Journal of Molecular Biology
Stereospecific Interactions of Proline Residues in Protein Structures and Complexes
Introduction
Pro is the only residue with an aliphatic ring that encompasses both the main and side-chains. As a result of the ring constraint the backbone torsion angle φ is restricted to a value around −60°,1 making it ideal for a location in β-turns2., 3. or at the N-terminal end of α-helices.4 Very often though, Pro is referred to in a negative sense, lacking an NH group, it cannot form a hydrogen bond and thus is unable to occur in an α-helix or in a β-strand.5 Nevertheless, Pro is found in the middle of α-helices and this has been explained by the existence of a non-conventional C–H⋯O hydrogen bond involving the ring C–H groups.6 This has prompted us to look into other specific interactions involving the Pro ring and see if they can be responsible for the occurrence of Pro in a given context of protein structures. We have recently analyzed the relative orientation between different aromatic residues7., 8., 9. and in the same vein we wanted to analyze the geometry of interaction of Pro and aromatic rings. Some of the unique structural features, such as the occurrence of cis peptide bonds involving Pro residues, have been explained by the stability that results from the stacking of Pro and aromatic rings and the concomitant C–H⋯π interaction.10 Though not as strong energetically as a conventional hydrogen bond, the non-conventional hydrogen bonds are quite ubiquitous.11., 12., 13. Here, we not only identify these interactions involving proline C–H groups in protein structures, we correlate their occurrence with the geometry of interaction of Pro with other aromatic residues. Structural motifs involving Pro–aromatic interactions and a novel use of C–H⋯O interaction in capping helical structures are presented. Finally, we show the importance of such interactions in molecular recognition, in particular the binding of Pro-containing protein/peptide to another protein molecule.
Section snippets
Results
A total of 555 chains in 531 PDB files were analyzed. There are 5166 Pro residues, out of which 2322 (45%) are involved in Pro–aromatic residue (Arom) interactions. Given that Pro residues are usually found near the protein surface and consequently have a smaller number of contacts with other protein atoms than expected from its size,14 it is rather interesting that such a large percentage of Pro residues have an aromatic residue in its neighborhood. An even larger percentage (74%) of Pro is
C–H⋯π and C–H⋯O interactions involving proline C–H groups
While conventional hydrogen bonds involve electronegative atoms like oxygen and nitrogen, weaker donors, such as the C–H group and acceptors like the π-electron cloud of an aromatic ring, can also be engaged by hydrogen bond interactions.54., 55., 56. Though weaker than conventional hydrogen bonds, the importance of C–H⋯π interactions are being increasingly recognized in protein structures10., 11., 12., 13. and in the binding of substrates and cofactors.57., 58. Likewise, a number of studies
Materials and Methods
Atomic coordinates were obtained from the Protein Data Bank (PDB) at the Research Collaboratory for Structural Bioinformatics (RCSB).67 A total of 555 chains (in 531 files) were selected using PDB_SELECT68 from PDB files (as of April, 2002) with an R-factor≤20%, and resolution of ≤2.0 Å and sequence identity less than 25%. Only those Pro and aromatic residues (Arom) were considered for which the fractional occupancies of all ring atoms were 1.00. As discussed by Samanta et al.,14 if the distance
Acknowledgements
R.B. was supported by a Senior Research Fellowship from the Council of Scientific and Industrial Research of India.
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