HOME HELP FEEDBACK SUBSCRIPTIONS ARCHIVE SEARCH TABLE OF CONTENTS		QUICK SEARCH:   [advanced] Author: Keyword(s): Year:  Vol:  Page:

This Article Full Text Full Text (PDF) Supplemental Research Data Alert me when this article is cited Alert me if a correction is posted Citation Map Services Email this article to a friend Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via Google Scholar Google Scholar Articles by Byerly, D. W. Articles by Foster, M. P. Search for Related Content PubMed PubMed Citation Articles by Byerly, D. W. Articles by Foster, M. P. Social Bookmarking                   What's this?

FOR THE RECORD

Mapping the surface of Escherichia coli peptide deformylase by NMR with organic solvents

¹ Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio 43210, USA
² Biophysics Program and Protein Research Group, Department of Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA

Reprint requests to: Mark P. Foster, Ohio State Biochemistry Program, Biophysics Program and Protein Research Group, Department of Biochemistry, The Ohio State University, Columbus, OH 43210, USA; e-mail: foster.281{at}osu.edu; fax: (614) 292-6773.

Identifying potential ligand binding sites on a protein surface is an important first step for targeted structure-based drug discovery. While performing control experiments with Escherichia coli peptide deformylase (PDF), we noted that the organic solvents used to solubilize some ligands perturbed many of the same resonances in PDF as the small molecule inhibitors. To further explore this observation, we recorded ¹⁵N HSQC spectra of E. coli peptide deformylase (PDF) in the presence of trace quantities of several simple organic solvents (acetone, DMSO, ethanol, isopropanol) and identified their sites of interaction from local perturbation of amide chemical shifts. Analysis of the protein surface structure revealed that the ligand-induced shift perturbations map to the active site and one additional surface pocket. The correlation between sites of solvent and inhibitor binding highlights the utility of organic solvents to rapidly and effectively validate and characterize binding sites on proteins prior to designing a drug discovery screen. Further, the solvent-induced perturbations have implications for the use of organic solvents to dissolve candidate ligands in NMR-based screens.

Keywords: Surface pockets; chemical shift perturbation; organic solvent; HSQC; peptide deformylase

Abbreviations: PDF, E. coli peptide deformylase • Fo-Met, formyl-methionine • HSQC, 2D 15N-edited 1H spectrum • DMSO, dimethyl sulfoxide

CiteULike    Connotea    Del.icio.us    Digg    Reddit    Technorati    What's this?