Conformational Rigidity and Protein Dynamics at Distinct Timescales Regulate PTP1B Activity and Allostery

Mol Cell. 2017 Feb 16;65(4):644-658.e5. doi: 10.1016/j.molcel.2017.01.014.

Abstract

Protein function originates from a cooperation of structural rigidity, dynamics at different timescales, and allostery. However, how these three pillars of protein function are integrated is still only poorly understood. Here we show how these pillars are connected in Protein Tyrosine Phosphatase 1B (PTP1B), a drug target for diabetes and cancer that catalyzes the dephosphorylation of numerous substrates in essential signaling pathways. By combining new experimental and computational data on WT-PTP1B and ≥10 PTP1B variants in multiple states, we discovered a fundamental and evolutionarily conserved CH/π switch that is critical for positioning the catalytically important WPD loop. Furthermore, our data show that PTP1B uses conformational and dynamic allostery to regulate its activity. This shows that both conformational rigidity and dynamics are essential for controlling protein activity. This connection between rigidity and dynamics at different timescales is likely a hallmark of all enzyme function.

Keywords: NMR spectroscopy; PTP1B; X-ray crystallography; allostery; enzyme; fast and intermediate timescale dynamics; protein dynamics; protein tyrosine phosphatase.

MeSH terms

  • Allosteric Regulation
  • Amino Acid Sequence
  • Binding Sites
  • Catalysis
  • Catalytic Domain
  • Conserved Sequence
  • Crystallography
  • Enzyme Inhibitors / metabolism
  • Enzyme Inhibitors / pharmacology
  • Genotype
  • Humans
  • Kinetics
  • Molecular Dynamics Simulation
  • Mutagenesis, Site-Directed
  • Mutation
  • Nuclear Magnetic Resonance, Biomolecular
  • Phenotype
  • Protein Binding
  • Protein Conformation, alpha-Helical
  • Protein Domains
  • Protein Tyrosine Phosphatase, Non-Receptor Type 1 / antagonists & inhibitors
  • Protein Tyrosine Phosphatase, Non-Receptor Type 1 / chemistry
  • Protein Tyrosine Phosphatase, Non-Receptor Type 1 / genetics
  • Protein Tyrosine Phosphatase, Non-Receptor Type 1 / metabolism*
  • Structure-Activity Relationship

Substances

  • Enzyme Inhibitors
  • PTPN1 protein, human
  • Protein Tyrosine Phosphatase, Non-Receptor Type 1