A molecular mechanism of P-loop pliability of Rho-kinase investigated by molecular dynamic simulation
A molecular mechanism of P-loop pliability of Rho-kinase investigated by molecular dynamic simulation
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DOI：
10.1007/s10822-008-9214-7
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发表时间：
2008-04
影响因子：
3.5
通讯作者：
K. Gohda;T. Hakoshima
中科院分区：
文献类型：
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作者：
K. Gohda;T. Hakoshima
rho激酶在细胞骨架事件（包括平滑肌收缩和神经突生长-锥体塌陷和收缩）的调控中起主导作用，是治疗血管和神经系统疾病的一个有希望的药物靶点。最近的rho激酶与小分子抑制剂法舒地尔络合的晶体结构揭示了atp结合位点的结构细节，atp结合位点代表了抑制剂的靶位点，并表明p环上保守的苯丙氨酸占据了口袋，导致蛋白质与配体接触增加。因此，p环柔韧性被认为在抑制剂结合亲和力和特异性中起重要作用。在本研究中，我们对具有两种不同p环构象（即伸展构象和折叠构象）的Rho-kinase-fasudil复合物进行了分子动力学模拟，以了解其在原子水平上的p环柔韧性和动力学。pka -法舒地尔复合物也用于比较。在MD模拟中，无法观察到从扩展构象或折叠构象开始的p环构象的触发器运动。然而，覆盖在p环上的长环区构象发生了明显的变化，法舒地尔与ATP结合位点酸性残基的离子相互作用方式也发生了变化，这仅在p环延伸构象的rho激酶-法舒地尔复合物中表现出来，而p环折叠构象的rho激酶和PKA复合物没有表现出大的波动。这表明具有扩展p环构象的rho激酶-法舒地尔复合物代表了一种亚稳定状态。本研究获得的p环柔韧性在原子水平上的信息可以为设计有效的和/或选择性的rho激酶抑制剂提供有价值的线索。
Rho-kinase is a leading player in the regulation of cytoskeletal events involving smooth muscle contraction and neurite growth-cone collapse and retraction, and is a promising drug target in the treatment of both vascular and neurological disorders. Recent crystal structure of Rho-kinase complexed with a small-molecule inhibitor fasudil has revealed structural details of the ATP-binding site, which represents the target site for the inhibitor, and showed that the conserved phenylalanine on the P-loop occupies the pocket, resulting in an increase of protein–ligand contacts. Thus, the P-loop pliability is considered to play an important role in inhibitor binding affinity and specificity. In this study, we carried out a molecular dynamic simulation for Rho-kinase–fasudil complexes with two different P-loop conformations, i.e., the extended and folded conformations, in order to understand the P-loop pliability and dynamics at atomic level. A PKA–fasudil complex was also used for comparison. In the MD simulation, the flip-flop movement of the P-loop conformation starting either from the extended or folded conformation was not able to be observed. However, a significant conformational change in a long loop region covering over the P-loop, and also alteration of ionic interaction-manner of fasudil with acidic residues in the ATP binding site were shown only in the Rho-kinase–fasudil complex with the extended P-loop conformation, while Rho-kinase with the folded P-loop conformation and PKA complexes did not show large fluctuations, suggesting that the Rho-kinase–fasudil complex with the extended P-loop conformation represents a meta-stable state. The information of the P-loop pliability at atomic level obtained in this study could provide valuable clues to designing potent and/or selective inhibitors for Rho-kinase.