NMR investigation of the solution conformation of oxidized flavodoxin from Desulfovibrio vulgaris. Determination of the tertiary structure and detection of protein-bound water molecules.

Abstract

Desulfovibrio vulgaris flavodoxin has been investigated with a combination of homo- and hetero-nuclear two-dimensional and three-dimensional NMR spectroscopy. The analysis of NOE, hydrogen exchange and J-coupling data led to a set of 1349 NOE, 63 hydrogen bond and 109 backbone phi-angle restraints which were used to determine the solution structure of the oxidized flavodoxin applying the distance geometry program DIANA combined with restrained energy minimization methods. Flavodoxin in solution consists of a five-stranded parallel beta-sheet which is pairwise flanked by four alpha-helices. The solution structure has been compared with the known crystal structure. While the global fold is identical, differences have been detected concerning local conformations. In addition, protein-bound water molecules have been localized by NOE effects which were detected in NMR experiments avoiding solvent suppression. The locations of these water molecules have been compared with those found in the X-ray structure.