Int. J. Mol. Sci. 2011, 12(12), 8449-8465; doi:10.3390/ijms12128449
Article

A Comparative Study of the Second-Order Hydrophobic Moments for Globular Proteins: The Consensus Scale of Hydrophobicity and the CHARMM Partial Atomic Charges

1 Department of Biotechnology, Asia University, Taichung 413, Taiwan 2 Department of Bioinformatics, Asia University, Taichung 413, Taiwan
* Author to whom correspondence should be addressed.
Received: 15 September 2011; Accepted: 15 November 2011 / Published: 29 November 2011
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Abstract: In this paper, the second-order hydrophobic moment for fifteen globular proteins in 150 nonhomologous protein chains was performed in a comparative study involving two sets of hydrophobicity: one selected from the consensus scale and the other derived from the CHARMM partial atomic charges. These proteins were divided into three groups, based on their number of residues (N) and the asphericity (δ). Proteins in Group I were spherical and those in Groups II and III were prolate. The size of the proteins is represented by the mean radius of gyration (Rg), which follows the Flory scaling law, Rg Nv. The mean value of v was 0.35, which is similar to a polymer chain in a poor solvent. The spatial distributions of the second-order moment for each of the proteins, obtained from the two sets of hydrophobicity, were compared using the Pearson correlation coefficient; the results reveal that there is a strong correlation between the two data sets for each protein structure when the CHARMM partial atomic charges, |qi|  ≥ 0.3, assigned for polar atoms, are used. The locations at which these distributions vanish and approach a negative value are at approximately 50% of the percentage of solvent accessibility, indicating that there is a transition point from hydrophobic interior to hydrophilic exterior in the proteins. This may suggest that there is a position for the proteins to determine the residues at exposed sites beyond this range.
Keywords: hydrophobicity consensus scale; CHARMM partial atomic charges; Second-order hydrophobic moment

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MDPI and ACS Style

Tsai, C.-F.; Lee, K.-J. A Comparative Study of the Second-Order Hydrophobic Moments for Globular Proteins: The Consensus Scale of Hydrophobicity and the CHARMM Partial Atomic Charges. Int. J. Mol. Sci. 2011, 12, 8449-8465.

AMA Style

Tsai C-F, Lee K-J. A Comparative Study of the Second-Order Hydrophobic Moments for Globular Proteins: The Consensus Scale of Hydrophobicity and the CHARMM Partial Atomic Charges. International Journal of Molecular Sciences. 2011; 12(12):8449-8465.

Chicago/Turabian Style

Tsai, Cheng-Fang; Lee, Kuei-Jen. 2011. "A Comparative Study of the Second-Order Hydrophobic Moments for Globular Proteins: The Consensus Scale of Hydrophobicity and the CHARMM Partial Atomic Charges." Int. J. Mol. Sci. 12, no. 12: 8449-8465.

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