On the Transferability of CHARMM36m Protein Force Field with LJ-PME: Hydrogen Bonding Dynamics under Elevated Pressures

10.26434/chemrxiv.13653203.v1 ◽

2021 ◽

Author(s):

You Xu ◽

Jing Huang

Keyword(s):

Phase Diagram ◽

Force Field ◽

Temperature Phase ◽

Elevated Pressures ◽

Nmr Data ◽

Wide Range ◽

Model Protein ◽

Temperature And Pressure ◽

Temperature Phase Diagram ◽

Hydrogen Bonding Dynamics

The pressure-temperature phase diagram is significant to understanding the physics of biomolecules. In this study we evaluated the transferability of CHARMM36m (C36m) protein force field (FF) in varied pressures using ubiquitin as a model protein compared with NMR data. We demonstrate that C36m FF combining with the LJ-PME method is suitable for simulations in a wide range of temperature and pressure.

Download Full-text

Validating the CHARMM36m Protein Force Field with LJ-PME Reveals Altered Hydrogen Bonding Dynamics under Elevated Pressures

10.26434/chemrxiv.13653203.v2 ◽

2021 ◽

Author(s):

You Xu ◽

Jing Huang

Keyword(s):

Hydrogen Bonds ◽

Force Field ◽

Md Simulations ◽

Temperature Phase ◽

Elevated Pressures ◽

Wide Range ◽

Thermodynamic Conditions ◽

Model Protein ◽

Temperature And Pressure ◽

Good Agreement

<p>The pressure-temperature phase diagram is important to our understanding of the physics of biomolecules. Compared to studies on temperature effects, studies of the pressure dependence of protein dynamic are rather limited. Molecular dynamics (MD) simulations with fine-tuned force fields (FFs) offer a powerful tool to explore the influence of thermodynamic conditions on proteins. Here we evaluate the transferability of the CHARMM36m (C36m) protein force field at varied pressures compared with NMR data using ubiquitin as a model protein. The pressure dependences of J couplings for hydrogen bonds and order parameters for internal motion are in good agreement with experiment. We demonstrate that the C36m FF combined with the LJ-PME method is suitable for simulations in a wide range of temperature and pressure. As the ubiquitin remains stable up to 2500 bar, we identify the mobility and stability of different hydrogen bonds in response to pressure. Based on those results, C36m is expected to be applied to more proteins in the future to further investigate protein dynamics under elevated pressures.</p>

Download Full-text

Validating the CHARMM36m protein force field with LJ-PME reveals altered hydrogen bonding dynamics under elevated pressures

Communications Chemistry ◽

10.1038/s42004-021-00537-8 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

You Xu ◽

Jing Huang

Keyword(s):

Hydrogen Bonds ◽

Force Field ◽

Md Simulations ◽

Temperature Phase ◽

Particle Mesh Ewald ◽

Elevated Pressures ◽

Wide Range ◽

Thermodynamic Conditions ◽

Model Protein ◽

Good Agreement

AbstractThe pressure-temperature phase diagram is important to our understanding of the physics of biomolecules. Compared to studies on temperature effects, studies of the pressure dependence of protein dynamic are rather limited. Molecular dynamics (MD) simulations with fine-tuned force fields (FFs) offer a powerful tool to explore the influence of thermodynamic conditions on proteins. Here we evaluate the transferability of the CHARMM36m (C36m) protein force field at varied pressures compared with NMR data using ubiquitin as a model protein. The pressure dependences of J couplings for hydrogen bonds and order parameters for internal motion are in good agreement with experiment. We demonstrate that the C36m FF combined with the Lennard-Jones particle-mesh Ewald (LJ-PME) method is suitable for simulations in a wide range of temperature and pressure. As the ubiquitin remains stable up to 2500 bar, we identify the mobility and stability of different hydrogen bonds in response to pressure. Based on those results, C36m is expected to be applied to more proteins in the future to further investigate protein dynamics under elevated pressures.

Download Full-text