title: Structure of RecX protein complex with the presynaptic RecA filament: Molecular dynamics simulations and small angle neutron scattering.
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.
authors: Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia; St. Petersburg State Polytechnical University, St. Petersburg, Russia. Electronic address: alexxy@omrb.pnpi.spb.ru.
authors: Alexey V
authors: AV
authors: Shvetsov
authors: Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia. Electronic address: dtry@omrb.pnpi.spb.ru.
authors: Dmitry V
authors: DV
authors: Lebedev
authors: Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia; Saint-Petersburg State University, Saint-Petersburg, Russia.
authors: Daria B
authors: DB
authors: Chervyakova
authors: Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia.
authors: Irina V
authors: IV
authors: Bakhlanova
authors: Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia; St. Petersburg State Polytechnical University, St. Petersburg, Russia.
authors: Igor A
authors: IA
authors: Yung
authors: Jülich Centre for Neutron Science Outstation at FRM II, Garching, Germany.
authors: Aurel
authors: A
authors: Radulescu
authors: Joint Centre for Nuclear Research, Dubna, Russia.
authors: Aleksandr I
authors: AI
authors: Kuklin
authors: Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia; St. Petersburg State Polytechnical University, St. Petersburg, Russia.
authors: Dmitry M
authors: DM
authors: Baitin
authors: Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia.
authors: Vladimir V
authors: VV
authors: Isaev-Ivanov
mesh_terms: D004277:DNA, Single-Stranded / Q000737:chemistry; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D033363:Neutron Diffraction; D020836:Protein Structure, Quaternary; D017433:Protein Structure, Secondary; D011938:Rec A Recombinases / Q000737:chemistry*; D053838:Scattering, Small Angle; D012996:Solutions
chemical_list: D004277:DNA, Single-Stranded; D029968:Escherichia coli Proteins; C531244:RecX protein, E coli; D012996:Solutions; D011938:Rec A Recombinases
keywords: GROMACS; Molecular dynamics; RecA; RecX; Small angle neutron scattering