Stereospecific Interactions of Proline Residues in Protein Structures and Complexes

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Abstract

The constrained backbone torsion angle of a proline (Pro) residue has usually been invoked to explain its three-dimensional context in proteins. Here we show that specific interactions involving the pyrrolidine ring atoms also contribute to its location in a given secondary structure and its binding to another molecule. It is adept at participating in two rather non-conventional interactions, C–H⋯π and C–H⋯O. The geometry of interaction between the pyrrolidine and aromatic rings, vis-à-vis the occurrence of the C–H⋯π interactions has been elucidated. Some of the secondary structural elements stabilized by Pro–aromatic interactions are β-turns, where a Pro can interact with an adjacent aromatic residue, and in antiparallel β-sheet, where a Pro in an edge strand can interact with an aromatic residue in the adjacent strand at a non-hydrogen-bonded site. The C–H groups at the Cα and Cδ positions can form strong C–H⋯O interactions (as seen from the clustering of points) and such interactions involving a Pro residue at C′ position relative to an α-helix can cap the hydrogen bond forming potentials of the free carbonyl groups at the helix C terminus. Functionally important Pro residues occurring at the binding site of a protein almost invariably engage aromatic residues (with one of them being held by C–H⋯π interaction) from the partner molecule in the complex, and such aromatic residues are highly conserved during evolution.

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.

References (91)

  • A Chakrabartty et al.

    Stability of α-helices

    Advan. Protein Chem.

    (1995)
  • L Serrano

    The relationship between sequence and structure in elementary folding units

    Advan. Protein Chem.

    (2000)
  • L Pal et al.

    Sequence and structure patterns in proteins from an analysis of the shortest helices: implications for helix nucleation

    J. Mol. Biol.

    (2003)
  • S Penel et al.

    Side-chain structures in the first turn of the α-helix

    J. Mol. Biol.

    (1999)
  • T Pawson

    SH2 and SH3 domains in signal transduction

    Advan. Cancer Res.

    (1994)
  • J Luban et al.

    Human-immunodeficiency-virus type-1 gag protein binds to cyclophilin-a and cyclophilin-b

    Cell

    (1993)
  • P Taylor et al.

    Structures of cyclophilin–ligand complexes

    Prog. Biophys. Mol. Biol.

    (1997)
  • B.K Kay et al.

    From peptides to drugs via phage display

    Drug Discov. Today

    (1998)
  • A Zucconi et al.

    Domain repertoires as a tool to derive protein recognition rules

    FEBS Letters

    (2000)
  • T.G.M Schmidt et al.

    Molecular interaction between the strep-tag affinity peptide and its cognate target, streptavidin

    J. Mol. Biol.

    (1996)
  • A Bottger et al.

    Molecular characterization of the hdm2-p53 interaction

    J. Mol. Biol.

    (1997)
  • T.E Meyer et al.

    Protein interaction sites obtained via sequence homology. The site of complexation of electron transfer partners of cytochrome c revealed by mapping amino acid substitutions onto three-dimensional protein surfaces

    Biochimie

    (1994)
  • F Pazos et al.

    Correlated mutations contain information about protein–protein interaction

    J. Mol. Biol.

    (1997)
  • B Kisters-Woike et al.

    On the conservation of protein sequences in evolution

    Trends Biochem. Sci.

    (2000)
  • X Gallet et al.

    A fast method to predict protein interaction sites from sequences

    J. Mol. Biol.

    (2000)
  • A.A Bogan et al.

    Anatomy of hot spots in protein interfaces

    J. Mol. Biol.

    (1998)
  • O Lichtarge et al.

    An evolutionary trace method defines binding surfaces common to protein families

    J. Mol. Biol.

    (1996)
  • A Armon et al.

    ConSurf: a algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information

    J. Mol. Biol.

    (2001)
  • P Chakrabarti et al.

    CH/π interaction in the packing of the adenine ring in protein structures

    J. Mol. Biol.

    (1995)
  • Y Umezawa et al.

    CH/π interactions in the crystal structure of class I MHC antigens and their complexes with peptides

    Bioorg. Med. Chem.

    (1998)
  • Z.S Derewenda et al.

    The occurrence of C–H⋯O hydrogen bonds in proteins

    J. Mol. Biol.

    (1995)
  • J Bella et al.

    Crystallographic evidence for Cα–H⋯O=C hydrogen bonds in a collagen triple helix

    J. Mol. Biol.

    (1996)
  • B.K Ho et al.

    Twist and shear in β-sheets and β-ribbons

    J. Mol. Biol.

    (2002)
  • S Scheiner et al.

    Strength of the CαH⋯O hydrogen bond of amino acid residues

    J. Biol. Chem.

    (2001)
  • R.M Kini et al.

    A hypothetical structural role for proline residues in the flanking segments of protein–protein interaction sites

    Biochem. Biophys. Res. Commun.

    (1995)
  • J.M Word et al.

    Asparagine and glutamine using hydrogen atom contacts in the choice of side chain amide orientation

    J. Mol. Biol.

    (1999)
  • M.T Pisabarro et al.

    Crystal structure of the Ab1-SH3 domain complexed with a designed high affinity peptide ligand: implications for SH3–ligand interactions

    J. Mol. Biol.

    (1998)
  • Y.D Zhao et al.

    Cyclophilin A complexed with a fragment of HIV-1 gag protein: insights into HIV-1 infectious activity

    Structure

    (1997)
  • T.R Gamble et al.

    Crystal structure of human cyclophilin A bound to the amino-terminal domain of HIV-1 capsid

    Cell

    (1996)
  • V Fulop et al.

    Structures of prolyl oligopeptidase substrate/inhibitor complexes

    J. Biol. Chem.

    (2001)
  • J Beneken et al.

    Structure of the Homer EVH1 domain-peptide complex reveals a new twist in polyproline recognition

    Neuron

    (2000)
  • C Sadasivan et al.

    Interaction of the factor XIII activation peptide with α-thrombin

    J. Biol. Chem.

    (2000)
  • R Friedrich et al.

    The methyl group of Nα(Me)Arg-containing peptides disturbs theactive-site geometry of thrombin, impairing efficient cleavage

    J. Mol. Biol.

    (2002)
  • E.G Hutchinson et al.

    A revised set of potentials for β-turn formation in proteins

    Protein Sci.

    (1994)
  • J.S Richardson et al.

    Amino acid preferences for specific locations at the ends of α-helices

    Science

    (1988)
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