Open AccessTertiary structure of two‐electron reduced Megasphaera elsdenii flavodoxin and some implications, as determined by two‐dimensional 1 H‐NMR and restrained molecular dynamics
Author(s) -
MIERLO Carlo P. M.,
LIJNZAAD Philip,
VERVOORT Jacques,
MÜLLER Franz,
BERENDSEN Herman J. C.,
VLIEG Jacob
Publication year - 1990
Publication title -
european journal of biochemistry
Language(s) - English
Resource type - Journals
eISSN - 1432-1033
pISSN - 0014-2956
DOI - 10.1111/j.1432-1033.1990.tb19444.x
Subject(s) - flavodoxin , flavin group , chemistry , crystallography , molecule , nmr spectra database , protein tertiary structure , amide , molecular dynamics , nuclear overhauser effect , proton nmr , stereochemistry , nuclear magnetic resonance spectroscopy , ferredoxin , spectral line , computational chemistry , physics , organic chemistry , biochemistry , astronomy , enzyme
The tertiary structure of the non‐crystallizable two‐electron‐reduced Megasphaera elsdenii flavodoxin (15 kDa, 137 amino acid residues) has been determined using nuclear Overhauser enhancement restraints extracted from two‐dimensional 1 H‐NMR spectra. A tertiary structure satisfying the experimental restraints very well (maximum NOE violation of 66 pm) was obtained with use of restrained molecular dynamics, using 509 distance restraints (including one non‐NOE) on a starting structure modeled from the crystal structure of one‐electron‐reduced Clostridium MP flavodoxin. The protein consists of a central parallel β‐sheet surrounded on both sides by two α‐helices. The flavin is positioned at the periphery of the molecule. The tertiary structure of the protein is highly defined with the exception of the flavin. The latter is expected to result from performing the restrained molecular dynamics simulation without water molecules and without proper charges on the flavin. The flavin, including the phosphate, the ribityl side chain and the isoalloxazine ring, is solvent accessible under the experimental conditions used and evidenced by a two‐dimensional amide exchange experiment. This accessibility is expected to be important in the redox potential regulation of the semiquinone hydroquinone couple of the protein. The amide exchange against deuterons and several typical line shapes in the two‐dimensional NMR spectra are consistent with the structure generated. The structure is discussed in detail.