Amide I Two-Dimensional Infrared Spectroscopy: Methods for Visualizing the Vibrational Structure of Large Proteins

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.