Abstract

Reduced point charge models of amino acids are used to model Ubiquitin (PDB: 1UBQ). They are designed (i) from local extremum positions in charge density (CD) distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential functions, or (ii) from local maximum positions in promolecular electron density distribution (ED) functions. Charge values are fitted versus all-atom Amber99 molecular electrostatic potentials. The program GROMACS is used to generate molecular dynamics trajectories of the protein, under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a null mass and radius. The results illustrate that secondary structure is best preserved with the CD-based model at low temperatures and in vacuum. This indicates that local potential energy wells are consistent with the all-atom model. However, at room temperature, the structure is best conserved when point charges are forced to be located on atoms, due to a better description of the Coulomb 1-4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrepancies versus the all-atom case. The CD-based model allows the formation of protein-water H-bonds with geometrical properties similar to the all-atom ones. Contrarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical properties of proteins modelled with reduced point charge models are also significantly affected by the choice of the solvent force field.

Original languageEnglish
Pages (from-to)1340-1354
Number of pages15
JournalSCIENCE CHINA Chemistry
Volume57
Issue number10
Early online date9 Aug 2014
DOIs
Publication statusPublished - 2014
Event2nd International Symposium of Theoretical Chemistry Center - Quantum Chemistry for Extended Systems - Tsinghua University, Beijing, China
Duration: 31 Mar 20142 Apr 2014

Fingerprint

Ubiquitin
Molecular dynamics
Computer simulation
Atoms
Charge density
Proteins
Electronic density of states
Probability density function
Distribution functions
Electrostatics
Poisson equation
Solvation
Potential energy
Temperature
Trajectories
Vacuum
Amino Acids
Water

Keywords

  • critical points
  • electron density
  • molecular electrostatic potential
  • point charge model
  • protein
  • smoothing of molecular fields
  • Ubiquitin

Cite this

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title = "Comparison of Reduced Point Charge Models of Proteins: Molecular Dynamics Simulations of Ubiquitin",
abstract = "Reduced point charge models of amino acids are used to model Ubiquitin (PDB: 1UBQ). They are designed (i) from local extremum positions in charge density (CD) distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential functions, or (ii) from local maximum positions in promolecular electron density distribution (ED) functions. Charge values are fitted versus all-atom Amber99 molecular electrostatic potentials. The program GROMACS is used to generate molecular dynamics trajectories of the protein, under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a null mass and radius. The results illustrate that secondary structure is best preserved with the CD-based model at low temperatures and in vacuum. This indicates that local potential energy wells are consistent with the all-atom model. However, at room temperature, the structure is best conserved when point charges are forced to be located on atoms, due to a better description of the Coulomb 1-4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrepancies versus the all-atom case. The CD-based model allows the formation of protein-water H-bonds with geometrical properties similar to the all-atom ones. Contrarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical properties of proteins modelled with reduced point charge models are also significantly affected by the choice of the solvent force field.",
keywords = "critical points, electron density, molecular electrostatic potential, point charge model, protein, smoothing of molecular fields, Ubiquitin",
author = "Laurence Leherte and Vercauteren, {Daniel P.}",
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T1 - Comparison of Reduced Point Charge Models of Proteins: Molecular Dynamics Simulations of Ubiquitin

AU - Leherte, Laurence

AU - Vercauteren, Daniel P.

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N2 - Reduced point charge models of amino acids are used to model Ubiquitin (PDB: 1UBQ). They are designed (i) from local extremum positions in charge density (CD) distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential functions, or (ii) from local maximum positions in promolecular electron density distribution (ED) functions. Charge values are fitted versus all-atom Amber99 molecular electrostatic potentials. The program GROMACS is used to generate molecular dynamics trajectories of the protein, under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a null mass and radius. The results illustrate that secondary structure is best preserved with the CD-based model at low temperatures and in vacuum. This indicates that local potential energy wells are consistent with the all-atom model. However, at room temperature, the structure is best conserved when point charges are forced to be located on atoms, due to a better description of the Coulomb 1-4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrepancies versus the all-atom case. The CD-based model allows the formation of protein-water H-bonds with geometrical properties similar to the all-atom ones. Contrarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical properties of proteins modelled with reduced point charge models are also significantly affected by the choice of the solvent force field.

AB - Reduced point charge models of amino acids are used to model Ubiquitin (PDB: 1UBQ). They are designed (i) from local extremum positions in charge density (CD) distribution functions built from the Poisson equation applied to smoothed molecular electrostatic potential functions, or (ii) from local maximum positions in promolecular electron density distribution (ED) functions. Charge values are fitted versus all-atom Amber99 molecular electrostatic potentials. The program GROMACS is used to generate molecular dynamics trajectories of the protein, under various implementation schemes, solvation, and temperature conditions. Point charges that are not located on atoms are considered as virtual sites with a null mass and radius. The results illustrate that secondary structure is best preserved with the CD-based model at low temperatures and in vacuum. This indicates that local potential energy wells are consistent with the all-atom model. However, at room temperature, the structure is best conserved when point charges are forced to be located on atoms, due to a better description of the Coulomb 1-4 energy terms. The ED-based model, generated at a lower resolution, led to the largest discrepancies versus the all-atom case. The CD-based model allows the formation of protein-water H-bonds with geometrical properties similar to the all-atom ones. Contrarily, intra-molecular H-bonds are not well described. Structural, thermodynamical, and dynamical properties of proteins modelled with reduced point charge models are also significantly affected by the choice of the solvent force field.

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