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) 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 Lin, L. Y.-C. Articles by Meighen, E. A. Search for Related Content PubMed PubMed Citation Articles by Lin, L. Y.-C. Articles by Meighen, E. A. Social Bookmarking                   What's this?

Modeling of the bacterial luciferase-flavin mononucleotide complex combining flexible docking with structure-activity data

¹ Department of Biochemistry, McGill University, Montreal, Quebec, Canada H3G 1Y6
² Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec, Canada H4P 2R2

Reprint requests to: Edward A. Meighen, McIntyre Medical Building, Room 813, Department of Biochemistry, McGill University, 3655 Promenade Sir William Osler, Montreal, PQ, Canada H3G 1Y6; e-mail: meighen{at}med.mcgill.ca; fax: 514-398-7384.

Although the crystal structure of Vibrio harveyi luciferase has been elucidated, the binding sites for the flavin mononucleotide and fatty aldehyde substrates are still unknown. The determined location of the phosphate-binding site close to Arg 107 on the subunit of luciferase is supported here by point mutagenesis. This information, together with previous structure-activity data for the length of the linker connecting the phosphate group to the isoalloxazine ring represent important characteristics of the luciferase-bound conformation of the flavin mononucleotide. A model of the luciferase–flavin complex is developed here using flexible docking supplemented by these structural constraints. The location of the phosphate moiety was used as the anchor in a flexible docking procedure performed by conformation search by using the Monte Carlo minimization approach. The resulting databases of energy-ranked feasible conformations of the luciferase complexes with flavin mononucleotide, -phosphopentylflavin, -phosphobutylflavin, and -phosphopropylflavin were filtered according to the structure-activity profile of these analogs. A unique model was sought not only on energetic criteria but also on the geometric requirement that the isoalloxazine ring of the active flavin analogs must assume a common orientation in the luciferase-binding site, an orientation that is also inaccessible to the inactive flavin analog. The resulting model of the bacterial luciferase–flavin mononucleotide complex is consistent with the experimental data available in the literature. Specifically, the isoalloxazine ring of the flavin mononucleotide interacts with the Ala 74–Ala 75 cis-peptide bond as well as with the Cys 106 side chain in the subunit of luciferase. The model of the binary complex reveals a distinct cavity suitable for aldehyde binding adjacent to the isoalloxazine ring and flanked by other key residues (His 44 and Trp 250) implicated in the active site.

Keywords: Bacterial luciferase; flavin mononucleotide; flexible docking; structural constraints

Abbreviations: FMN, flavin mononucleotide • FMNH2, reduced FMN

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