Computational Analysis on the Formation of Metal-Binding Pterin (MPT) from cyclic Pyranopterin Monophosphate (cPMP) in Molybdenum Cofactor Biosynthesis

Abstract

Formation of molybdopterin (MPT) from cyclic Pyranopterin Mono-Phosphate (cPMP) is the second step in Molybdenum cofactor (MoCo) biosynthesis, which is important for molybdo-enzymes of all organisms. Deficiency of MoCo can cause serious neurological disorders. The focus of this work was to understand the biosynthesis of MPT from cPMP using MPT synthase with the help of computational techniques. Binding pocket for cPMP in MPT synthase was identified using binding pocket prediction software followed by molecular docking. Quantum Mechanical Calculations were performed to understand the reaction mechanism of MPT formation from cPMP using Density Functional Theory (DFT) methods. For Quantum Mechanical Calculations all geometries involved in the reaction mechanism of MPT formation from cPMP were modeled. Geometry optimization and single point energy calculations were performed on all the modeled geometries using B3LYP (Becke, 3-parameter, Lee–Yang–Parr)/ SDD(Stuttgart/Dresden) and B3LYP/LANL2DZ (Los Alamos Na-La 2-Double-zeta) levels of DFT. Keeping the possibility of phosphate group attached with the cPMP, to be protonated or un-protonated, the overall geometry charge and multiplicity of 0,1 and -1,1 were considered, respectively. After analyzing and comparing the results obtained from computational analysis using different levels of DFT on the reaction mechanism of MPT synthase, it has been observed that LANL2DZ gives more feasible results, low energy pathway on the potential energy surface as compared to SDD basis set. In addition, it has also been revealed that cPMP is present in its unprotonated/ anionic form 1 when attached with the MPT synthase for the formation of MPT. When analyzing the role of copper in the MPT formation, computational results indicated that copper plays no specific role in the formation of MPT from cPMP, however, it can provide the place of attachment for molybdate which is the next step of biosynthetic pathway of Moco.