Distance mapping in proteins using fluorescence spectroscopy: tyrosine, like tryptophan, quenches bimane fluorescence in a distance-dependent manner

Biochemistry. 2014 Oct 14;53(40):6290-301. doi: 10.1021/bi500493r. Epub 2014 Oct 1.

Abstract

Tryptophan-induced quenching of fluorophores (TrIQ) uses intramolecular fluorescence quenching to assess distances in proteins too small (<15 Å) to be easily probed by traditional Forster resonance energy transfer methods. A powerful aspect of TrIQ is its ability to obtain an ultrafast snapshot of a protein conformation, by identifying "static quenching" (contact between the Trp and probe at the moment of light excitation). Here we report new advances in this site-directed fluorescence labeling (SDFL) approach, gleaned from recent studies of T4 lysozyme (T4L). First, we show that like TrIQ, tyrosine-induced quenching (TyrIQ) occurs for the fluorophore bimane in a distance-dependent fashion, although with some key differences. The Tyr "sphere of quenching" for bimane (≤10 Å) is smaller than for Trp (≤15 Å, Cα-Cα distance), and the size difference between the quenching residue (Tyr) and control (Phe) differs by only a hydroxyl group. Second, we show how TrIQ and TyrIQ can be used together to assess the magnitude and energetics of a protein movement. In these studies, we placed a bimane (probe) and Trp or Tyr (quencher) on opposite ends of a "hinge" in T4L and conducted TrIQ and TyrIQ measurements. Our results are consistent with an ∼5 Å change in Cα-Cα distances between these sites upon substrate binding, in agreement with the crystal structures. Subsequent Arrhenius analysis suggests the activation energy barrier (Ea) to this movement is relatively low (∼1.5-2.5 kcal/mol). Together, these results demonstrate that TyrIQ, used together with TrIQ, significantly expands the power of quenching-based distance mapping SDFL studies.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Boron Compounds / chemistry
  • Bridged Bicyclo Compounds, Heterocyclic / chemistry*
  • Energy Transfer
  • Fluorescent Dyes / chemistry*
  • Hydrogen-Ion Concentration
  • Hydrolysis
  • Kinetics
  • Models, Molecular
  • Muramidase / chemistry
  • Peptidoglycan / chemistry
  • Protein Binding
  • Protein Structure, Tertiary
  • Spectrometry, Fluorescence
  • Tryptophan / chemistry
  • Tyrosine / chemistry

Substances

  • 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene
  • Boron Compounds
  • Bridged Bicyclo Compounds, Heterocyclic
  • Fluorescent Dyes
  • Peptidoglycan
  • bimanes
  • Tyrosine
  • Tryptophan
  • Muramidase