Kinetic and structural changes in HsmtPheRS, induced by pathogenic mutations in human FARS2

Protein Sci. 2017 Aug;26(8):1505-1516. doi: 10.1002/pro.3176. Epub 2017 May 3.

Abstract

Mutations in the mitochondrial aminoacyl-tRNA synthetases (mtaaRSs) can cause profound clinical presentations, and have manifested as diseases with very selective tissue specificity. To date most of the mtaaRS mutations could be phenotypically recognized, such that clinicians could identify the affected mtaaRS from the symptoms alone. Among the recently reported pathogenic variants are point mutations in FARS2 gene, encoding the human mitochondrial PheRS. Patient symptoms range from spastic paraplegia to fatal infantile Alpers encephalopathy. How clinical manifestations of these mutations relate to the changes in three-dimensional structures and kinetic characteristics remains unclear, although impaired aminoacylation has been proposed as possible etiology of diseases. Here, we report four crystal structures of HsmtPheRS mutants, and extensive MD simulations for wild-type and nine mutants to reveal the structural changes on dynamic trajectories of HsmtPheRS. Using steady-state kinetic measurements of phenylalanine activation and tRNAPhe aminoacylation, we gained insight into the structural and kinetic effects of mitochondrial disease-related mutations in FARS2 gene.

Keywords: X-ray structures; kinetic experiments; mitochondrial PheRS; mitochondrial diseases; molecular dynamic simulations; mutants.

Publication types

  • Case Reports

MeSH terms

  • Adolescent
  • Amino Acid Motifs
  • Aminoacylation
  • Binding Sites
  • Child, Preschool
  • Crystallography, X-Ray
  • Diffuse Cerebral Sclerosis of Schilder / diagnosis
  • Diffuse Cerebral Sclerosis of Schilder / genetics*
  • Diffuse Cerebral Sclerosis of Schilder / metabolism
  • Diffuse Cerebral Sclerosis of Schilder / pathology
  • Female
  • Humans
  • Kinetics
  • Male
  • Mitochondria / genetics
  • Mitochondria / metabolism
  • Mitochondria / pathology
  • Mitochondrial Proteins / chemistry*
  • Mitochondrial Proteins / genetics
  • Mitochondrial Proteins / metabolism
  • Molecular Dynamics Simulation
  • Mutation*
  • Paraplegia / diagnosis
  • Paraplegia / genetics*
  • Paraplegia / metabolism
  • Paraplegia / pathology
  • Phenylalanine-tRNA Ligase / chemistry*
  • Phenylalanine-tRNA Ligase / genetics
  • Phenylalanine-tRNA Ligase / metabolism
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Conformation, beta-Strand
  • Protein Interaction Domains and Motifs
  • RNA, Transfer, Phe / chemistry*
  • RNA, Transfer, Phe / metabolism
  • Sequence Alignment
  • Substrate Specificity
  • Thermodynamics

Substances

  • Mitochondrial Proteins
  • RNA, Transfer, Phe
  • FARS2 protein, human
  • Phenylalanine-tRNA Ligase