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Article Dans Une Revue Journal of Chemical Physics Année : 1999

A simplified force field for describing vibrational protein dynamics over the whole frequency range

Konrad Hinsen
Gérald Kneller

Résumé

The empirical force fields used for protein simulations contain short-ranged terms (chemical bond structure, steric effects, van der Waals interactions) and long-ranged electrostatic contributions. It is well known that both components are important for determining the structure of a protein. We show that the dynamics around a stable equilibrium state can be described by a much simpler midrange force field made up of the chemical bond structure terms plus unspecific harmonic terms with a distance-dependent force constant. A normal mode analysis of such a model can reproduce the experimental density of states as well as a conventional molecular dynamics simulation using a standard force field with long-range electrostatic terms. This finding is consistent with a recent observation that effective Coulomb interactions are short ranged for systems with a sufficiently homogeneous charge distribution.
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hal-02155539 , version 1 (13-06-2019)

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Konrad Hinsen, Gérald Kneller. A simplified force field for describing vibrational protein dynamics over the whole frequency range. Journal of Chemical Physics, 1999, 111 (24), pp.10766-10769. ⟨10.1063/1.480441⟩. ⟨hal-02155539⟩
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