Folding dynamics of a small protein at room temperature via simulated coherent two-dimensional infrared spectroscopy

Abstract

Understanding protein folding is of fundamental and practical importance in chemistry and biology. Despite the great success that has been made in tackling this problem, a detailed knowledge of how the elementary processes such as hydrogen-bond formation occur during protein folding has remained largely elusive. Using the combined power of molecular dynamics simulation with electrostatic polarization and coherent two-dimensional infrared spectroscopy, we are able to delineate the order of the hydrogen-bond formation event of a 17-residue peptide during its folding from an extended state to the native α-helix state. The folding is carried out by a single trajectory room-temperature molecular dynamics simulation that includes the polarization effect of hydrogen bonding, which is critical to the successful folding of the peptide. The onset and evolution of the isotope-labeled amide I vibration diagonal and cross peaks on the simulated 2DIR spectra allow us to build a structure-spectrum connection, and thus provide a microscopic picture of the helix folding process.