Insights on the structural perturbations in human MTHFR Ala222Val mutant by protein modeling and molecular dynamics

J Biomol Struct Dyn. 2016;34(4):892-905. doi: 10.1080/07391102.2015.1057866. Epub 2015 Aug 14.

Abstract

Methylenetetrahydrofolate reductase (MTHFR) protein catalyzes the only biochemical reaction which produces methyltetrahydrofolate, the active form of folic acid essential for several molecular functions. The Ala222Val polymorphism of human MTHFR encodes a thermolabile protein associated with increased risk of neural tube defects and cardiovascular disease. Experimental studies have shown that the mutation does not affect the kinetic properties of MTHFR, but inactivates the protein by increasing flavin adenine dinucleotide (FAD) loss. The lack of completely solved crystal structure of MTHFR is an impediment in understanding the structural perturbations caused by the Ala222Val mutation; computational modeling provides a suitable alternative. The three-dimensional structure of human MTHFR protein was obtained through homology modeling, by taking the MTHFR structures from Escherichia coli and Thermus thermophilus as templates. Subsequently, the modeled structure was docked with FAD using Glide, which revealed a very good binding affinity, authenticated by a Glide XP score of -10.3983 (kcal mol(-1)). The MTHFR was mutated by changing Alanine 222 to Valine. The wild-type MTHFR-FAD complex and the Ala222Val mutant MTHFR-FAD complex were subjected to molecular dynamics simulation over 50 ns period. The average difference in backbone root mean square deviation (RMSD) between wild and mutant variant was found to be ~.11 Å. The greater degree of fluctuations in the mutant protein translates to increased conformational stability as a result of mutation. The FAD-binding ability of the mutant MTHFR was also found to be significantly lowered as a result of decreased protein grip caused by increased conformational flexibility. The study provides insights into the Ala222Val mutation of human MTHFR that induces major conformational changes in the tertiary structure, causing a significant reduction in the FAD-binding affinity.

Keywords: Folate; MTHFR Ala222Val polymorphism; flavin adenine dinucleotide (FAD); methylenetetrahydrofolate reductase (MTHFR); modeling; molecular dynamics; structural perturbation analysis.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Catalysis
  • Catalytic Domain
  • Codon
  • Flavin-Adenine Dinucleotide / chemistry
  • Humans
  • Hydrogen Bonding
  • Kinetics
  • Methylenetetrahydrofolate Reductase (NADPH2) / chemistry*
  • Methylenetetrahydrofolate Reductase (NADPH2) / genetics
  • Molecular Docking Simulation
  • Molecular Dynamics Simulation*
  • Mutant Proteins*
  • Mutation
  • Protein Binding
  • Protein Conformation*
  • Structure-Activity Relationship

Substances

  • Codon
  • Mutant Proteins
  • Flavin-Adenine Dinucleotide
  • Methylenetetrahydrofolate Reductase (NADPH2)