A possible folding and missfolding explanation of a single point mutation in human galactokinase - A combined theoretical study

Molecular dynamics calculations (MD) were performed (10 ns) for the wild‑type (WT) and the Pro²⁸Thr point mutated (MT) human galactokinase enzyme (GALK1). Comparative analysis of the equilibrated trajectory (last 4 ns) revealed, in different global motions, compared the WT and MT forms of GALK1. The explanation of this behavior was found to be the alteration of the local interaction sites. This was reconfirmed by using quantum chemistry method (B3LYP/6-31G(d)) as well as analysis of the bond critical point using Atoms in Molecules (AIM) theory around the point mutation region.

Both the MD results and AIM analysis have shown that bifurcated H-bond of Glu²⁷ and Thr²⁸ is formed in chain A of the MT (MTA). This can cause the MTA structure more rigid compared to the wild-type one (both WTA and WTB). This type of stabilization was not observed in the case of chain B of MT, eventhough, the primary structure of MTB is the same as that of MTA.

B3LYP level of theory was also used to find the closest minima to native‑like structures of both WT and MT oligopeptide chains as well as their extended structures. Thermodynamic functions (H°, G° and S°) were computed up to hepta-peptide for both wild and mutated oligomers. The change of thermodynamic functions (∆H°, ∆G° and ∆S°) for the folding process was analyzed as a function of mutation. Furthermore, a linear relationship was found between the entropies obtained from quasi-harmonic MD and B3LYP calculations. Entropy was computed at ab initio molecular computation for a short segment (n=7) and by molecular dynamic for a longer segment (n=41) of the enzyme in the vicinity of the site of point mutation (Pro²⁸Thr). The results indicated a changing degree of order or disorder upon mutation in chains A and B. The entropy change was related to relative structural information content.