Proton transport in a membrane protein channel: two-dimensional infrared spectrum modeling

We model the two-dimensional infrared (2DIR) spectrum of a proton channel to investigate its applicability as a spectroscopy tool to study the proton transport process in biological systems. Proton transport processes in proton channels are involved in numerous fundamental biochemical reactions. However, probing the proton transport process at the molecular level is challenging, because of the limitation in both spatial and time resolution of the traditional experimental approaches. In this paper, we perform proton transport molecular dynamics simulations and model the amide I region of the 2DIR spectrum of a proton channel to examine its sensitivity to the proton transport process. We first report the position dependent proton transfer rates along the channel. The rates in the middle of the channel are larger than those in the entrance. In the presence of protons, we find that the antidiagonal line width of the 2DIR spectrum is larger, and the time evolution of the 2DIR spectrum is slower than that without proton. The time evolution of the 2DIR spectrum with different isotope-labeled residues is similar, even if the local proton transfer rates are different. This results from the proton hopping and the channel water rotation being collective mechanisms, and these effects are convoluted in the spectra.