title: Ligand-induced changes in the structure and dynamics of Escherichia coli peptide deformylase.
abstract: 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.
authors.affiliation: Biophysics Program, The Ohio StateUniversity, Columbus, Ohio 43210, USA.
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Amero
authors.forename: Douglas W
authors.initials: DW
authors.lastname: Byerly
authors.forename: Craig A
authors.initials: CA
authors.lastname: McElroy
authors.forename: Amber
authors.initials: A
authors.lastname: Simmons
authors.forename: Mark P
authors.initials: MP
authors.lastname: Foster
mesh_terms: D000577:Amides / Q000737:chemistry; D000581:Amidohydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000378:metabolism; D002151:Calorimetry; D020134:Catalytic Domain; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000201:enzymology*; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006877:Hydroxamic Acids / Q000737:chemistry / Q000378:metabolism; D008024:Ligands; D008670:Metals / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D019906:Nuclear Magnetic Resonance, Biomolecular; D011485:Protein Binding; D011487:Protein Conformation; D013816:Thermodynamics
chemical_list: D000577:Amides; D000900:Anti-Bacterial Agents; D029968:Escherichia coli Proteins; D006877:Hydroxamic Acids; D008024:Ligands; D008670:Metals; D000581:Amidohydrolases; C084507:peptide deformylase; C010531:actinonin