title: QSE: A new 3-D solvent exposure measure for the analysis of protein structure.
abstract: 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.
authors.affiliation: College of Electrical and Computer Engineering, Chungbuk National University, Chungbuk, Korea.
authors.forename: Peipei
authors.initials: P
authors.lastname: Li
authors.forename: Gouchol
authors.initials: G
authors.lastname: Pok
authors.forename: Kwang Su
authors.initials: KS
authors.lastname: Jung
authors.forename: Ho Sun
authors.initials: HS
authors.lastname: Shon
authors.forename: Keun Ho
authors.initials: KH
authors.lastname: Ryu
mesh_terms: D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D030562:Databases, Protein; D008969:Molecular Sequence Data; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012997:Solvents / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins; D012997:Solvents