H-bonds in Protein-Nucleic Acid Complexes

Of central importance for the formation of a specific protein-DNA complex are hydrogen bonds. The H-bonds are clearly identifiable in high resolution structures. H-bonds occur where a H-bond donor and acceptor he with 0.27-0.31 nm of each other. Energetically most favorable is the hnear arrangement of the H-bond, with deviations from hnearity leading to a reduction in energy. This characteristic is responsible for the stereospecific orientation of H-bond acceptors and donors. The H-bond thus contributes significantly to the spatial orientation between protein and nucleic acid. 

There are many different H-bond donors as well as acceptors in proteins and nucleic acids which contribute to the specific recognition. Important H-bond donors and acceptors in proteins are Asn, Gin, Ser, Thr, Tyr, Glu, Asp, Arg, Lys, Cys and His. The peptide bonds of the backbone often participate, as well. 

The heteroatoms and exocyclic fimctional groups of the bases within the nucleic acid can form H-bonds to residues of a binding protein, in addition to base pairing. Also, the oxygen of the ribose or deoxyribose and the phosphate moiety of DNA can be used as H-bond acceptors. 

The various base pairs, e.g. A T vs G C, can be individually distinguished based on their pattern of H-bond donors and H-bond acceptors, as viewed from the major groove (Fig. 1.11). 

The available structural information on protein-DNA complexes shows that mother nature uses the spectrum of possible H-bond interaction in a flexible manner. Originally it was assumed that, similar to the genetic code, a specific code for contacting a base pair by amino acids existed. 

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