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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

Potential of mean force (PMF) results for the backbone torsion(ϕ/ψ) distributions of amino acids, calculated from theexperimental protein structures (Dunbrack Library). The color barsrepresent the free energy in the unit of kcal/mol.
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fig7: Potential of mean force (PMF) results for the backbone torsion(ϕ/ψ) distributions of amino acids, calculated from theexperimental protein structures (Dunbrack Library). The color barsrepresent the free energy in the unit of kcal/mol.

Mentions: From the data gathered from Dunbrack Library,61 (see Figure 7), it appears that,in the β basin, alanine (Ala), arginine (Arg), cysteine (Cys),glutamine (Gln), glutamic acid (Glu), histidine (His), leucine (Leu),lysine (Lys), methionine (Met), phenylalanine (Phe), serine (Ser),threonine (Thr), and tyrosine (Tyr) follow a similar energy patternthat two minima are separated by a very shallow barrier. From theGBEMP results (Figure 8), two minima were alsofound in the β basin for arginine (Arg), glutamic acid (Glu),phenylalanine (Phe), serine (Ser), threonine (Thr), and tyrosine (Tyr),but only one minimum was observed for alanine (Ala), cysteine (Cys),glutamine (Gln), histidine (His), leucine (Leu), lysine (Lys), andmethionine (Met). However, the relative populations of the βregion for these amino acids are matched reasonably well between theGBEMP model and experimental results, see Table 3.


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)

Potential of mean force (PMF) results for the backbone torsion(ϕ/ψ) distributions of amino acids, calculated from theexperimental protein structures (Dunbrack Library). The color barsrepresent the free energy in the unit of kcal/mol.
© Copyright Policy
Related In: Results  -  Collection

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

fig7: Potential of mean force (PMF) results for the backbone torsion(ϕ/ψ) distributions of amino acids, calculated from theexperimental protein structures (Dunbrack Library). The color barsrepresent the free energy in the unit of kcal/mol.
Mentions: From the data gathered from Dunbrack Library,61 (see Figure 7), it appears that,in the β basin, alanine (Ala), arginine (Arg), cysteine (Cys),glutamine (Gln), glutamic acid (Glu), histidine (His), leucine (Leu),lysine (Lys), methionine (Met), phenylalanine (Phe), serine (Ser),threonine (Thr), and tyrosine (Tyr) follow a similar energy patternthat two minima are separated by a very shallow barrier. From theGBEMP results (Figure 8), two minima were alsofound in the β basin for arginine (Arg), glutamic acid (Glu),phenylalanine (Phe), serine (Ser), threonine (Thr), and tyrosine (Tyr),but only one minimum was observed for alanine (Ala), cysteine (Cys),glutamine (Gln), histidine (His), leucine (Leu), lysine (Lys), andmethionine (Met). However, the relative populations of the βregion for these amino acids are matched reasonably well between theGBEMP model and experimental results, see Table 3.

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