Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism
Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism
复制标题
DOI：
10.1073/pnas.1404220111
复制
发表时间：
2014-07-15
影响因子：
11.1
通讯作者：
Vendruscolo, Michele
中科院分区：
文献类型：
--
作者：
Camilloni, Carlo;Sahakyan, Aleksandr B.;Vendruscolo, Michele
脯氨酸异构化是一个普遍存在的过程，在蛋白质的折叠及其功能的调节中起着关键作用。不同家族的酶，称为“肽基脯氨酰异构酶”（PPI酶），催化该反应，该反应涉及氨基酸脯氨酸的N-末端酰胺键的顺式和反式异构体之间的相互转化。然而，这些酶的功能机制的完整描述仍然难以捉摸。我们在这里表明，亲环素A，最常见的PPIases之一，提供了一个催化环境，通过静电处理机制作用于基板上。在这种机制中，催化位点中的静电场使与底物中脯氨酸之前的氨基酸的羰基相关的电偶极子转动，从而导致两个残基之间的肽键旋转。我们确定了这种机制，使用NMR测量，分子动力学模拟和密度泛函理论计算的组合，同时确定亲环素A及其底物的顺式结合和反式结合构象的酶促反应发生。我们预计，这种方法将有助于阐明我们在这里描述的静电处理机制是否是常见的其他PPIases，更一般地说，在表征其他酶的过程。
Proline isomerization is a ubiquitous process that plays a key role in the folding of proteins and in the regulation of their functions. Different families of enzymes, known as "peptidyl-prolyl isomerases" (PPIases), catalyze this reaction, which involves the interconversion between the cis and trans isomers of the N-terminal amide bond of the amino acid proline. However, complete descriptions of the mechanisms by which these enzymes function have remained elusive. We show here that cyclophilin A, one of the most common PPIases, provides a catalytic environment that acts on the substrate through an electrostatic handle mechanism. In this mechanism, the electrostatic field in the catalytic site turns the electric dipole associated with the carbonyl group of the amino acid preceding the proline in the substrate, thus causing the rotation of the peptide bond between the two residues. We identified this mechanism using a combination of NMR measurements, molecular dynamics simulations, and density functional theory calculations to simultaneously determine the cis-bound and trans-bound conformations of cyclophilin A and its substrate as the enzymatic reaction takes place. We anticipate that this approach will be helpful in elucidating whether the electrostatic handle mechanism that we describe here is common to other PPIases and, more generally, in characterizing other enzymatic processes.