Computing infrared spectra of proteins using the exciton model

Area of Science:

• Computational chemistry
• Biophysics
• Spectroscopy

Background:

• First-principles computation of protein infrared spectra connects atomistic models to biological systems.
• Infrared spectroscopy, particularly 2D IR, requires interpretation via detailed structural and dynamical information.

Purpose of the Study:

• To compute and analyze one- and two-dimensional infrared (IR) spectra for nine well-characterized proteins in solution.
• To interpret spectral features in terms of protein conformational dynamics and solvent effects.
• To demonstrate the utility of computed spectra in complementing experimental measurements.

Main Methods:

• Molecular dynamics (MD) simulations in an explicit point charge water model.
• Computation of 1D and 2D IR spectra in the Amide I region using an exciton approach.
• Analysis of spectra based on local mode basis of carbonyl stretches.

Main Results:

• Solvent effects shift the Amide I band by 30-50 cm⁻¹.
• Protein conformational dynamics contribute to spectral peak broadening.
• Inhomogeneous broadening in 1D and 2D spectra correlates with simulated conformational diversity.
• Computed 2D cross-peak spectra reveal information on coupled vibrations.

Conclusions:

• First-principles IR spectral calculations provide valuable insights into protein structure and dynamics.
• Simulations accurately capture solvent and dynamic contributions to spectral properties.
• 2D IR spectroscopy, aided by computation, offers detailed understanding of molecular vibrations.