Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 456296
Title Molecular dynamics simulation of energy migration between tryptophan residues in apoflavodoxin
Author(s) Nunthaboot, N.; Tanaka, F.; Kokpol, S.; Visser, N.V.; Amerongen, H. van; Visser, A.J.W.G.
Source RSC Advances : An international journal to further the chemical sciences 4 (2014). - ISSN 2046-2069 - p. 31443 - 31451.
DOI https://doi.org/10.1039/c4ra03779k
Department(s) Biophysics
Biochemistry
Publication type Refereed Article in a scientific journal
Publication year 2014
Keyword(s) time-resolved fluorescence - azotobacter-vinelandii - anisotropy decay - force-field - flavodoxin - proteins - water - pathway - system - state
Abstract 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.
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