A Survey of Aspartate鈭扨henylalanine and Glutamate鈭扨henylalanine Interactions in the Protein Data Bank: Searching for Anion鈭捪€ Pairs

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• 作者：Vivek Philip ; Jason Harris ; Rachel Adams ; Don Nguyen ; Jeremy Spiers ; Jerome Baudry ; Elizabeth E. Howell ; Robert J. Hinde
• 刊名：Biochemistry
• 出版年：2011
• 出版时间：April 12, 2011
• 年：2011
• 卷：50
• 期：14
• 页码：2939-2950
• 全文大小：1052K
• 年卷期：v.50,no.14(April 12, 2011)
• ISSN：1520-4995

文摘

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion鈭捪€ pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion鈭抭uadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242鈭?249]. To study the role of anion鈭捪€ interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification of Phe鈭扐sp or 鈭扜lu pairs separated by less than 7 脜 in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura鈭扢orokuma energy calculations were performed on roughly 19000 benzene鈭抐ormate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (鈭? to 鈭?.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion鈭捪€ pairs are found throughout protein structures, in helices as well as 尾 strands. Numerous pairs also had nearby cation鈭捪€ interactions as well as potential 蟺鈭捪€ stacking. While more than 1000 structures did not contain an anion鈭捪€ pair, the 3134 remaining structures contained approximately 2.6 anion鈭捪€ pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.