HYDROGEN-BONDING MOTIFS OF PROTEIN SIDE-CHAINS - DESCRIPTIONS OF BINDING OF ARGININE AND AMIDE GROUPS

The modes of hydrogen bonding of arginine, asparagine, and glutamine s ide chains and of urea have been examined in small-molecule crystal st ructures in the Cambridge Structural Database and in crystal structure s of protein nucleic acid and protein-protein complexes. Analysis of t he hydrogen bonding patterns of each by graph-set theory shows three p atterns of rings (R) with one or two hydrogen bond accepters and two d onors and with eight, nine, or six atoms in the ring, designated R(2)( 2)(8), R(2)(2)(9), and R(2)(1)(6). These three patterns are found for arginine-like groups and for urea, whereas only the first two patterns R(2)(2)(8) and R(2)(2)(9) are found for asparagine- and glutamine-lik e groups. In each case, the entire system is planar within 0.7 Angstro m or less. On the other hand, in macromolecular crystal structures, th e hydrogen bonding patterns in protein-nucleic acid complexes between the nucleic acid base and the protein are all R(2)(2)(9), whereas hydr ogen bonding between Watson-Crick-like pairs of nucleic acid bases is R(2)(2)(8). These two hydrogen bonding arrangements [R(2)(2)(9) and R( 2)(2)(8)] are predetermined by the nature of the groups available for hydrogen bonding. The third motif identified, R(2)(1)(6), involves hyd rogen bonds that are less linear than in the other two motifs and is f ound in proteins.