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Structural analysis of ABAD point mutations causing 2‐methyl‐3‐hydroxylbutyryl‐coA deficiency
Author(s) -
Marques Alexandra T.,
Fernandes Pedro A.,
Ramos Maria João
Publication year - 2010
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.22091
Subject(s) - alanine scanning , tetramer , mutation , point mutation , mutagenesis , chemistry , molecular dynamics , molecular mechanics , mutant , hydrogen bond , genetics , stereochemistry , enzyme , biophysics , biochemistry , biology , computational chemistry , gene , molecule , organic chemistry
Abstract 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