caa a22 4500 605512477 CHVBK 20210128100655.0 cr unu---uuuuu 210128e20150401xx s 000 0 eng 10.1007/s00894-015-2602-8 doi (NATIONALLICENCE)springer-10.1007/s00894-015-2602-8 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 [Elektronische Daten] [M. Sobieraj, K. Krzyśko, A. Jarmuła, M. Kalinowski, B. Lesyng, M. Prokopowicz, J. Cieśla, A. Gojdź, B. Kierdaszuk] 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 < k2 < 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 mutants at pH 7 and above. The presence of the tyrosinate anion results in a competitive energy dissipation channel and red-shifted 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 wild-type 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. The Author(s), 2015 Deprotonation nationallicence Emission spectroscopy nationallicence Excited state nationallicence Formycin A nationallicence FRET nationallicence PNP nationallicence QC-MD nationallicence SCF-CI nationallicence Simulations nationallicence Tyrosinate anion nationallicence Ado : Adenosine nationallicence CI : Configurational interaction nationallicence DTT : Dithiotreitol nationallicence EDTA : Ethylenediaminetetraacetic acid nationallicence ESP charges : Electrostatic potential charges nationallicence ETDM : Electronic transition dipole moments nationallicence ETP : Energy transfer probabilities nationallicence FA : Formycin A, 3-(β-D-ribofuranosyl)-7-aminopyrazolo [4,3-d] pyrimidine nationallicence FB : Formycin B nationallicence FPLC : Fast protein liquid chromatography nationallicence FRET : Fluorescence resonance energy transfer or Förester resonance energy transfer nationallicence Guo : Guanosine nationallicence Hepes : N-2-hydroxyethylpiperazine-N'-2-ethanesulfonic acid nationallicence Ino : Inosine nationallicence m7Guo : N (7)-methylguanosine nationallicence MD : Molecular dynamics nationallicence MM : Molecular mechanics nationallicence Pi : Orthophosphate nationallicence PMSF : Phenylmethanesulfonyl fluoride nationallicence PNP : Purine nucleoside phosphorylase nationallicence PNP : Escherichia coli hexameric PNP, the product of the deoD gene nationallicence SA : Ammonium sulfate nationallicence SCF : Self consistent field nationallicence SDS-PAGE : Sodium dodecyl sulfate polyacrylamide gel electrophoresis nationallicence TCSPC : Time-correlated single-photon counting nationallicence Tris-HCl : Tris (hydroxymethyl) aminomethane hydrochloride nationallicence TZVP : Split valence, triple zeta basis set nationallicence Xao : Xanthosine nationallicence Sobieraj M. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut Krzyśko K. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut Jarmuła A. Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093, Warsaw, Poland aut Kalinowski M. Bioinformatics Laboratory, Medical Research Centre, Polish Academy of Sciences, 02-106, Warsaw, Poland aut Lesyng B. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut Prokopowicz M. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut Cieśla J. Department of Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664, Warsaw, Poland aut Gojdź A. Department of Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664, Warsaw, Poland aut Kierdaszuk B. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut Journal of Molecular Modeling Springer Berlin Heidelberg 21/4(2015-04-01), 1-14 1610-2940 21:4<1 2015 21 894 https://doi.org/10.1007/s00894-015-2602-8 text/html Onlinezugriff via DOI BK010053 XK010053 XK010000 Metadata rights reserved Springer special CC-BY-NC licence nationallicence 1 research-article jats NATIONALLICENCE NATIONALLICENCE NL-springer NATIONALLICENCE 856 40 https://doi.org/10.1007/s00894-015-2602-8 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Sobieraj M. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut NATIONALLICENCE 700 1- Krzyśko K. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut NATIONALLICENCE 700 1- Jarmuła A. Department of Biochemistry, Nencki Institute of Experimental Biology, Polish Academy of Sciences, 02-093, Warsaw, Poland aut NATIONALLICENCE 700 1- Kalinowski M. Bioinformatics Laboratory, Medical Research Centre, Polish Academy of Sciences, 02-106, Warsaw, Poland aut NATIONALLICENCE 700 1- Lesyng B. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut NATIONALLICENCE 700 1- Prokopowicz M. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut NATIONALLICENCE 700 1- Cieśla J. Department of Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664, Warsaw, Poland aut NATIONALLICENCE 700 1- Gojdź A. Department of Technology and Biotechnology, Faculty of Chemistry, Warsaw University of Technology, 00-664, Warsaw, Poland aut NATIONALLICENCE 700 1- Kierdaszuk B. Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, 02-089, Warsaw, Poland aut NATIONALLICENCE 773 0- Journal of Molecular Modeling Springer Berlin Heidelberg 21/4(2015-04-01), 1-14 1610-2940 21:4<1 2015 21 894