The specificity of protein-nucleic acid recognition is believed to originate largely from hydrogen bonding between protein polar atoms, primarily side-chain and polar atoms of nucleic acid bases. One way to design new nucleic acid binding proteins of novel specificity is by structure-guided alterations of the hydrogen bonding patterns of a nucleic acid-protein complex. We have used cI repressor of bacteriophage λ as a model system. In the λ-repressor-DNA complex, the ε-NH2 group (hydrogen bond donor) of lysine-4 of λ-repressor forms hydrogen bonds with the amide carbonyl atom of asparagine-55 (acceptor) and the O6 (acceptor) of CG6 of operator site OL1. Substitution of lysine-4 (two donors) by iso-steric S-(2-hydroxyethyl)-cysteine (one donor and one acceptor), by site-directed mutagenesis and chemical modification, leads to switch of binding specificity of λ-repressor from C:G to T:A at position 6 of OL1. This suggests that unnatural amino acid substitutions could be a simple way of generating nucleic acid binding proteins of altered specificity.
Bibliographical noteFunding Information:
This work was funded by a grant from Department of Science and Technology, Government of India. We also acknowledge CSIR (India) fellowship to A.M. Funding to pay the Open Access publication charges for this article was provided by CSIR, New Delhi, India.