CH···O Hydrogen Bonds at Protein-Protein Interfaces

Abstract

For the first time, a statistical potential has been developed to quantitatively describe the CH⅐⅐⅐O hydrogen bonding interaction at the protein-protein interface. The calculated energies of the CH⅐⅐⅐O pair interaction show a favorable valley at ϳ3.3 Å, exhibiting a feature typical of an H-bond and similar to the ab initio quantum calculation result (Scheiner, S., Kar, T., and Gu, Y. (2001) J. Biol. Chem. 276, 9832-9837). The potentials have been applied to a set of 469 protein-protein complexes to calculate the contribution of different types of interactions to each protein complex: the average energy contribution of a conventional H-bond is ϳ30%; that of a CH⅐⅐⅐O H-bond is 17%; and that of a hydrophobic interaction is 50%. In some protein-protein complexes, the contribution of the CH⅐⅐⅐O H-bond can reach as high as ϳ40 -50%, indicating the importance of the CH⅐⅐⅐O H-bond at the protein interface. At the interfaces of these complexes, C ␣ H⅐⅐⅐O H-bonds frequently occur between adjacent strands in both parallel and antiparallel orientations, having the obvious structural motif of bifurcated H-bonds. Our study suggests that the weak CH⅐⅐⅐O Hbond makes an important contribution to the association and stability of protein complexes and needs more attention in protein-protein interaction studies.The conventional hydrogen bonds of the type X-H⅐⅐⅐Y (where X and Y ϭ N or O) have been widely found and thoroughly studied in macromolecular structures from both experimental and theoretical perspectives (1, 2, 7-9). On the other hand, close CH⅐⅐⅐O contacts occur often in protein structures and are considered as hydrogen bonds. It is increasingly recognized that weak CH⅐⅐⅐O hydrogen bonds play an important role in the stabilization and function of biological macromolecules (3-6).CH⅐⅐⅐O contacts are now being increasingly widely accepted as genuine hydrogen bonds (10, 11). Much of the evidence for the CH⅐⅐⅐O hydrogen bond comes from the observation that short intermolecular CH⅐⅐⅐O contacts are well established in many small molecule crystals (12, 13). In more recent years, neutron diffraction studies of amino acid crystals (which yield highly accurate positions of hydrogen atoms experimentally) have provided convincing evidence in favor of the ability of the carbon atoms to function directly as hydrogen bond donors in CH⅐⅐⅐O contacts (14). Recently, there have been surveys of high resolution protein structures that reveal the widespread occurrence of weak CH⅐⅐⅐O hydrogen bonds (15-21, 59, 60). Various studies have reported the existence of a weak C ␣ H⅐⅐⅐O hydrogen bond between the parallel ␤-sheets in proteins (17,59,60). At the same time, some mutation studies on protein-ligand interactions have reported that weak CH⅐⅐⅐O bonds stabilize proteinligand complexes (10,22,23). Similar to protein-ligand interfaces, close CH⅐⅐⅐O contacts abound at protein-protein interfaces. Although CH⅐⅐⅐O H-bonds are normally weaker than conventional hydrogen bonds, their number cannot be neglected. The CH⅐⅐⅐O hydrogen bonding interaction is als...

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