Search

Here, we report a structural analysis of three human amyloid-beta binding alcohol dehydrogenase (ABAD) mutations, identified in patients with 2-methyl-3-hydroxylbutyryl-coA dehydrogenase (MHBD) deficiency. Mapping of the mutations (R130C, L122V, and N247S) on ABAD crystal structure revealed that they occur in the interfaces of the enzyme tetramer. The wild-type and mutant enzymes were then subjected to molecular dynamics simulations with the intention of studying the local effects of the mutations on protein structure. A computational alanine scanning mutagenesis study has been carried out to study the possible impact of the mutations in the energetic contribution of the mutation sites to the binding free energy of ABAD subunit association. In this study, the MMPB-SA (molecular mechanics/Poisson-Boltzmann surface area) approach has been used to calculate the free energy differences on alanine mutation. The interactions and conservation of the mutation sites have been also evaluated. Our results provide an explanation for the strong effect of the R130C mutation on protein stability, evidenced from experimental results. Possibly, the primary effect of this mutation is to impair dimer assembly, as it changes the hot spot character of position 130 to null spot and causes the loss of important hydrogen bonds mediated by the R130 side chain, including a conserved interface hydrogen bond. The other two mutations do not significantly change the energetic contribution of residues 122 and 247 to subunit association, but they are predicted to cause structural changes that affect the enzymatic activity. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [ABSTRACT FROM AUTHOR]

Seven nucleoside reverse transcriptase (RT) inhibitors are currently used in the clinical treatment of acquired immunodeficiency syndrome (AIDS). These substrate analogues block DNA synthesis by the viral enzyme RT. However, the emergence of resistant variants of RT allied to their long-term toxicity requires the design of new and better RT inhibitors, with long-term in vivo efficacy. In this work we used density functional theory (DFT) calculations to develop a set of molecular mechanics (MM) parameters committed to the AMBER force field for one of the most used in the clinic nucleoside reverse transcriptase inhibitors (NRTIs): zidovudine (AZT). These parameters were tested by comparing the optimized geometries of AZT at both the DFT and MM levels of theory. The ability of the new parameters to reproduce the torsional energy of the azide group was also verified by scanning the surface in MM with the new parameters and comparing the results with the same potential energy surface (PES) at the DFT level. Finally, the parameters were validated through classical MD simulations of AZT in aqueous environment. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [ABSTRACT FROM AUTHOR]