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An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.

Shen H, Li Y, Ren P, Zhang D, Li G - J Chem Theory Comput (2014)

Bottom Line: As a result, the coarse-grained protein model presented an accurate description of non-bonded interactions (particularly electrostatic component) between hetero-/homo-dimers (such as peptide-peptide, peptide-water).In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides.In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China.

ABSTRACT
Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay-Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library) as well as from atomistic force field simulations (using AMOEBA, AMBER and CHARMM force fields) while saving the computational cost by a factor of about 10~200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of non-bonded interactions (particularly electrostatic component) between hetero-/homo-dimers (such as peptide-peptide, peptide-water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems.

No MeSH data available.


Related in: MedlinePlus

Correlationsbetween the GBEMP and AMOEBA results for the magnitudeof the dipole moment of different dipeptide models (20 kinds of dipeptidesin total). In the calculations of the dipole moment for each dipeptidemodel, various conformations were chosen randomly from the atomisticstructures generated from atomistic MD simulation (using AMOEBA forcefield).
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fig4: Correlationsbetween the GBEMP and AMOEBA results for the magnitudeof the dipole moment of different dipeptide models (20 kinds of dipeptidesin total). In the calculations of the dipole moment for each dipeptidemodel, various conformations were chosen randomly from the atomisticstructures generated from atomistic MD simulation (using AMOEBA forcefield).

Mentions: The quality of theoptimized EMP parameters for different dipeptidemodels have been further evaluated by calculating their dipole momentsusing both GBEMP and AMOEBA models. The correlations between the twomodels for the magnitude of dipeptide dipole moment and x, y, and z components have beencalculated respectively, as shown in Figure 4 and Supporting Information Figure S2,demonstrating good quality of the GBEMP model, especially for hydrophobicamino acid residues. In the calculations of the dipole moment foreach dipeptide, the atomistic configurations were chosen randomlyfrom the structures generated from atomistic MD simulations (usingAMOEBA force field), and the correlations did not vary significantlyby randomly selecting different sets of conformations. Furthermore,for each dipeptide model, a number of waters were generated randomlysurrounding it (any heavy atom in a dipeptide molecule was separatedfrom an oxygen atom of the water molecule in the range of 3.0–5.0Å), and then the electrostatic interaction energies were calculatedbetween the dipeptide and a single water being placed at differentpositions, showing rather encouraging agreement between GBEMP andAMOEBA models, as seen in Figure 5.


An Anisotropic Coarse-Grained Model for Proteins Based On Gay-Berne and Electric Multipole Potentials.

Shen H, Li Y, Ren P, Zhang D, Li G - J Chem Theory Comput (2014)

Correlationsbetween the GBEMP and AMOEBA results for the magnitudeof the dipole moment of different dipeptide models (20 kinds of dipeptidesin total). In the calculations of the dipole moment for each dipeptidemodel, various conformations were chosen randomly from the atomisticstructures generated from atomistic MD simulation (using AMOEBA forcefield).
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3958967&req=5

fig4: Correlationsbetween the GBEMP and AMOEBA results for the magnitudeof the dipole moment of different dipeptide models (20 kinds of dipeptidesin total). In the calculations of the dipole moment for each dipeptidemodel, various conformations were chosen randomly from the atomisticstructures generated from atomistic MD simulation (using AMOEBA forcefield).
Mentions: The quality of theoptimized EMP parameters for different dipeptidemodels have been further evaluated by calculating their dipole momentsusing both GBEMP and AMOEBA models. The correlations between the twomodels for the magnitude of dipeptide dipole moment and x, y, and z components have beencalculated respectively, as shown in Figure 4 and Supporting Information Figure S2,demonstrating good quality of the GBEMP model, especially for hydrophobicamino acid residues. In the calculations of the dipole moment foreach dipeptide, the atomistic configurations were chosen randomlyfrom the structures generated from atomistic MD simulations (usingAMOEBA force field), and the correlations did not vary significantlyby randomly selecting different sets of conformations. Furthermore,for each dipeptide model, a number of waters were generated randomlysurrounding it (any heavy atom in a dipeptide molecule was separatedfrom an oxygen atom of the water molecule in the range of 3.0–5.0Å), and then the electrostatic interaction energies were calculatedbetween the dipeptide and a single water being placed at differentpositions, showing rather encouraging agreement between GBEMP andAMOEBA models, as seen in Figure 5.

Bottom Line: As a result, the coarse-grained protein model presented an accurate description of non-bonded interactions (particularly electrostatic component) between hetero-/homo-dimers (such as peptide-peptide, peptide-water).In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides.In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems.

View Article: PubMed Central - PubMed

Affiliation: Laboratory of Molecular Modeling and Design, State key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Rd. Dalian 116023, PR China.

ABSTRACT
Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay-Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-grained model, namely GBEMP model, is able to reproduce many key features observed from experimental protein structures (Dunbrack Library) as well as from atomistic force field simulations (using AMOEBA, AMBER and CHARMM force fields) while saving the computational cost by a factor of about 10~200 depending on specific cases and atomistic models. More importantly, unlike other coarse-grained approaches, our framework is based on the fundamental intermolecular forces with explicit treatment of electrostatic and repulsion-dispersion forces. As a result, the coarse-grained protein model presented an accurate description of non-bonded interactions (particularly electrostatic component) between hetero-/homo-dimers (such as peptide-peptide, peptide-water). In addition, the encouraging performance of the model was reflected by the excellent correlation between GBEMP and AMOEBA models in the calculations of the dipole moment of peptides. In brief, the GBEMP model given here is general and transferable, suitable for simulating complex biomolecular systems.

No MeSH data available.


Related in: MedlinePlus