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Updated: Jun 10, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web
Published on: July 16, 2017
A local-mode model for understanding the dependence of the extended amide III vibrations on protein secondary
Thomas Weymuth1, Christoph R Jacob, Markus Reiher
1ETH Zurich, Laboratorium für Physikalische Chemie, Wolfgang-Pauli-Strasse 10, 8093 Zurich, Switzerland.
Abstract:
The extended amide III region in vibrational spectra of polypeptides and proteins is particularly sensitive to changes in secondary structure. To investigate this structural sensitivity, we have performed density-functional calculations on the small model compound N-acetyl-l-alanine-N-methylamide, which are analyzed using the recently developed analysis in terms of localized modes [J. Chem. Phys. 2009, 130, 084106]. We find that the local modes obtained for different backbone conformations are actually rather similar. To probe the secondary structure sensitivity, we investigate the dependence of the local-mode frequencies and coupling constants on the torsional angles phi and psi. This enables us to set up a local-mode model of the extended amide III region for better understanding its structural sensitivity.
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