Conformational difference between two subunits in flavin mononucleotide binding protein dimers from Desulfovibrio vulgaris (MF): molecular dynamics simulation.
The structural and dynamical properties of five FMN binding protein (FBP) dimers, WT (wild type), E13K (Glu13 replaced by Lys), E13R (Glu13 replaced by Arg), E13T (Glu13 replaced by Thr) and E13Q (Glu13 replaced by Gln), were investigated using a method of molecular dynamics simulation (MDS). In crystal structures, subunit A (Sub A) and subunit B (Sub B) were almost completely equivalent in all of the five FBP dimers. However, the predicted MDS structures of the two subunits were not equivalent in solution, revealed by the distances and inter-planar angles between isoalloxazine (Iso) and aromatic amino acids (Trp32, Tyr35 and Trp106) as well as the hydrogen bonding pairs between Iso and nearby amino acids. Residue root of mean square fluctuations (RMSF) also displayed considerable differences between Sub A and Sub B and in the five FBP dimers. The dynamics of the whole protein structures were examined with the distance (RNN) between the peptide N atom of the N terminal (Met1) and the peptide N atom of the C terminal (Leu122). Water molecules were rarely accessible to Iso in all FBP dimers which are in contrast with other flavoenzymes.
Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahasarakham University, Mahasarakham, 44150, Thailand. Electronic address: nadtanet@gmail.com.
Nadtanet
N
Nunthaboot
Program of Chemistry, Faculty of Science and Technology, Bansomdej Chaopraya Rajabhat University, Bangkok 10600, Thailand.
Kiattisak
K
Lugsanangarm
Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
Somsak
S
Pianwanit
Department of Chemistry, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
Sirirat
S
Kokpol
Division of Laser Biochemistry, Institute for Laser Technology, Utsubo-Honmachi, 1-8-4, Nishiku, Osaka 550-0004, Japan.
Fumio
F
Tanaka
Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Osaka 558-8585, Japan.
Takeshi
T
Nakanishi
Department of Applied Chemistry and Bioengineering, Graduate School of Engineering, Osaka City University, Osaka 558-8585, Japan.
Masaya
M
Kitamura
D001426:Bacterial Proteins / Q000737:chemistry*; D016969:Desulfovibrio vulgaris / Q000737:chemistry*; D019281:Dimerization; D005486:Flavin Mononucleotide / Q000737:chemistry*; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D013050:Spectrometry, Fluorescence
D001426:Bacterial Proteins; D005486:Flavin Mononucleotide
FMN binding proteins; Hydrogen bond; Isoalloxazine; Molecular dynamics simulation; Protein dynamics; RMSF