Salt bridge formation

The functionalization of folded motifs is based on an understanding of secondary and tertiary structures (Fig. 2) and must take into account the relative positions of the residues, their rotamer populations and possible interactions with residues that do not form part of the site. For example, glutamic acid in position i has a strong propensity for salt-bridge formation, and thus reduced reactivity, if there is a Lys residue available i-4 in the sequence, but the probabihty is much less if the base is i-3 [60]. Fortunately, there is a wealth of structural information on the structural properties of the common amino acids from studies of natural proteins that provides considerable support for the design of new proteins. The naturally occurring amino acids have so far been used to construct reactive sites for catalysis [11-13], metal- and heme-binding sites [14,15,19,21,22] and for the site-selective functionalization of folded proteins [24,25]. 

Ghosh, T., Grade, S. and Garcia, A.E. (2003) Role of Backbone Hydration and Salt-Bridge Formation in Stability of Alpha-Helix in Solution. Biophys. J., 85, 3187-3193. 

The C-helix is positioned for salt bridge formation to a P-strand of the N-terminal lobe... 

DDC belongs to fold-type I of PLP-dependent enzymes and to group II of PLP-dependent decarboxylases/ In tbe human DDC, as observed for all fold-type I enzymes, tbe aspartate involved in salt bridge formation with tbe pyridine nitrogen (D271) precedes the amino acid sequence in the aaive-site lysine (K303). 

Salt bridge formation between He 16 and Asp 194 (next to the active site) and... 

DNA. Since polylysine binds preferentially to AT-rich DNA, hydrogen bonding in addition to salt bridge formation is likely to occur. Complex formation between polylysine or polycytosine is also reversible and may lead to rod-like structures (Haynes et al., 1970). Small cationic peptides with an aromatic amino acid, e.g., the tripeptide Lys-Tep.Lys, first add to double-stranded DNA and then force the aromatic side chain to intercalate between two nucleic base pairs. Bending of the DNA is then observed (Gabbay et al., 1973). 

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