Article

Energy relaxation of the amide-I mode in hydrogen-bonded peptide units: a route to conformational change.

Institut UTINAM, Université de Franche-Comté, UMR CNRS 6213, 25030 Besançon Cedex, France.
The Journal of Chemical Physics (Impact Factor: 3.12). 03/2008; 128(6):065101. DOI: 10.1063/1.2831508
Source: PubMed

ABSTRACT A one-site Davydov model involving a C[Double Bond]O group engaged in a hydrogen bond is used to study the amide-I relaxation due to Fermi resonances with a bath of intramolecular normal modes. In the amide-I ground state, the hydrogen bond behaves as a harmonic oscillator whose eigenstates are phonon number states. By contrast, in the amide-I first excited state, the hydrogen bond experiences a linear distortion so that the eigenstates are superimpositions of number states. By assuming the hydrogen bond in thermal equilibrium at biological temperature, it is shown that the amide-I excitation favors the population of these excited states and the occurrence of coherences. Due to the interaction with the bath, the vibron decays according to an exponential or a biexponential law depending on whether the Fermi resonance is wide or narrow. Therefore, each excited state relaxes over a set of number states according to specific pathways. The consequence is twofold. First, the relaxation leads to a redistribution of the number state population which differs from the initial Boltzmann distribution. Then, it allows for coherence transfers so that, although the vibron has disappeared, the hydrogen keeps the memory of its initial distortion and it develops free oscillations.

0 Followers
 · 
85 Views
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Electron capture dissociation (ECD) of peptides and proteins in the gas phase is a powerful tool in tandem mass spectrometry whose current description is not sufficient to explain many experimental observations. Here, we attempt to bridge the current understanding of the vibrational dynamics in alpha-helices with the recent experimental results on ECD of alpha-helical peptides through consideration of amide-I relaxation-induced hydrogen bond distortion. Based on a single spine of H-bonded peptide units, we assume that charge neutralization upon electron capture by a charged alpha-helix excites a nearby amide-I mode, which relaxes over a few picoseconds due to Fermi resonances with intramolecular normal modes. The amide-I population plays the role of an external force, which drives the displacements of each peptide unit. It induces a large immobile contraction of the H bonds surrounding the excited site whose lifetime is about the amide-I lifetime. In addition, it creates two lattice deformations describing H bond stretchings, which propagate from the excited region toward both termini of the alpha-helix, get reflected at the termini and yield H bond contractions which move back to the excited region. Consequently, we show that H bonds experience rather large contractions whose amplitude depends on general features such as the position of the amide-I mode, the peptide length and the H bond force constants. When an H bond contraction is sufficiently large, it may promote a hydrogen atom transfer between two neighboring peptide units leading to the formation of a radical at charge site remote carbonyl carbon which is known to be a precursor to the rupture of the corresponding N[Single Bond]C(alpha) bond. The introduced here way of excitation energy generation and transfer may significantly advance ECD understanding and complement existing ECD mechanisms.
    The Journal of Chemical Physics 10/2008; 129(9):095106. DOI:10.1063/1.2965525 · 3.12 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: A time-convolutionless master equation is established for describing the amide-I vibrational energy flow in a lattice of H-bonded peptide units. The dynamics is addressed within the small polaron formalism to account for the strong coupling between the amide-I vibron and the phonons describing the H-bond vibrations. Therefore, special attention is paid to characterize the influence of the amide-I relaxation on the polaron transport properties. This relaxation is modeled by assuming that each amide-I mode interacts with a bath of intramolecular normal modes whose displacements are strongly localized on the C=O groups. It has been shown that the energy relaxation occurs over a very short time scale which prevents any significant delocalization of the polaron. At biological temperature, the polaron explores a finite region around the excited site whose size is about one or two lattice parameters. However, two regimes occur depending on whether the vibron-phonon coupling is weak or strong. For a weak coupling, the energy propagates coherently along the lattice until the polaron disappears. By contrast, for a strong coupling, a diffusive regime occurs so that the polaron explores a finite size region incoherently. In both cases, the finite polaron lifetime favors the localization of the vibron density whose amplitude decreases exponentially.
    Physical Review E 01/2009; 78(6 Pt 1):061909. DOI:10.1103/PhysRevE.78.061909 · 2.33 Impact Factor
  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: Employing extensive quantum-chemical calculations at the DFT/B3LYP and MP2 level, a quartic force field of isolated N-methylacetamide is constructed. Taking into account 24 vibrational degrees of freedom, the model is employed to perform numerically exact vibrational configuration interaction calculations of the vibrational energy relaxation of the amide I mode. It is found that the energy transfer pathways may sensitively depend on details of the theoretical description. Moreover, the exact reference calculations were used to study the applicability and accuracy of (i) the quasiclassical trajectory method, (ii) time-dependent second-order perturbation theory, and (iii) the instantaneous normal mode description of frequency fluctuations. Based on the results, several strategies to describe vibrational energy relaxation in biomolecular systems are discussed.
    International Journal of Quantum Chemistry 01/2009; 109(10). DOI:10.1002/qua.22061 · 1.17 Impact Factor
Show more

Preview

Download
0 Downloads
Available from