Computational analyses, molecular dynamics, and mutagenesis studies of unprocessed form of [NiFe] hydrogenase reveal the role of disorder for efficient enzyme maturation
Computational analyses, molecular dynamics, and mutagenesis studies of unprocessed form of [NiFe] hydrogenase reveal the role of disorder for efficient enzyme maturation
复制标题
DOI：
10.1016/j.bbabio.2019.01.001
复制
发表时间：
2019-04-01
影响因子：
4.3
通讯作者：
Palacios, Jose M.
中科院分区：
文献类型：
--
作者：
Albareda, Marta;Pacios, Luis F.;Palacios, Jose M.
氢的生物生产和氧化是由氢化酶介导的，氢化酶是这些能量相关反应的关键酶。[NiFe]氢化酶的合成涉及一系列复杂的生化反应，以组装酶功能所需的蛋白质亚基和金属辅因子。该生物合成途径的最后一步是处理其大亚基的c末端尾部（CTT），从而允许将镍适当插入这些酶中独特的NiFe(CN)(2)CO辅因子中。在计算机模拟和分子动力学（MD）分析处理和未处理形式的legttminosarum。viciae （Rlv）氢化酶大亚基HupL显示其CTT（残基582-596）是一个内在无序区（IDR），可能为蛋白质水解成熟的最后步骤提供所需的灵活性。对两种形式的酶大亚基的可电离侧链的pKa值的预测也表明，CTT的存在强烈地改变了活性位点周围一些关键残基的质子化状态。此外，MD模拟和突变体分析显示，两个谷氨酸残基（位于n端区域的E27和位于CTT内的E589）可能参与了镍融入酶的过程。计算分析还揭示了Rlv氢化酶LSU与负责去除CTT的内源性蛋白酶HupD相互作用的结构细节。
Biological production and oxidation of hydrogen is mediated by hydrogenases, key enzymes for these energy relevant reactions. Synthesis of [NiFe] hydrogenases involves a complex series of biochemical reactions to assemble protein subunits and metallic cofactors required for enzyme function. A final step in this biosynthetic pathway is the processing of a C-terminal tail (CTT) from its large subunit, thus allowing proper insertion of nickel in the unique NiFe(CN)(2)CO cofactor present in these enzymes. In silico modelling and Molecular Dynamics (MD) analyses of processed vs. unprocessed forms of Rhizobium legttminosarum by. viciae (Rlv) hydrogenase large subunit HupL showed that its CTT (residues 582-596) is an intrinsically disordered region (IDR) that likely provides the required flexibility to the protein for the final steps of proteolytic maturation. Prediction of pKa values of ionizable side chains in both forms of the enzyme's large subunit also revealed that the presence of the CTT strongly modify the protonation state of some key residues around the active site. Furthermore, MD simulations and mutant analyses revealed that two glutamate residues (E27 in the N-terminal region and E589 inside the CTT) likely contribute to the process of nickel incorporation into the enzyme. Computational analysis also revealed structural details on the interaction of Rlv hydrogenase LSU with the endoprotease HupD responsible for the removal of CTT.