Flexibility of prolyl oligopeptidase:: Molecular dynamics and molecular framework analysis of the potential substrate pathways
Flexibility of prolyl oligopeptidase:: Molecular dynamics and molecular framework analysis of the potential substrate pathways
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DOI：
10.1002/prot.20508
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发表时间：
2005-08-15
影响因子：
2.9
通讯作者：
Simon, I
中科院分区：
文献类型：
--
作者：
Fuxreiter, M;Magyar, C;Simon, I
利用分子动力学（MD）和分子框架方法研究了脯氨酰寡肽酶的柔韧性，以描绘底物到活性位点的路线。酶的选择性是由七叶β -推进器介导的，在晶体结构中，它不指示底物到达催化中心的可能通道。然而，它的开放式拓扑结构可以让叶片分开，让基底进入大的中心腔。利用FIRST （Floppy Inclusion and Rigid Substructure Topology）方法对脯氨酸寡肽酶结构进行柔韧性分析，通过MD模拟得到的原子波动证明了螺旋桨结构域的刚性，这使得底物不允许通过该结构域接近活性位点。相反，通过相互关联分析和基本动力学，在区域间区域有一个较小的通道，包括肽酶结构域的高度柔性n端段和螺旋桨（残基192-205）的亲水性环，这是底物的唯一潜在途径。柔性环的功能重要性也通过酶的动力学分析得到了验证。通过表征两个结构域的协同运动来合理化工程二硫桥的催化作用。
The flexibility of prolyl oligopeptidase has been investigated using molecular dynamics (MD) and molecular framework approaches to delineate the route of the substrate to the active site. The selectivity of the enzyme is mediated by a seven-bladed beta-propeller that in the crystal structure does not indicate the possible passage for the substrate to the catalytic center. Its open topology however, could allow the blades to move apart and let the substrate into the large central cavity. Flexibility analysis of prolyl oligopeptidase structure using the FIRST (Floppy Inclusion and Rigid Substructure Topology) approach and the atomic fluctuations derived from MD simulations demonstrated the rigidity of the propeller domain, which does not permit the substrate to approach the active site through this domain. Instead, a smaller tunnel at the inter-domain region comprising the highly flexible N-terminal segment of the peptidase domain and a facing hydrophilic loop from the propeller (residues 192-205) was identified by cross-correlation analysis and essential dynamics as the only potential pathway for the substrate. The functional importance of the flexible loop has been also verified by kinetic analysis of the enzyme with a split loop. Catalytic effect of engineered disulfide bridges was rationalized by characterizing the concerted motions of the two domains.