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Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering |
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| Authors: | Alexey V Shvetsov Dmitry V Lebedev Daria B Chervyakova Irina V Bakhlanova Igor A Yung Aurel Radulescu Aleksandr I Kuklin Dmitry M Baitin Vladimir V Isaev-Ivanov |
| Institution: | 1. Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia;2. Saint-Petersburg State University, Saint-Petersburg, Russia;3. St. Petersburg State Polytechnical University, St. Petersburg, Russia;4. Joint Centre for Nuclear Research, Dubna, Russia;5. Jülich Centre for Neutron Science Outstation at FRM II, Garching, Germany |
| Abstract: | Using molecular modeling techniques we have built the full atomic structure and performed molecular dynamics simulations for the complexes formed by Escherichia coli RecX protein with a single-stranded oligonucleotide and with RecA presynaptic filament. Based on the modeling and SANS experimental data a sandwich-like filament structure formed two chains of RecX monomers bound to the opposite sides of the single stranded DNA is proposed for RecX::ssDNA complex. The model for RecX::RecA::ssDNA include RecX binding into the grove of RecA::ssDNA filament that occurs mainly via Coulomb interactions between RecX and ssDNA. Formation of RecX::RecA::ssDNA filaments in solution was confirmed by SANS measurements which were in agreement with the spectra computed from the molecular dynamics simulations. |
| Keywords: | RecX RecA Molecular dynamics GROMACS Small angle neutron scattering |
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