School of Life Sciences, Centre for Protein Science and Crystallography, State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Hong Kong, China.
Methods Mol Biol. 2024;2841:49-66. doi: 10.1007/978-1-0716-4059-3_4.
In this chapter, we predict the structure of the Arabidopsis receptor-homology-transmembrane-RING-H2 isoform 1 (RMR1) in complex with the C-terminal sorting determinant of cruciferin (CRU1) by AlphaFold2 using the ColabFold web interface and to perform molecular dynamics simulation to probe the dynamics of the predicted structures. Our results predict that the C-terminal carboxylate group of ctVSD of CRU1 is recognized by the conserved Arg89 of the cargo-binding loop of RMR1 and Arg468 of CRU1 by negative charge residues in the cargo-binding pocket of RMR1. The procedures described here are useful for modeling of other protein complexes.
在本章中，我们使用 ColabFold 网络界面中的 AlphaFold2 预测拟南芥受体同源跨膜环指蛋白 1（RMR1）与芸薹素 C 端分选决定因子（CRU1）复合物的结构，并进行分子动力学模拟，以探测预测结构的动力学。我们的结果预测，CRU1 的 ctVSD 的 C 端羧基基团被 RMR1 的货物结合环的保守 Arg89 和 RMR1 的货物结合口袋中的负电荷残基识别Arg468。这里描述的步骤对于其他蛋白质复合物的建模是有用的。
