title: Assessing Spectral Simulation Protocols for the Amide I Band of Proteins.
abstract: We present a benchmark study of spectral simulation protocols for the amide I band of proteins. The amide I band is widely used in infrared spectroscopy of proteins due to the large signal intensity, high sensitivity to hydrogen bonding, and secondary structural motifs. This band has, thus, proven valuable in many studies of protein structure-function relationships. We benchmark spectral simulation protocols using two common force fields in combination with several electrostatic mappings and coupling models. The results are validated against experimental linear absorption and two-dimensional infrared spectroscopy for three well-studied proteins. We find two-dimensional infrared spectroscopy to be much more sensitive to the simulation protocol than linear absorption and report on the best simulation protocols. The findings demonstrate that there is still room for ideas to improve the existing models for the amide I band of proteins.
authors.affiliation: Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Ana V
authors.initials: AV
authors.lastname: Cunha
authors.affiliation: Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Anna S
authors.initials: AS
authors.lastname: Bondarenko
authors.affiliation: Zernike Institute for Advanced Materials, University of Groningen , Nijenborgh 4, 9747 AG Groningen, The Netherlands.
authors.forename: Thomas L C
authors.initials: TL
authors.lastname: Jansen
mesh_terms: D000577:Amides / Q000737:chemistry*; D003208:Concanavalin A / Q000737:chemistry / Q000378:metabolism; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry / Q000378:metabolism; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012259:Ribonuclease, Pancreatic / Q000737:chemistry / Q000378:metabolism; D017550:Spectroscopy, Fourier Transform Infrared
chemical_list: D000577:Amides; D011506:Proteins; D003208:Concanavalin A; D012259:Ribonuclease, Pancreatic; D009113:Muramidase