Amide I two-dimensional infrared spectroscopy: methods for visualizing the vibrational structure of large proteins

J Phys Chem A. 2013 Jul 25;117(29):5955-61. doi: 10.1021/jp310689a. Epub 2012 Dec 27.

Abstract

Network layouts are introduced as a method to visualize couplings between local amide I vibrations in proteins. The method is used to identify groups of strongly coupled oscillators to block-diagonalize the Hamiltonians, considerably reducing the expense associated with computing infrared spectra of large proteins. The quality of linear and nonlinear spectra generated from block-diagonal Hamiltonians is demonstrated by comparison with spectra generated from full Hamiltonian trajectories. A library of six proteins reveals that vibrational couplings within hydrogen-bonded residues in specific secondary structures give rise to the characteristic amide I line shapes whereas other couplings play a minor role. Exciton delocalization analyses indicate that amide I vibrations in proteins remain largely localized to groups of less than ten residues.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Absorption
  • Amides / chemistry*
  • Molecular Dynamics Simulation
  • Protein Structure, Secondary
  • Proteins / chemistry*
  • Spectrophotometry, Infrared
  • Vibration*

Substances

  • Amides
  • Proteins