A QM-MD simulation approach to the analysis of FRET processes in (bio)molecular systems. A case study: complexes of E. coli purine nucleoside phosphorylase and its mutants with formycin A

Journal of Molecular Modeling
M SobierajBorys Kierdaszuk

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 SCF-CI level. FRET probability W F depends on the inverse six-power of the D*-A distance, R da . The orientational factor 0 < k(2) < 4 between D* and A is computed and included in the analysis. Finally W F is time-averaged over the MD trajectories resulting in its mean value. The red-shift 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 mutan...Continue Reading

References

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Aug 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·M S HershfieldS A Short
Jan 1, 1990·Zeitschrift Für Naturforschung. C, a Journal of Biosciences·A BzowskaD Shugar
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Aug 26, 2003·The Journal of Biological Chemistry·Eric M BennettSteven E Ealick

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Methods Mentioned

BETA
FRET
fluorescence microscopy
fluorescence resonance
FRETs

Software Mentioned

TURBOMOLE
CHARMM
egrad
dscf

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