粘性介质中蛋白质分子诱导的DNA双螺旋结构的碱基对开放和气泡输运
Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium
摘要：
研究了在粘性介质中，在生理温度下，蛋白质-DNA分子系统的非线性动力学，将DNA看作是一组耦合的线性链，蛋白质以线性链的形式沿着DNA滑动.上述分子系统的非线性动力学一般由扰动的非线性薛定谔方程控制。在非粘性极限下，方程化为完全可积的非线性薛定谔方程，该方程存在N个孤子解。DNA碱基的孤立子激发使DNA碱基对局部打开，并以气泡的形式沿DNA链传播。这可能代表在转录过程中当RNA聚合酶结合到DNA双螺旋链中的启动子位点时产生的气泡。通过将周围环境的粘性效应视为弱扰动，利用微扰理论求解了扰动的NLS方程，结果表明，溶剂在周围环境中的粘性对孤子的振幅有阻尼作用。
英文摘要：
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous medium. The nonlinear dynamics of the above molecular system in general is governed by a perturbed nonlinear Schrödinger equation. In the non-viscous limit, the equation reduces to the completely integrable nonlinear Schrödinger (NLS) equation which admits N-soliton solutions. The soliton excitations of the DNA bases make localized base pair opening and travel along the DNA chain in the form of a bubble. This may represent the bubble generated during the transcription process when an RNA-polymerase binds to a promoter site in the DNA double helical chain. The perturbed NLS equation is solved using a perturbation theory by treating the viscous effect due to surrounding as a weak perturbation and the results show that the viscosity of the solvent in the surrounding damps out the amplitude of the soliton.
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