Department of Physiology and Biophysics, Boston University School of Medicine, 72 East Concord Street, Boston, MA 02118, USA.
J Struct Biol. 2010 May;170(2):313-8. doi: 10.1016/j.jsb.2010.01.016. Epub 2010 Feb 1.
The inherent flexibility of rod-like tropomyosin coiled-coils is a significant factor that constrains tropomyosin's complex positional dynamics on actin filaments. Flexibility of elongated straight molecules typically is assessed by persistence length, a measure of lengthwise thermal bending fluctuations. However, if a molecule's equilibrium conformation is curved, this formulation yields an "apparent" persistence length ( approximately 100nm for tropomyosin), measuring deviations from idealized straight conformations which then overestimate actual dynamic flexibility. To obtain the "dynamic" persistence length, a true measurement of flexural stiffness, the average curvature of the molecule must be taken into account. Different methods used in our studies for measuring the dynamic persistence length directly from Molecular Dynamics (MD) simulations of tropomyosin are described here in detail. The dynamic persistence length found, 460+/-40nm, is approximately 12-times longer than tropomyosin and 5-times the apparent persistence length, showing that tropomyosin is considerably stiffer than previously thought. The longitudinal twisting behavior of tropomyosin during MD shows that the amplitude of end-to-end twisting fluctuation is approximately 30 degrees when tropomyosin adopts its near-average conformation. The measured bending and twisting flexibilities are used to evaluate different models of tropomyosin motion on F-actin.
肌球蛋白原丝上的旋绕肌动蛋白的固有灵活性是限制肌球蛋白原丝在肌动蛋白丝上复杂位置动态的一个重要因素。长而直的分子的灵活性通常通过持久长度来评估，这是衡量沿长度方向热弯曲波动的一个指标。然而，如果分子的平衡构象是弯曲的，那么这种公式就会产生一个“表观”持久长度（肌球蛋白原丝约为 100nm），测量与理想直构象的偏差，从而高估实际的动态灵活性。为了获得“动态”持久长度，即真正的弯曲刚度测量值，必须考虑分子的平均曲率。这里详细描述了我们在研究中用于直接从肌球蛋白原丝的分子动力学（MD）模拟中测量动态持久长度的不同方法。发现的动态持久长度为 460+/-40nm，大约是肌球蛋白原丝的 12 倍，是表观持久长度的 5 倍，这表明肌球蛋白原丝比之前认为的要硬得多。肌球蛋白原丝在 MD 过程中的纵向扭曲行为表明，当肌球蛋白原丝采用其接近平均的构象时，其末端到末端的扭曲波动幅度约为 30 度。测量的弯曲和扭曲灵活性用于评估肌球蛋白原丝在 F-肌动蛋白上运动的不同模型。
