title: Proton transport in biological systems can be probed by two-dimensional infrared spectroscopy.
abstract: We propose a new method to determine the proton transfer (PT) rate in channel proteins by two-dimensional infrared (2DIR) spectroscopy. Proton transport processes in biological systems, such as proton channels, trigger numerous fundamental biochemical reactions. Due to the limitation in both spatial and time resolution of the traditional experimental approaches, describing the whole proton transport process and identifying the rate limiting steps at the molecular level is challenging. In the present paper, we focus on proton transport through the Gramicidin A channel. Using a kinetic PT model derived from all-atom molecular dynamics simulations, we model the amide I region of the 2DIR spectrum of the channel protein to examine its sensitivity to the proton transport process. We demonstrate that the 2DIR spectrum of the isotope-labeled channel contain information on the PT rate, which may be extracted by analyzing the antidiagonal linewidth of the spectral feature related to the labeled site. Such experiments in combination with detailed numerical simulations should allow the extraction of site dependent PT rates, providing a method for identifying possible rate limiting steps for proton channel transfer.
authors.affiliation: Center for Theoretical Physics and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Chungwen
authors.initials: C
authors.lastname: Liang
authors.forename: Thomas L C
authors.initials: TL
authors.lastname: Jansen
authors.forename: Jasper
authors.initials: J
authors.lastname: Knoester
mesh_terms: D000465:Algorithms; D000577:Amides / Q000737:chemistry; D004735:Energy Transfer; D006096:Gramicidin / Q000737:chemistry*; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D018892:Proton-Motive Force; D011522:Protons; D013055:Spectrophotometry, Infrared / Q000379:methods*; D014867:Water / Q000737:chemistry
chemical_list: D000577:Amides; D011522:Protons; D014867:Water; D006096:Gramicidin