International School for Advanced Studies (SISSA/ISAS), CNR-INFM-Democritos National Simulation Center, and Italian Institute of Technology (IIT), Trieste, Italy.
J Chem Theory Comput. 2008 Oct 14;4(10):1745-56. doi: 10.1021/ct8001877.
The anthrax disease is caused by the lethal toxin secreted by the bacterium Bacillus anthracis. The toxin is a protein aggregate which contains a Zn-based hydrolase called anthrax Lethal Factor (LF). In this work, we investigate the structure of its Michaelis complex with an optimized MAPKK-like substrate using several computational methods including density functional theory, molecular dynamics, and coarse grained techniques. Our calculations suggest that (i) the presence of second-shell ligands is crucial for tuning the structure, energetics, and protonation state of the metal binding site, as found in other Zn-based enzymes; (ii) the nucleophilic agent is a Zn-bound water molecule; (iii) substrate binding to the active site groove is mainly stabilized by van der Waals interactions; (iv) the bonds most likely involved in the substrate hydrolysis are only mildly polarized by the protein scaffold; and (v) part of helix α19, which is present in one solid state structure of LF (PDB: 1JKY ), assumes a coiled conformation.
炭疽病是由炭疽杆菌分泌的致死毒素引起的。这种毒素是一种蛋白质聚集体，其中包含一种名为炭疽致死因子（LF）的基于锌的水解酶。在这项工作中，我们使用几种计算方法，包括密度泛函理论、分子动力学和粗粒技术，研究了其与优化的 MAPKK 样底物的迈克尔复合体的结构。我们的计算表明：（i） 第二壳层配体的存在对于调节金属结合位点的结构、能量和质子化状态至关重要，这在其他基于锌的酶中也有发现；（ii） 亲核试剂是一个 Zn 结合的水分子；（iii） 底物结合到活性位点凹槽主要通过范德华相互作用稳定；（iv） 最有可能参与底物水解的键仅被蛋白质支架轻微极化；（v） 存在于 LF 的一个固态结构（PDB：1JKY）中的α19 螺旋的一部分，呈现出卷曲构象。
