Path Ensembles for Pin1-Catalyzed Cis-Trans Isomerization of a Substrate Calculated by Weighted Ensemble Simulations
Path Ensembles for Pin1-Catalyzed Cis-Trans Isomerization of a Substrate Calculated by Weighted Ensemble Simulations
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DOI：
10.1021/acs.jctc.0c01280
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发表时间：
2021-03-26
影响因子：
5.5
通讯作者：
Fujisaki, Hiroshi
中科院分区：
文献类型：
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作者：
Moritsugu, Kei;Yamamoto, Norifumi;Fujisaki, Hiroshi
Pin 1酶蛋白特异性识别磷酸化丝氨酸/苏氨酸（pSer/pThr），并催化顺式和反式之间肽基脯氨酰键的缓慢相互转化。顺式和反式之间的结构动力学对于揭示催化的潜在分子机理是必不可少的。在这项研究中，我们应用加权系综（WE）模拟方法，以获得全面的路径系综的Pin 1催化异构化过程。相关的速率常数为顺式-反式和反式-顺式异构化计算为亚微秒的时间尺度，这是在良好的协议与计算的自由能景观的顺式形式是稍微不太有利。类似委员会的分析表明，与隔离底物的固有位置（ω类似于90度）相比，过渡态向反式（在异构化角度ω类似于110度）的转变。计算出的结构系综澄清了双组氨酸基序，His 59/His 157，和碱性残基，Lys 63/Arg 68/Arg 69，锚的肽基脯氨酰键，在Pro中的芳环，和磷酸在pSer，分别两侧的作用。扭转角的旋转被发现是通过中继pSer中的主链氧的氢键伴侣从Cys 113在顺式到Arg 68在反式，通过Ser 154在过渡态，这是真正的原因，在过渡态的移动。Ser 154作为异构化的驱动力的作用被证实了额外的WE和自由能计算S154 A突变体的异构化发生稍慢，通过突变的自由能垒增加。本研究表明，有效的WE模拟反应物和产物状态之间的大量路径采样，解开酶催化的分子机制。
Pin1 enzyme protein recognizes specifically phosphorylated serine/threonine (pSer/pThr) and catalyzes the slow interconversion of the peptidylprolyl bond between cis and trans forms. Structural dynamics between the cis and trans forms are essential to reveal the underlying molecular mechanism of the catalysis. In this study, we apply the weighted ensemble (WE) simulation method to obtain comprehensive path ensembles for the Pin1-catalyzed isomerization process. Associated rate constants for both cis-to-trans and trans-to-cis isomerization are calculated to be submicroseconds time scales, which are in good agreement with the calculated free energy landscape where the cis form is slightly less favorable. The committor-like analysis indicates the shift of the transition state toward trans form (at the isomerization angle omega similar to 110 degrees) compared to the intrinsic position for the isolated substrate (omega similar to 90 degrees). The calculated structural ensemble clarifies a role of both the dual-histidine motif, His59/His157, and the basic residues, Lys63/Arg68/Arg69, to anchor both sides of the peptidyl-prolyl bond, the aromatic ring in Pro, and the phosphate in pSer, respectively. The rotation of the torsion angle is found to be facilitated by relaying the hydrogen-bond partner of the main-chain oxygen in pSer from Cys113 in the cis form to Arg68 in the trans form, through Ser154 at the transition state, which is really the cause of the shift in the transition state. The role of Ser154 as a driving force of the isomerization is confirmed by additional WE and free energy calculations for S154A mutant where the isomerization takes place slightly slower and the free energy barrier increases through the mutation. The present study shows the usefulness of the WE simulation for substantial path samplings between the reactant and product states, unraveling the molecular mechanism of the enzyme catalysis.