Phosphate recognition, electrostatic

The ct-3 helix of cl is called the recognition helix, because when cl is bound to DNA, its position deep within the major groove allows it to contact specific DNA bases and hence to determine sequence specificity of binding. The cn-2 helix is in contact primarily with DNA phosphates. These electrostatic contacts strengthen binding but do not contribute to specificity. 

Phosphate Recognition by Electrostatic Interactions and Hydrogen Bonds... 

Pattern recognition using cahxarene receptors that bind to proteins via surface electrostatic interaction has been used to identify a variety of proteins (Kolusheva et al. 2006). Amphiphilic calixarenes terminated with either amino or phosphate groups were incorporated into mixed PDA/phospholipid vesicles, which were incubated with various proteins that differed in their isoelectric points (pi). As expected, proteins with low pi values resulted in a large CR with liposomes containing cationic calixarene receptors. Each protein was characterized by a unique ACR value, where... 

The helix-turn-helix motif is comprised of two a-helices connected by a turn. One a-helix, the recognition helix, binds in the major groove of B-form DNA, forming hydrophobic contacts with the base pairs and electrostatic interactions between the a-helix dipole and the DNA phosphates. The amino-acid side-chains of the recognition... 

Phosphonates may be viewed as structural analogues of phosphate or carboxylates. They are chosen as inhibitors of enzymes which catalyse reactions of carboxylates or phosphates following the recognition that ionic interactions are an important component in enzymic specificity and thus a major factor in the design of inhibitors. They may be expected to interfere with enzymatic processes involving phosphates due to the substitution of the P—O—C bond by the hydrolytically stable P—C bond. On the other hand, the combination of the electrostatic similarity with the stereochemical difference between the tetrahedral phosphonic groups and the planar carboxy groups makes it likely that phosphonates can inhibit enzymes which catalyse reactions of carboxylic acids. 

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