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.

  • Source
    [Show abstract] [Hide abstract]
    ABSTRACT: The bio-energy transport is a basic problem in life science and related to many biological processes. Therefore to establish the mechanism of bio-energy transport and its theory have an important significance. Based on different properties of structure of α-helical protein molecules some theories of bio-energy transport along the molecular chains have been proposed and established, where the energy is released by hydrolysis of adenosine triphosphate (ATP). A brief survey of past researches on different models and theories of bio-energy, including Davydov's, Takeno's, Yomosa's, Brown et al.'s, Schweitzer's, Cruzeiro-Hansson's, Forner's and Pang's models were first stated in this paper. Subsequently we studied and reviewed mainly and systematically the properties, thermal stability and lifetimes of the carriers (solitons) transporting the bio-energy at physiological temperature 300 K in Pang's and Davydov's theories. From these investigations we know that the carrier (soliton) of bio-energy transport in the α-helical protein molecules in Pang's model has a higher binding energy, higher thermal stability and larger lifetime at 300 K relative to those of Davydov's model, in which the lifetime of the new soliton at 300 K is enough large and belongs to the order of 10(-10) s or τ/τ(0)≥700. Thus we can conclude that the soliton in Pang's model is exactly the carrier of the bio-energy transport, Pang's theory is appropriate to α-helical protein molecules.
    Physics of Life Reviews 06/2011; 8(3):264-86. · 9.48 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: The changes of property of solitons in α-helix protein molecules with three channels under influences of fluctuations of structure parameters and thermal perturbation of medium are extensively investigated using dynamic equations in the improved theory, numerical simulation and Runge-Kutta method. In this investigation the peculiarities of the solitons are given first in the motions of short-time and long-time and its collision features at T = 0 K and biological temperature T = 300 K. This study shows that the solutions of dynamic equations are solitons, which are very stable at T = 0 and 300 K, although its amplitudes and velocity are somewhat decreased relative to that at T = 0 K, the soliton can transport over 1000 amino acid residues, its lifetime is, at least, 120 ps. Subsequently, studies are made of the changes of properties of the soliton with variations of temperature of the medium and fluctuations of structure parameters including mass sequence of amino acid residues and the coupling constant, force constant, dipole–dipole interaction, chain–chain interaction and ground state energy in the α-helix proteins. The investigations indicate that the soliton has high thermal stability and can transport along the molecular chains retaining amplitude, energy and velocity, although the fluctuations of the structure parameters and temperature of the medium increase continually. However, the solitons disperse in larger fluctuations at T = 300 K and higher temperatures than 315 K. Thus it is determined that the critical temperature of the soliton is 315 K. Finally reasons are given for the generation of high thermal stability of the soliton and the correctness of the improved model is demonstrated. It is concluded that the soliton in the improved model is very robust against structure disorder and thermal perturbation of the α-helix protein molecules at 300 K, and is a possible carrier of bio-energy transport, and the improved model is maybe a candidate for the mechanism of this transport.
    Molecular Physics 05/2010; 108(10):1297-1315. · 1.64 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: In this paper, we firstly derive non-Markovian operator Langevin equations of the Davydov monomer in its environment. Next, we replace the equations with the c-number quantum general Langevin equations (QGLEs) by calculating statistical and quantum averages of the operator Langevin equations. Then, by using the c-number QGLEs we investigate the evolutions of the subsystems amide-I and amide-site. The evolution of a parameter θ describing quantum entanglement of the coupling subsystems with continuous variable Hamiltonian has also been investigated. It is shown that there is certain entanglement between the amide-I and amide-site in the Davydov-Scott monomer.
    The European Physical Journal D 01/2014; · 1.40 Impact Factor


Available from