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A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.

Yamagishi J, Okimoto N, Morimoto G, Taiji M - J Comput Chem (2014)

Bottom Line: The presented PB radii were optimized using results from explicit solvent simulations of the large systems.The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment.The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules.

View Article: PubMed Central - PubMed

Affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-15 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; Laboratory for Computational Molecular Design, Quantitative Biology Center (QBiC), RIKEN, 1-6-5 Minatojima-Minatomachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.

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Example of compensations of per-atom errors in the solvation free energies within small molecular fragments. Per-atom errors for the tyrosine residue from PDB ID: 2DX446 are illustrated. Small errors (under ± 1.0 kcal mol−1) are omitted for clarity.
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fig06: Example of compensations of per-atom errors in the solvation free energies within small molecular fragments. Per-atom errors for the tyrosine residue from PDB ID: 2DX446 are illustrated. Small errors (under ± 1.0 kcal mol−1) are omitted for clarity.

Mentions: Further analysis of our PB results at the atomic level can provide more useful and interesting information. Figure 5 shows the distribution of errors in the solvation free energies on a per-atom basis, indicating relatively large errors on a per-atom basis as compared with those on a per-residue basis; large errors over ± 3.0 kcal mol−1 were concentrated on atoms in polar or charged functional groups, while moderate errors (≈ ± 2.0 kcal mol−1) were also observed for atoms in nonpolar groups. Nevertheless, the errors on a per-residue basis for our PB were quite small. This can be attributed to compensations of errors within a small fragment or a functional group of the molecule. For example (Fig. 6), the error on the hydrogen atom in the hydroxyl group was almost compensated by that on the neighboring oxygen atom. Similarly, the errors on aromatic hydrogen atoms were compensated by those on the neighboring carbons. These data indicated that our PB can provide reliable results at the level of the small molecular fragment or the functional group.


A new set of atomic radii for accurate estimation of solvation free energy by Poisson-Boltzmann solvent model.

Yamagishi J, Okimoto N, Morimoto G, Taiji M - J Comput Chem (2014)

Example of compensations of per-atom errors in the solvation free energies within small molecular fragments. Per-atom errors for the tyrosine residue from PDB ID: 2DX446 are illustrated. Small errors (under ± 1.0 kcal mol−1) are omitted for clarity.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4263261&req=5

fig06: Example of compensations of per-atom errors in the solvation free energies within small molecular fragments. Per-atom errors for the tyrosine residue from PDB ID: 2DX446 are illustrated. Small errors (under ± 1.0 kcal mol−1) are omitted for clarity.
Mentions: Further analysis of our PB results at the atomic level can provide more useful and interesting information. Figure 5 shows the distribution of errors in the solvation free energies on a per-atom basis, indicating relatively large errors on a per-atom basis as compared with those on a per-residue basis; large errors over ± 3.0 kcal mol−1 were concentrated on atoms in polar or charged functional groups, while moderate errors (≈ ± 2.0 kcal mol−1) were also observed for atoms in nonpolar groups. Nevertheless, the errors on a per-residue basis for our PB were quite small. This can be attributed to compensations of errors within a small fragment or a functional group of the molecule. For example (Fig. 6), the error on the hydrogen atom in the hydroxyl group was almost compensated by that on the neighboring oxygen atom. Similarly, the errors on aromatic hydrogen atoms were compensated by those on the neighboring carbons. These data indicated that our PB can provide reliable results at the level of the small molecular fragment or the functional group.

Bottom Line: The presented PB radii were optimized using results from explicit solvent simulations of the large systems.The performances using our PB radii showed high accuracy for the estimation of solvation free energies at the level of the molecular fragment.The obtained PB radii are effective for the detailed analysis of the solvation effects of biomolecules.

View Article: PubMed Central - PubMed

Affiliation: Department of Computational Biology, Graduate School of Frontier Sciences, The University of Tokyo, 5-15 Kashiwanoha, Kashiwa, Chiba, 277-8561, Japan; Laboratory for Computational Molecular Design, Quantitative Biology Center (QBiC), RIKEN, 1-6-5 Minatojima-Minatomachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan.

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