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Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations.

Spiriti J, Zuckerman DM - J Chem Theory Comput (2014)

Bottom Line: For a greater amount of smoothing, multiple folding-unfolding transitions of the peptide were observed, along with a factor of 10-100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations.Chem.Theory Comput.2006, 2, 656-666).

View Article: PubMed Central - PubMed

Affiliation: Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, Pennsylvania 15213, United States.

ABSTRACT
Many commonly used coarse-grained models for proteins are based on simplified interaction sites and consequently may suffer from significant limitations, such as the inability to properly model protein secondary structure without the addition of restraints. Recent work on a benzene fluid (Lettieri S.; Zuckerman D. M.J. Comput. Chem.2012, 33, 268-275) suggested an alternative strategy of tabulating and smoothing fully atomistic orientation-dependent interactions among rigid molecules or fragments. Here we report our initial efforts to apply this approach to the polar and covalent interactions intrinsic to polypeptides. We divide proteins into nearly rigid fragments, construct distance and orientation-dependent tables of the atomistic interaction energies between those fragments, and apply potential energy smoothing techniques to those tables. The amount of smoothing can be adjusted to give coarse-grained models that range from the underlying atomistic force field all the way to a bead-like coarse-grained model. For a moderate amount of smoothing, the method is able to preserve about 70-90% of the α-helical structure while providing a factor of 3-10 improvement in sampling per unit computation time (depending on how sampling is measured). For a greater amount of smoothing, multiple folding-unfolding transitions of the peptide were observed, along with a factor of 10-100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations. For a β hairpin, secondary structure is also preserved, albeit for a narrower range of the smoothing parameter and, consequently, for a more modest improvement in sampling. We have also applied the new method in a "resolution exchange" setting, in which each replica runs a Monte Carlo simulation with a different degree of smoothing. We obtain exchange rates that compare favorably to our previous efforts at resolution exchange (Lyman E.; Zuckerman D. M.J. Chem. Theory Comput.2006, 2, 656-666).

No MeSH data available.


Related in: MedlinePlus

Secondary structure in tabulated and smoothedsimulations. (a)Average fraction of α-helical structure in Leu12 as determinedeither by regions of the Ramachandran plot or using STRIDE.65 Thin horizontal lines indicate result for simulationwithout tables. (b) Average fraction of β-sheet structure inGB1 hairpin as determined by STRIDE. (c, d) Contour plot of averagefraction of (c) α-helical structure in Leu12 and (d) β-sheetstructure in the GB1 hairpin, both as a function of interaction smoothingand covalent smoothing.
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fig4: Secondary structure in tabulated and smoothedsimulations. (a)Average fraction of α-helical structure in Leu12 as determinedeither by regions of the Ramachandran plot or using STRIDE.65 Thin horizontal lines indicate result for simulationwithout tables. (b) Average fraction of β-sheet structure inGB1 hairpin as determined by STRIDE. (c, d) Contour plot of averagefraction of (c) α-helical structure in Leu12 and (d) β-sheetstructure in the GB1 hairpin, both as a function of interaction smoothingand covalent smoothing.

Mentions: Just as a careful choice of lattice was needed to obtain secondarystructures in lattice-based coarse-grained models,17 it is possible for the finite resolution of our tablesto destabilize secondary structure in our models. To investigate this,we compared the average α-helical or β-sheet fractionand the distribution of backbone RMSD in simulations with and withouttables. The results are shown in Figures 3 and 4. For Leu12, both the fraction of α-helicalstructure and the distribution of backbone RMSDs did not change whentables were used.


Tunable Coarse Graining for Monte Carlo Simulations of Proteins via Smoothed Energy Tables: Direct and Exchange Simulations.

Spiriti J, Zuckerman DM - J Chem Theory Comput (2014)

Secondary structure in tabulated and smoothedsimulations. (a)Average fraction of α-helical structure in Leu12 as determinedeither by regions of the Ramachandran plot or using STRIDE.65 Thin horizontal lines indicate result for simulationwithout tables. (b) Average fraction of β-sheet structure inGB1 hairpin as determined by STRIDE. (c, d) Contour plot of averagefraction of (c) α-helical structure in Leu12 and (d) β-sheetstructure in the GB1 hairpin, both as a function of interaction smoothingand covalent smoothing.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4230378&req=5

fig4: Secondary structure in tabulated and smoothedsimulations. (a)Average fraction of α-helical structure in Leu12 as determinedeither by regions of the Ramachandran plot or using STRIDE.65 Thin horizontal lines indicate result for simulationwithout tables. (b) Average fraction of β-sheet structure inGB1 hairpin as determined by STRIDE. (c, d) Contour plot of averagefraction of (c) α-helical structure in Leu12 and (d) β-sheetstructure in the GB1 hairpin, both as a function of interaction smoothingand covalent smoothing.
Mentions: Just as a careful choice of lattice was needed to obtain secondarystructures in lattice-based coarse-grained models,17 it is possible for the finite resolution of our tablesto destabilize secondary structure in our models. To investigate this,we compared the average α-helical or β-sheet fractionand the distribution of backbone RMSD in simulations with and withouttables. The results are shown in Figures 3 and 4. For Leu12, both the fraction of α-helicalstructure and the distribution of backbone RMSDs did not change whentables were used.

Bottom Line: For a greater amount of smoothing, multiple folding-unfolding transitions of the peptide were observed, along with a factor of 10-100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations.Chem.Theory Comput.2006, 2, 656-666).

View Article: PubMed Central - PubMed

Affiliation: Department of Computational and Systems Biology, University of Pittsburgh , Pittsburgh, Pennsylvania 15213, United States.

ABSTRACT
Many commonly used coarse-grained models for proteins are based on simplified interaction sites and consequently may suffer from significant limitations, such as the inability to properly model protein secondary structure without the addition of restraints. Recent work on a benzene fluid (Lettieri S.; Zuckerman D. M.J. Comput. Chem.2012, 33, 268-275) suggested an alternative strategy of tabulating and smoothing fully atomistic orientation-dependent interactions among rigid molecules or fragments. Here we report our initial efforts to apply this approach to the polar and covalent interactions intrinsic to polypeptides. We divide proteins into nearly rigid fragments, construct distance and orientation-dependent tables of the atomistic interaction energies between those fragments, and apply potential energy smoothing techniques to those tables. The amount of smoothing can be adjusted to give coarse-grained models that range from the underlying atomistic force field all the way to a bead-like coarse-grained model. For a moderate amount of smoothing, the method is able to preserve about 70-90% of the α-helical structure while providing a factor of 3-10 improvement in sampling per unit computation time (depending on how sampling is measured). For a greater amount of smoothing, multiple folding-unfolding transitions of the peptide were observed, along with a factor of 10-100 improvement in sampling per unit computation time, although the time spent in the unfolded state was increased compared with less smoothed simulations. For a β hairpin, secondary structure is also preserved, albeit for a narrower range of the smoothing parameter and, consequently, for a more modest improvement in sampling. We have also applied the new method in a "resolution exchange" setting, in which each replica runs a Monte Carlo simulation with a different degree of smoothing. We obtain exchange rates that compare favorably to our previous efforts at resolution exchange (Lyman E.; Zuckerman D. M.J. Chem. Theory Comput.2006, 2, 656-666).

No MeSH data available.


Related in: MedlinePlus