Molecular dynamics simulation of truncated bovine adrenodoxin.
The 128 amino acid long soluble protein adrenodoxin (Adx) is a typical member of the ferredoxin protein family that are electron carrier proteins with an iron-sulfur cofactor. Adx carries electrons from adrenodoxin reductase (AdR) to cytochrome P450s. Its binding modes to these proteins were previously characterized by site-directed mutagenesis, by X-ray crystallography for the complex Adx:AdR, and by NMR. However, no clear evidence has been provided for the driving force that promotes Adx detachment from AdR upon reduction. Here, we characterized the conformational dynamics of unbound Adx in the oxidized and reduced forms using 2-20 ns long molecular dynamics simulations. The most noticeable difference between both forms is the enhanced flexibility of the loop (47-51) surrounding the iron-sulfur cluster in the reduced form. Together with several structural displacements at the binding interface, this increased flexibility may be the key factor promoting unbinding of reduced Adx from AdR. This points to an intrinsic property of reduced Adx that drives dissociation.
Shakya
Saurabh Kumar
SK
Center for Bioinformatics, Saarland University, D-66041 Saarbrücken, Germany.
Gu
Wei
W
Helms
Volkhard
V
D000325:Adrenodoxin / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D001665:Binding Sites; D002417:Cattle; D003198:Computer Simulation; D004355:Drug Stability; D006860:Hydrogen Bonding; D007700:Kinetics; D008958:Models, Molecular; D010084:Oxidation-Reduction; D011485:Protein Binding; D011487:Protein Conformation; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013696:Temperature
D000596:Amino Acids; D000325:Adrenodoxin