title: Computational Amide I 2D IR Spectroscopy as a Probe of Protein Structure and Dynamics.
abstract: Two-dimensional infrared spectroscopy of amide I vibrations is increasingly being used to study the structure and dynamics of proteins and peptides. Amide I, a primarily carbonyl stretching vibration of the protein backbone, provides information on secondary structures as a result of vibrational couplings and on hydrogen-bonding contacts when isotope labeling is used to isolate specific sites. In parallel with experiments, computational models of amide I spectra that use atomistic structures from molecular dynamics simulations have evolved to calculate experimental spectra. Mixed quantum-classical models use spectroscopic maps to translate the structural information into a quantum-mechanical Hamiltonian for the spectroscopically observed vibrations. This allows one to model the spectroscopy of large proteins, disordered states, and protein conformational dynamics. With improvements in amide I models, quantitative modeling of time-dependent structural ensembles and of direct feedback between experiments and simulations is possible. We review the advances in developing these models, their theoretical basis, and current and future applications.
authors.affiliation: Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637; email: tokmakoff@uchicago.edu.|Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139.
authors.forename: Mike
authors.initials: M
authors.lastname: Reppert
authors.affiliation: Department of Chemistry, James Franck Institute, Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637; email: tokmakoff@uchicago.edu.
authors.forename: Andrei
authors.initials: A
authors.lastname: Tokmakoff
mesh_terms: D000577:Amides / Q000737:chemistry; D000818:Animals; D006801:Humans; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D013055:Spectrophotometry, Infrared / Q000379:methods*
chemical_list: D000577:Amides; D011506:Proteins
keywords: conformational heterogeneity; molecular dynamics simulations; protein folding; structural ensembles; ultrafast spectroscopy