Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia; St. Petersburg State Polytechnical University, St. Petersburg, Russia.
Petersburg Nuclear Physics Institute, NRC Kurchatov Institute, Gatchina, Russia.
FEBS Lett. 2014 Mar 18;588(6):948-55. doi: 10.1016/j.febslet.2014.01.053. Epub 2014 Feb 13.
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.
利用分子建模技术，我们构建了完整的原子结构，并对大肠杆菌 RecX 蛋白与单链寡核苷酸和 RecA 预链形成的复合物进行了分子动力学模拟。基于建模和 SANS 实验数据，提出了 RecX::ssDNA 复合物的三明治状细丝结构，其中两个 RecX 单体链结合在单链 DNA 的相对侧。RecX::RecA::ssDNA 的模型包括 RecX 结合到 RecA::ssDNA 细丝的沟槽中，这主要是通过 RecX 和 ssDNA 之间的库仑相互作用发生的。溶液中 RecX::RecA::ssDNA 细丝的形成通过 SANS 测量得到了证实，该测量结果与从分子动力学模拟计算出的光谱一致。
