Predicting the assembly/disassembly order of protein complexes via coarse-grained simulations  

基于粗粒化模拟预测蛋白质复合物的组装/去组装顺序

作　　者：Yunxiao Lu Xin Liu Zhiyong Zhang 卢芸笑;刘欣;张志勇(中国科学技术大学无膜细胞器与细胞动力学教育部重点实验室,生命科学与医学部,安徽合肥230026;中国科学技术大学大数据学院,安徽合肥230026;中国科学技术大学物理系,安徽合肥230026)

机构地区：[1]MOE Key Laboratory for Cellular Dynamics,Division of Life Sciences and Medicine,University of Science and Technology of China,Hefei 230026,China [2]School of Data Science,University of Science and Technology of China,Hefei 230026,China [3]Department of Physics,University of Science and Technology of China,Hefei 230026,China

出　　处：《中国科学技术大学学报》2024年第12期7-15,I0002,I0008,共11页JUSTC

基　　金：This work was supported by the National Key Research and Development Program of China(2021YFA1301504);the Chinese Academy of Sciences Strategic Priority Research Program(XDB37040202);the National Natural Science Foundation of China(91953101).

摘　　要：The assembly of a protein complex is very important for its biological function,which can be investigated by determining the order of assembly/disassembly of its protein subunits.Although static structures of many protein com-plexes are available in the protein data bank,their assembly/disassembly orders of subunits are largely unknown.In addition to experimental techniques for studying subcomplexes in the assembly/disassembly of a protein complex,computational methods can be used to predict the assembly/disassembly order.Since sampling is a nontrivial issue in simulating the assembly/disassembly process,coarse-grained simulations are more efficient than atomic simulations are.In this work,we developed computational protocols for predicting the assembly/disassembly orders of protein complexes via coarse-grained simulations.The protocols were illustrated via two protein complexes,and the predicted assembly/disassembly orders were consistent with the available experimental data.蛋白质复合物的组装对其生物学功能非常重要,我们可以通过确定蛋白质亚基的组装和去组装顺序来研究复合物的组装。虽然蛋白质数据库中已有许多蛋白质复合物的静态结构,但大多数蛋白质复合物的亚基组装和去组装顺序未知。除了利用实验技术研究蛋白质复合物组装和去组装过程中的亚复合物外,我们还可以利用计算模拟方法预测其组装和去组装顺序。由于在模拟蛋白质复合物组装和去组装过程中存在着构象空间采样的问题,因此粗粒化模拟比全原子模拟更有效率。本文开发了利用粗粒化模拟预测蛋白质复合物组装和去组装顺序的计算工具。我们使用两种蛋白质复合物对计算工具进行了初步测试,结果表明预测的组装和去组装顺序与已有的实验数据一致。

关 键 词：protein complexes assembly/disassembly order coarse-grained simulations native contacts 

分 类 号：Q617[生物学—生物物理学]