Pietropaolo Adriana, Muccioli Luca, Berardi Roberto, Zannoni Claudio
Dipartimento di Chimica Fisica ed Inorganica and INSTM, Università di Bologna, V.le Risorgimento, 4, I-40136 Bologna, Italy.
Proteins. 2008 Feb 15;70(3):667-77. doi: 10.1002/prot.21578.
We propose a methodology for the description of the secondary structure of proteins, based on assigning a chirality parameter to short aminoacid sequences according to their arrangement in space at a certain time. We validated the method on ideal and crystalline structures, showing that it can assign secondary structures and that this assignment is robust with respect to random conformational perturbations. From the values of the index and its pattern along a sequence it is possible to recognize many structural motifs of a protein, and in particular poly-L-proline II left-handed helices, often not detected by secondary structure assignment algorithms. Assigning an instantaneous chirality index to the fragments also allows the dynamics to be studied. With this purpose, molecular dynamics simulations were carried out in water for selected hemoglobin (110 ns) and immunoglobulin antigen fragments (50 ns), showing the capability of the chiral index in identifying the stable secondary structure elements, as well as in following their time evolution and conformational changes during the trajectory.
我们提出了一种描述蛋白质二级结构的方法，该方法基于根据短氨基酸序列在特定时间的空间排列为其分配一个手性参数。我们在理想结构和晶体结构上验证了该方法，结果表明它能够分配二级结构，并且这种分配对于随机构象扰动具有鲁棒性。从沿着序列的指数值及其模式可以识别蛋白质的许多结构基序，特别是多聚-L-脯氨酸II型左手螺旋，而二级结构分配算法通常无法检测到这种结构。为片段分配瞬时手性指数还可以研究动力学。为此，我们在水中对选定的血红蛋白（110纳秒）和免疫球蛋白抗原片段（50纳秒）进行了分子动力学模拟，结果表明手性指数能够识别稳定的二级结构元件，以及跟踪它们在轨迹中的时间演化和构象变化。
