Homology modeling of human serum carnosinase, a potential medicinal target, and MD simulations of its allosteric activation by citrate

Recent biochemical and clinical evidence implicates human serum carnosinase in a variety of pathological conditions, such as neurological disorders and diabetic nephropathy, suggesting that this enzyme is of potential interest as a novel medicinal target. The present study was undertaken with a view to model the serum carnosinase and its catalytic site and to unravel the molecular mechanism by which citrate ions increase the catalytic efficiency of serum carnosinase. A homology model of the enzyme was obtained on the basis of β-alanine synthetase, and its active center was found to bind known substrates carnosine, homocarnosine, and anserine in a binding mode conducive to catalysis. Citrate ions were shown to bind at only three well-defined sites involving both ion pairs and hydrogen bonds. Molecular dynamics simulations evidenced that citrate binding had a remarkable conformational influence on the 3D structure of carnosinase, increasing the binding affinity (i.e., binding score) of carnosine to the catalytic site. This is one of the first reports documenting the molecular mechanism of an allosteric enzyme activator using MD simulations