Molecular dynamics simulation of energy migration between tryptophan residues in apoflavodoxin

N. Nunthaboot, F. Tanaka, S. Kokpol, N.V. Visser, H. van Amerongen, A.J.W.G. Visser

Research output: Contribution to journalArticleAcademicpeer-review

2 Citations (Scopus)


Molecular dynamics (MD) simulations over a 30 ns trajectory have been carried out on apoflavodoxin from Azotobacter vinelandii to compare with the published, experimental time-resolved fluorescence anisotropy results of F¨orster Resonance Energy Transfer (FRET) between the three tryptophan residues. MD analysis of atomic coordinates yielding both the time course of geometric parameters and the time-correlated second-order Legendre polynomial functions reflects immobilization of tryptophans in the protein matrix. However, one tryptophan residue (Trp167) undergoes flip-flop motion on the nanosecond timescale. The simulated time-resolved fluorescence anisotropy of tryptophan residues in apoflavodoxin implying a model of two unidirectional FRET pathways is in very good agreement with the experimental time-resolved fluorescence anisotropy, although the less efficient FRET pathway cannot be resolved and is hidden in the contribution of a slow protein motion.
Original languageEnglish
Pages (from-to)31443-31451
JournalRSC Advances : An international journal to further the chemical sciences
Publication statusPublished - 2014


  • time-resolved fluorescence
  • azotobacter-vinelandii
  • anisotropy decay
  • force-field
  • flavodoxin
  • proteins
  • water
  • pathway
  • system
  • state

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