Ming Dengming, Kong Yifei, Wu Yinghao, Ma Jianpeng
Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas, USA.
Biophys J. 2003 Jul;85(1):27-35. doi: 10.1016/S0006-3495(03)74451-8.
Here we report the results of applying substructure synthesis method to the simulation of F-actin filaments of several microns in length. The elastic deformational modes of long F-actin filaments were generated from the vibrational modes of the 13-subunit repeat of F-actin using a hierarchical synthesis scheme. The computationally synthesized deformational modes, in the very low-frequency regime, are in good agreement with theoretical solutions for long homogeneous elastic rods, which confirmed the usefulness of substructure synthesis method. Other low-frequency modes carry rich local deformational features that are unique to F-actins. All these modes thus provide a theoretical basis set for a description of spontaneously occurring thermal deformations, such as undulations, of the filaments. The results demonstrate that substructure synthesis method, as a method for computational modal analysis, is capable of scaling up the microscopic dynamic information, obtained from atomistic simulations, to a wide range of macroscopic length scale. Moreover, the combination of substructure synthesis method and hierarchical synthesis scheme provides an effective way in dealing with complex systems of periodic repeats that are abundant in cells.
在此，我们报告将子结构合成方法应用于模拟长度为几微米的F-肌动蛋白丝的结果。使用分层合成方案，从F-肌动蛋白13亚基重复序列的振动模式生成了长F-肌动蛋白丝的弹性变形模式。在极低频范围内，通过计算合成的变形模式与长均匀弹性杆的理论解高度吻合，这证实了子结构合成方法的有效性。其他低频模式具有F-肌动蛋白特有的丰富局部变形特征。因此，所有这些模式为描述细丝自发出现的热变形（如波动）提供了一套理论基础。结果表明，子结构合成方法作为一种计算模态分析方法，能够将从原子模拟获得的微观动态信息扩展到广泛的宏观长度尺度。此外，子结构合成方法与分层合成方案的结合为处理细胞中大量存在的周期性重复复杂系统提供了一种有效方法。
