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Peptide deformylase (PDF) is an enzyme that is responsible for removing the
formyl group from nascently synthesized polypeptides in bacteria, attracting
much attention as a potential target for novel antibacterial agents. Efforts to
develop potent inhibitors of the enzyme have progressed on the basis of
classical medicinal chemistry, combinatorial chemistry, and structural
approaches, yet the validity of PDF as an antibacterial target hangs, in part,
on the ability of inhibitors to selectively target this enzyme in favor of
structurally related metallohydrolases. We have used (15)N NMR spectroscopy and
isothermal titration calorimetry to investigate the high-affinity interaction of
EcPDF with actinonin, a naturally occurring potent EcPDF inhibitor. Backbone
amide chemical shifts, residual dipolar couplings, hydrogen-deuterium exchange,
and (15)N relaxation reveal structural and dynamic effects of ligand binding in
the immediate vicinity of the ligand-binding site as well as at remote sites. A
comparison of the crystal structures of free and actinonin-bound EcPDF with the
solution data suggests that most of the consequences of the ligand binding to
the protein are lost or obscured during crystallization. The results of these
studies improve our understanding of the thermodynamic global minimum and have
important implications for structure-based drug design.
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