Metadynamics simulations of twist in ApT and GpC sequence with and without H-NS bound

<br>Metadynamics production runs were conducted using GROMACS 2023.2 patched with PLUMED-2.9.0, incorporating the RBB-NA code available on GitHub. The RBB-NA algorithm enables control of rigid base parameters in all-atom nucleic acid simulations, allowing manipulation of DNA’s six rotational parameters (tilt, roll, twist, buckle, propeller, and opening) and six translational parameters (shift, slide, rise, shear, stretch, and stagger). The twist of the central step (6th base pair) was used as the collective variable (CV). Gaussian potentials with a width of 0.04 radians and a height of 0.1 kJ/mol were deposited every 4 ps, with the bias applied only within the 10°–60° interval to prevent complete DNA denaturation at extreme twist values.

元动力学生产模拟采用打有PLUMED-2.9.0补丁的GROMACS 2023.2完成，并集成了GitHub平台开源的RBB-NA代码。RBB-NA算法可在全原子核酸模拟中调控刚性碱基参数，实现对DNA的6种旋转参数（倾斜（tilt）、滚动（roll）、扭转（twist）、扣合（buckle）、螺旋桨扭转（propeller）和张开（opening））及6种平移参数（移位（shift）、滑动（slide）、堆叠高度（rise）、剪切（shear）、拉伸（stretch）和交错（stagger））的精准操控。本研究以第6个碱基对所在的碱基阶梯的扭转角作为集体变量（collective variable, CV）。每4 ps施加一次宽度为0.04弧度、高度为0.1 kJ/mol的高斯势函数，且仅在10°至60°的区间内施加偏置势，以避免极端扭转角下DNA发生完全变性。