Walker Kenneth T, Nan Ruodan, Wright David W, Gor Jayesh, Bishop Anthony C, Makhatadze George I, Brodsky Barbara, Perkins Stephen J
Department of Structural and Molecular Biology, Darwin Building, University College London, Gower Street, London WC1E 6BT, U.K.
Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, NY 12180-3590, U.S.A.
Biochem J. 2017 Jun 16;474(13):2203-2217. doi: 10.1042/BCJ20170217.
Collagen adopts a characteristic supercoiled triple helical conformation which requires a repeating (Xaa-Yaa-Gly) sequence. Despite the abundance of collagen, a combined experimental and atomistic modelling approach has not so far quantitated the degree of flexibility seen experimentally in the solution structures of collagen triple helices. To address this question, we report an experimental study on the flexibility of varying lengths of collagen triple helical peptides, composed of six, eight, ten and twelve repeats of the most stable Pro-Hyp-Gly (POG) units. In addition, one unblocked peptide, (POG), was compared with the blocked (POG) as a control for the significance of end effects. Complementary analytical ultracentrifugation and synchrotron small angle X-ray scattering data showed that the conformations of the longer triple helical peptides were not well explained by a linear structure derived from crystallography. To interpret these data, molecular dynamics simulations were used to generate 50 000 physically realistic collagen structures for each of the helices. These structures were fitted against their respective scattering data to reveal the best fitting structures from this large ensemble of possible helix structures. This curve fitting confirmed a small degree of non-linearity to exist in these best fit triple helices, with the degree of bending approximated as 4-17° from linearity. Our results open the way for further studies of other collagen triple helices with different sequences and stabilities in order to clarify the role of molecular rigidity and flexibility in collagen extracellular and immune function and disease.
胶原蛋白采用特征性的超螺旋三螺旋构象，这需要一个重复的（Xaa - Yaa - Gly）序列。尽管胶原蛋白含量丰富，但到目前为止，结合实验和原子模型方法尚未对胶原蛋白三螺旋溶液结构中实验观察到的柔性程度进行量化。为了解决这个问题，我们报告了一项关于不同长度胶原蛋白三螺旋肽柔性的实验研究，这些肽由最稳定的Pro - Hyp - Gly（POG）单元的六个、八个、十个和十二个重复组成。此外，将一个未封闭的肽（POG）与封闭的（POG）进行比较，作为末端效应重要性的对照。互补的分析超速离心和同步加速器小角X射线散射数据表明，较长的三螺旋肽的构象不能用晶体学推导的线性结构很好地解释。为了解释这些数据，使用分子动力学模拟为每个螺旋生成50000个符合物理现实的胶原蛋白结构。将这些结构与它们各自的散射数据进行拟合，以从这一大组可能的螺旋结构中揭示最佳拟合结构。这种曲线拟合证实了这些最佳拟合三螺旋中存在一定程度的非线性，弯曲程度相对于线性近似为4 - 17°。我们的结果为进一步研究具有不同序列和稳定性的其他胶原蛋白三螺旋开辟了道路，以便阐明分子刚性和柔性在胶原蛋白细胞外和免疫功能及疾病中的作用。
