Wolgemuth Charles W, Sun Sean X
Department of Cell Biology and Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut 06030-3505, USA.
Phys Rev Lett. 2006 Dec 15;97(24):248101. doi: 10.1103/PhysRevLett.97.248101.
Predicting large scale conformations of protein structures is computationally demanding. Here we compute the conformation and elasticity of double-stranded coiled coils using a simple coarse-grained elastic model. By maximizing the contact between hydrophobic residues and minimizing the elastic energy, we show that the minimum energy structure of a coiled coil is a supercoiled double helix of alpha helices. For realistic binding energies, the elastic energy of the alpha helices requires binding every 7th residue, which leads to a pitch and helix angle for the structure that is consistent with experimental measurements. Analysis of the model equations shows how the pitch varies with the helical repeat of the hydrophobic residues and with the ratio of the twisting modulus to the bending modulus and provides an estimate of the persistence length of around 150 nm, in agreement with previous experimental estimates.
预测蛋白质结构的大规模构象对计算要求很高。在此，我们使用一个简单的粗粒度弹性模型来计算双链卷曲螺旋的构象和弹性。通过最大化疏水残基之间的接触并最小化弹性能量，我们表明卷曲螺旋的最低能量结构是α螺旋的超螺旋双螺旋。对于实际的结合能，α螺旋的弹性能量要求每隔7个残基进行结合，这导致该结构的螺距和螺旋角与实验测量结果一致。对模型方程的分析表明螺距如何随疏水残基的螺旋重复以及扭转模量与弯曲模量的比值而变化，并给出了约150 nm的持久长度估计值，这与先前的实验估计相符。
