title: Molecular Dynamics and Room Temperature Vibrational Properties of Deprotonated Phosphorylated Serine.
abstract: The local structure of phosphorylated residues in peptides and proteins may have a decisive role on their functional properties. Recent IRMPD experiments have started to provide spectroscopic signatures of such structural details; however, a proper modeling of these signatures beyond the harmonic approximation, taking into account temperature and entropic effects, is still lacking. In order to bridge this gap, DFT-based Car-Parrinello molecular dynamics simulations have been carried out for the first time on a phosphorylated amino acid, gaseous deprotonated phosphoserine. It is found that all vibrational signatures are successfully reproduced, and new deconvolution techniques enable the assignment of the vibrational spectrum directly from the dynamics results and the comparison of vibrational modes at several temperatures. The lowest energy structure is found to involve a strong hydrogen bond between the deprotonated phosphate and the acid with relatively small free energy barriers to proton transfer; however, we find that proton shuttling between the two sites does not occur frequently. Anharmonicities turn out to be important to reproduce the frequencies and shapes of several experimental bands. Comparison of room temperature and 13 K, effectively harmonic dynamics, allows insight to be obtained into vibrational anharmonicities. In particular, a significant blue-shift and broadening of the C═O stretching frequency from 13 to 300 K can be ascribed to intrinsic anharmonicity rather than to anharmonic coupling to other modes. On the other hand, significant couplings are found for the stretching motions of the hydrogen bonded P-O bond and of the free P-OH bond, mainly with modes within the phosphate group.
authors.affiliation: Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR8587 CNRS, Université d'Evry val d'Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France.
authors.forename: A
authors.initials: A
authors.lastname: Cimas
authors.affiliation: Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR8587 CNRS, Université d'Evry val d'Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France.
authors.forename: P
authors.initials: P
authors.lastname: Maitre
authors.affiliation: Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR8587 CNRS, Université d'Evry val d'Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France.
authors.forename: G
authors.initials: G
authors.lastname: Ohanessian
authors.affiliation: Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement, UMR8587 CNRS, Université d'Evry val d'Essonne, boulevard F. Mitterrand, Bat. Maupertuis, 91025 Evry Cedex, France, Laboratoire de Chimie Physique, Université Paris Sud 11, UMR8000 CNRS, Faculté des sciences, bâtiment 350, 91405 Orsay Cedex, France, and Laboratoire des Mécanismes réactionnels, Département de Chimie, Ecole Polytechnique, CNRS, 91128 Palaiseau Cedex, France.
authors.forename: M-P
authors.initials: MP
authors.lastname: Gaigeot