Understanding normal modes of proteins

Area of Science:

• Computational chemistry
• Molecular dynamics
• Spectroscopy

Background:

• Accurate normal modes are crucial for analyzing protein vibrational spectroscopy.
• Reliable conformation-dependent force fields are necessary for obtaining these normal modes.
• Empirical polypeptide force fields have shown success in reproducing synthetic polypeptide spectra.

Purpose of the Study:

• To discuss the utility of empirical polypeptide force fields for protein normal mode analysis.
• To illustrate the insights gained from empirical force fields using deoxymyoglobin calculations.
• To investigate the influence of helix irregularity and force constant variation on protein vibrational spectra.

Main Methods:

• Utilizing empirical polypeptide force fields for normal mode calculations.
• Performing ab initio dipole derivative calculations.
• Computing amide I and amide II infrared band profiles for deoxymyoglobin.
• Examining the influence of rigid peptide group geometry on low-frequency density-of-states.

Main Results:

• Empirical force fields provide valuable insights into protein normal modes despite limitations.
• Calculations on deoxymyoglobin demonstrate the impact of helix irregularity and force constant variation on mode delocalization.
• Computed IR band profiles correlate with eigenvectors, explaining band shape and breadth.
• Rigid peptide group geometry significantly influences low-frequency density-of-states.

Conclusions:

• Empirical force fields are useful for understanding protein normal modes and vibrational spectra.
• The study highlights the importance of force field accuracy and conformation dependence for spectroscopic analyses.
• Further development of spectroscopically determined force fields (SDFF) is motivated by limitations of current empirical models.