In vitro selection of nicotinamide-binding peptides

Massachusetts General Hospital, Boston MA

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Abstract

DESCRIPTION (provided by applicant): We propose to use mRNA display to select for a synthetic protein that specifically binds nicotinamide adenine dinucleotide (NAD), and to compare and contrast the structural and biochemical characteristics of the selected protein with natural NAD proteins. These proteins will be evaluated by a variety of criteria, including those that will assess NAD affinity, structural stability, and the elucidation of the tertiary fold. Comparisons between this NAD-binding peptide with the previously selected ATP-binding peptide will be informative since NAD is essentially an ATP derivative, and ATP-binding and NAD-binding proteins share many structural features. Interestingly, analogous comparisons between in vitro selected RNAs show a propensity for adenosine recognition. Whether similar preferences exist for in vitro evolved proteins has yet to be determined. Additionally, in vitro selected cofactor binding motifs can subsequently be used as starting points for selections of catalytic activity or for targets of protein-protein interaction domains. Such progressions may ultimately allow for the generation of synthetic pathways that could either be inserted into bacterial chromosomes or encapsulated in artificial membranes.