Laboratory for Biomolecular Function Simulation, RIKEN Center for Biosystems Dynamics Research, Kobe, Hyogo, Japan.
Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, USA.
Nat Commun. 2021 Jul 2;12(1):4099. doi: 10.1038/s41467-021-24349-5.
The inside of a cell is highly crowded with proteins and other biomolecules. How proteins express their specific functions together with many off-target proteins in crowded cellular environments is largely unknown. Here, we investigate an inhibitor binding with c-Src kinase using atomistic molecular dynamics (MD) simulations in dilute as well as crowded protein solution. The populations of the inhibitor, 4-amino-5-(4-methylphenyl)-7-(t-butyl)pyrazolo[3,4-d]pyrimidine (PP1), in bulk solution and on the surface of c-Src kinase are reduced as the concentration of crowder bovine serum albumins (BSAs) increases. This observation is consistent with the reduced PP1 inhibitor efficacy in experimental c-Src kinase assays in addition with BSAs. The crowded environment changes the major binding pathway of PP1 toward c-Src kinase compared to that in dilute solution. This change is explained based on the population shift mechanism of local conformations near the inhibitor binding site in c-Src kinase.
细胞内部高度拥挤着蛋白质和其他生物分子。在拥挤的细胞环境中，蛋白质如何与许多非靶标蛋白质一起表达其特定功能，在很大程度上尚不清楚。在这里，我们使用稀溶液和拥挤的蛋白质溶液中的原子分子动力学（MD）模拟研究了与 c-Src 激酶结合的抑制剂。随着牛血清白蛋白（BSA）浓度的增加，抑制剂 4-氨基-5-(4-甲基苯基）-7-(叔丁基）吡唑并[3,4-d]嘧啶（PP1）在本体溶液和 c-Src 激酶表面上的浓度降低。这一观察结果与实验 c-Src 激酶测定中 BSAs 存在时 PP1 抑制剂效力降低的结果一致。与稀溶液相比，拥挤的环境改变了 PP1 与 c-Src 激酶的主要结合途径。这种变化基于 c-Src 激酶中抑制剂结合位点附近局部构象的种群转移机制来解释。
