title: Amide I two-dimensional infrared spectroscopy: methods for visualizing the vibrational structure of large proteins.
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.
authors.affiliation: Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
authors.forename: Carlos R
authors.initials: CR
authors.lastname: Baiz
authors.forename: Mike
authors.initials: M
authors.lastname: Reppert
authors.forename: Andrei
authors.initials: A
authors.lastname: Tokmakoff
mesh_terms: D000042:Absorption; D000577:Amides / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D013055:Spectrophotometry, Infrared; D014732:Vibration
chemical_list: D000577:Amides; D011506:Proteins