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...

Calculating protein-protein interaction energies is crucial for understanding protein-protein associations. On the basis of the methodology of mean-field potential, we have developed an empirical approach to estimate binding free energy for protein-protein interactions. This knowledge-based approach has been used to derive distance-dependent free energies of protein complexes from a nonredundant training set in the Protein Data Bank (PDB), with a careful treatment of homology. We calculate atom pair potentials for 16 pair interactions, which can reflect the importance of hydrophobic interactions and specific hydrogen-bonding interactions. The derived potentials for hydrogen-bonding interactions show a valley of favorable interactions at a distance of approximately 3 A, corresponding to that of an established hydrogen bond. For the test set of 28 protein complexes, the calculated energies have a correlation coefficient of 0.75 compared with experimental binding free energies. The performance of the method in ranking the binding energies of different protein-protein complexes shows that the energy estimation can be applied to value binding free energies for protein-protein associations.

No abstract

RNAi is a major antiviral defense response in plant and animal model systems. RNA-dependent RNA polymerase 6 (RDR6) is an essential component of RNAi, which plays an important role in the resistance against viruses in the model plants. We found previously that rice RDR6 (OsRDR6) functioned in the defense against Rice stripe virus (RSV), and Rice Dwarf Phytoreovirus (RDV) infection resulted in down-regulation of expression of RDR6. Here we report our new findings on the function of OsRDR6 against RDV. Our result showed that down-regulation of OsRDR6 through the antisense (OsRDR6AS) strategy increased rice susceptibility to RDV infection while over-expression of OsRDR6 had no effect on RDV infection. The accumulation of RDV vsiRNAs was reduced in the OsRDR6AS plants. In the OsRDR6 over-expressed plants, the levels of OsRDR6 RNA transcript and protein were much higher than that in the control plants. Interestingly, the accumulation level of OsRDR6 protein became undetectable after RDV infection. This finding indicated that the translation and/or stability of OsRDR6 protein were negatively impacted upon RDV infection. This new finding provides a new light on the function of RDR6 in plant defense response and the cross-talking between factors encoded by host plant and double-stranded RNA viruses.