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QSE: A new 3‐D solvent exposure measure for the analysis of protein structure
Author(s) -
Li Peipei,
Pok Gouchol,
Jung Kwang Su,
Shon Ho Sun,
Ryu Keun Ho
Publication year - 2011
Publication title -
proteomics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.26
H-Index - 167
eISSN - 1615-9861
pISSN - 1615-9853
DOI - 10.1002/pmic.201100189
Subject(s) - accessible surface area , measure (data warehouse) , quadrant (abdomen) , protein tertiary structure , solvent , surface (topology) , geometry , amino acid residue , protein structure , histogram , radius , atom (system on chip) , mathematics , biological system , physics , chemistry , biology , computer science , computational chemistry , data mining , artificial intelligence , peptide sequence , computer security , image (mathematics) , pathology , embedded system , biochemistry , medicine , nuclear magnetic resonance , gene , organic chemistry
Solvent exposure of amino acids measures how deep residues are buried in tertiary structure of proteins, and hence it provides important information for analyzing and predicting protein structure and functions. Existing methods of calculating solvent exposure such as accessible surface area, relative accessible surface area, residue depth, contact number, and half‐sphere exposure still have some limitations. In this article, we propose a novel solvent exposure measure named quadrant‐sphere exposure (QSE) based on eight quadrants derived from spherical neighborhood. The proposed measure forms a microenvironment around Cα atom as a sphere with a radius of 13 Å, and subdivides it into eight quadrants according to a rectangular coordinate system constructed based on geometric relationships of backbone atoms. The number of neighboring Cα atoms whose labels are the same is given as the QSE value of the center Cα atom at hand. As evidenced by histograms that show very different distributions for different structure configurations, the proposed measure captures local properties that are characteristic for a residue's eight‐directional neighborhood within a sphere. Compared with other measures, QSE provides a different view of solvent exposure, and provides information that is specific for different tertiary structure. As the experimental results show, QSE measure can potentially be used in protein structure analysis and predictions.