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A Survey of Aspartate−Phenylalanine and Glutamate−Phenylalanine Interactions in the Protein Data Bank: Searching for Anion−π Pairs

Philip, Vivek, Harris, Jason, Adams, Rachel, Nguyen, Don, Spiers, Jeremy, Baudry, Jerome, Howell, Elizabeth E., Hinde, Robert J.·2011·Biochemistry
DOI 10.1021/bi200066k
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Abstract

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-π pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-π 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-Asp or -Glu pairs separated by less than 7 Å 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-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 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-π pairs are found throughout protein structures, in helices as well as β strands.…

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  • Edge-on aromatic liganding of anions is rare but not unprecedented in proteins, and F- coordination by aromatic edges appears in many small-molecule structures.

    “Edge-on aromatic liganding of anions is rare but not unprecedented in proteins19, and F- coordination by aromatic edges appears in many small-molecule structures20.”

    From Crystal structures of a double-barrelled fluoride ion channel (2015) · cites this paper as [19]

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Metadata

Authors
Philip, V., Harris, J., Adams, R., Nguyen, D., Spiers, J., Baudry, J., Howell, E. E., & Hinde, R. J.
Venue
Biochemistry
Publisher
American Chemical Society (ACS)
Published
2011-03-18
Volume
50
Issue
14
Pages
2939-2950
ISSN
  • 0006-2960
  • 1520-4995
DOI
10.1021/bi200066k
Cited by
109
References
1
Language
en

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