A QMMD simulation approach to the analysis of FRE

Authors: M Sobieraj K A Krzyśko A Jarmuła M W Kalinowski B Lesyng M Prokopowicz J Cieśla A Gojdź B Kierdaszuk

Publish Date: 2015/03/10

Volume: 21, Issue: 4, Pages: 75-

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Abstract

Predicting FRET pathways in proteins using computer simulation techniques is very important for reliable interpretation of experimental data A novel and relatively simple methodology has been developed and applied to purine nucleoside phosphorylase PNP complexed with a fluorescent ligand — formycin A FA FRET occurs between an excited Tyr residue D and FA A This study aims to interpret experimental data that among others suggests the absence of FRET for the PNPF159A mutant in complex with FA based on novel theoretical methodology MD simulations for the protein molecule containing D and complexed with A are carried out Interactions of D with its molecular environment are accounted by including changes of the ESP charges in S1 compared to S0 and computed at the SCFCI level FRET probability W F depends on the inverse sixpower of the DA distance R da The orientational factor 0  k2  4 between D and A is computed and included in the analysis Finally W F is timeaveraged over the MD trajectories resulting in its mean value The redshift of the tyrosinate anion emission and thus lack of spectral overlap integral and thermal energy dissipation are the reasons for the FRET absence in the studied mutants at pH 7 and above The presence of the tyrosinate anion results in a competitive energy dissipation channel and redshifted emission thus in consequence in the absence of FRET These studies also indicate an important role of the phenyl ring of Phe159 for FRET in the wildtype PNP which does not exist in the Ala159 mutant and for the effective association of PNP with FA In a more general context our observations point out very interesting and biologically important properties of the tyrosine residue in its excited state which may undergo spontaneous deprotonation in the biomolecular systems resulting further in unexpected physical and/or biological phenomena Until now this observation has not been widely discussed in the literature

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