:

• Developed experimental and computational tools for IDP ensemble characterization.
• Analyzed short elastin-like peptides (ELPs) containing the Pro-Gly turn motif.
• Found that Ala or Val side chains preceding the Pro-Gly unit promote extended structures compared to Gly-Pro-Gly motifs.

Conclusions:

• Steric interactions play a significant role in modulating the molecular properties of elastin.
• Vibrational spectroscopy provides a viable method for experimentally testing structural models of IDPs.
• The developed tools advance the characterization of complex protein systems like IDPs.