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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

(A) RMSDvalues of the backbone Cα atoms from the crystalstructure (PDB ID 2M6O) and (B) RMSF values of the backbone Cα atoms were calculatedusing AMBER 03 atomistic force field (in black) and GBEMP coarse-grainedforce field (in red).
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fig12: (A) RMSDvalues of the backbone Cα atoms from the crystalstructure (PDB ID 2M6O) and (B) RMSF values of the backbone Cα atoms were calculatedusing AMBER 03 atomistic force field (in black) and GBEMP coarse-grainedforce field (in red).

Mentions: The backbone Cα root-mean-squaredeviations (RMSDs) of two proteins, plotted in Figures 12A and 13A, were measured as of around4.0 Å, indicating that the overall native structures of the proteinswere reasonably maintained throughout the coarse-grained MD simulations.Figures 12A and 13Ashow that the coarse-grained MD simulations reached equilibrium within10 ns while the equilibrium can be obtained within 2 ns as for theatomistic MD simulations. So, the last 10 and 3 ns were consideredas the production runs for the coarse-grained and atomistic MD simulationsrespectively. Although larger RMSD values were observed for the GBEMPmodel when comparing to atomistic AMBER model, the difference of theequilibrated RMSD values between the GBEMP and atomistic AMBER modelsis about 1.5 Å, acceptable for a coarse-grained model.


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)

(A) RMSDvalues of the backbone Cα atoms from the crystalstructure (PDB ID 2M6O) and (B) RMSF values of the backbone Cα atoms were calculatedusing AMBER 03 atomistic force field (in black) and GBEMP coarse-grainedforce field (in red).
© Copyright Policy
Related In: Results  -  Collection

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

fig12: (A) RMSDvalues of the backbone Cα atoms from the crystalstructure (PDB ID 2M6O) and (B) RMSF values of the backbone Cα atoms were calculatedusing AMBER 03 atomistic force field (in black) and GBEMP coarse-grainedforce field (in red).
Mentions: The backbone Cα root-mean-squaredeviations (RMSDs) of two proteins, plotted in Figures 12A and 13A, were measured as of around4.0 Å, indicating that the overall native structures of the proteinswere reasonably maintained throughout the coarse-grained MD simulations.Figures 12A and 13Ashow that the coarse-grained MD simulations reached equilibrium within10 ns while the equilibrium can be obtained within 2 ns as for theatomistic MD simulations. So, the last 10 and 3 ns were consideredas the production runs for the coarse-grained and atomistic MD simulationsrespectively. Although larger RMSD values were observed for the GBEMPmodel when comparing to atomistic AMBER model, the difference of theequilibrated RMSD values between the GBEMP and atomistic AMBER modelsis about 1.5 Å, acceptable for a coarse-grained model.

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