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
| Autor: | Bogdan Lesyng, M. W. Kalinowski, K. A. Krzyśko, Małgorzata Prokopowicz, Joanna Cieśla, M. Sobieraj, Adrian Gojdź, Borys Kierdaszuk, Adam Jarmuła |
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| Jazyk: | angličtina |
| Rok vydání: | 2015 |
| Předmět: |
Simulations
Stereochemistry Protein Conformation Purine nucleoside phosphorylase Context (language use) QC-MD Ligands PNP Catalysis Substrate Specificity Inorganic Chemistry Excited state Protein structure Formycin A Tyrosinate anion Escherichia coli Fluorescence Resonance Energy Transfer Molecule Computer Simulation Physical and Theoretical Chemistry Original Paper Binding Sites Chemistry Ligand Organic Chemistry Deprotonation Emission spectroscopy SCF-CI Fluorescence Computer Science Applications Förster resonance energy transfer Spectrometry Fluorescence Computational Theory and Mathematics Purine-Nucleoside Phosphorylase Mutation FRET Formycins |
| Zdroj: | Journal of Molecular Modeling |
| ISSN: | 0948-5023 1610-2940 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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