Significant fluctuations of the vibrational free energy in conformational samples of proteins
Abstract
Vibrational free energy (VFE), a quantum contribution to the free energy of any molecular system, is usually ignored in studies of biomolecular systems. In the present work, the fluctuation of the VFE of protein conformers is studied, for close conformers coming from Molecular Dynamics simulations or for conformers coming from CASP prediction experiments. In both cases, VFE fluctuations are large (6-10 kcal/mole), strongly suggesting that VFE should not be ignored, either when looking for a fair sampling of the conformational space or for ranking protein conformers. Interestingly, there is a strong correlation between VFE and vibrational entropy, as well as with zero-point energy. A simple approximation is proposed for the later, which does not involve any costly matrix diagonalization and even does not require prior energy-minimization. Being analytically derivable, it provides a straightforward way to take VFE into account within the frame of standard forceelds. As such, it should allow to assess the possible effects of VFE on the stability and dynamics of molecular systems.
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BibTeX
@misc{sanejouand2026significant,
title = {{Significant fluctuations of the vibrational free energy in conformational samples of proteins}},
author = {Yves-Henri Sanejouand},
howpublished = {HAL},
year = {2026},
month = oct,
url = {https://hal.science/hal-05785557v1},
note = {CC BY-ND 4.0},
}
RIS
TY - UNPB
TI - Significant fluctuations of the vibrational free energy in conformational samples of proteins
AU - Yves-Henri Sanejouand
PY - 2026
DA - 2026/10/01
PB - HAL
UR - https://hal.science/hal-05785557v1
AB - Vibrational free energy (VFE), a quantum contribution to the free energy of any molecular system, is usually ignored in studies of biomolecular systems. In the present work, the fluctuation of the VFE of protein conformers is studied, for close conformers coming from Molecular Dynamics simulations or for conformers coming from CASP prediction experiments. In both cases, VFE fluctuations are large (6-10 kcal/mole), strongly suggesting that VFE should not be ignored, either when looking for a fair sampling of the conformational space or for ranking protein conformers. Interestingly, there is a strong correlation between VFE and vibrational entropy, as well as with zero-point energy. A simple approximation is proposed for the later, which does not involve any costly matrix diagonalization and even does not require prior energy-minimization. Being analytically derivable, it provides a straightforward way to take VFE into account within the frame of standard forceelds. As such, it should allow to assess the possible effects of VFE on the stability and dynamics of molecular systems.
ER -