Interconversion of functional motions between mesophilic and thermophilic adenylate kinases.
Interconversion of functional motions between mesophilic and thermophilic adenylate kinases.
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DOI：
10.1371/journal.pcbi.1002103
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发表时间：
2011-07
影响因子：
4.3
通讯作者：
Cui Q
中科院分区：
文献类型：
--
作者：
Daily MD;Phillips GN Jr;Cui Q
动态性质在许多蛋白质中具有重要的功能，包括腺苷酸激酶（AK），其打开/关闭的转变限制了催化周转的速度。在这里，我们比较了我们之前发表的粗粒度（双孔ggi）模拟大肠杆菌（AKmeso）的中温AK和Aquifex aeolicus （AKthermo）的嗜热AK的模拟。在AKthermo中，与AKmeso一样，在配体存在的情况下，LID结构域倾向于在NMP结构域之前关闭，但开放(O)系综中的LID刚体柔韧性显著降低。O和/或过渡态（TS）系综中的主链折叠性在一些域间主链铰链和LID内相对于AKmeso显著增加。在接触空间中，AKthermo的TS在CORE-LID界面上的接触较少，但在CORE-NMP界面周围的接触网络比AKmeso的TS更强。根据“对应状态”假设，AKthermo在375K下的“加热”模拟略微增加了LID刚体柔韧性。此外，虽然AKthermo中的7个脯氨酸突变为AKmeso对应的脯氨酸会产生类似的小扰动，但要实现与AKmeso相当的LID刚体柔韧性和铰链柔韧性，需要将这些位点（尤其是位置8和155）突变为甘氨酸。将AKmeso中的7个位点突变为脯氨酸会降低一些铰链的柔韧性，尤其是铰链2，但不会降低LID刚体的柔韧性，这表明这两种类型的运动在AKmeso中是解耦的。总之，我们的结果表明，铰链灵活性和整体功能运动都是相关的，但不是完全由铰链残数决定的。这种突变框架可以为其他蛋白质的重要功能柔韧性和变构的合理设计提供信息，从而实现新的生物化学途径。动态特性在许多蛋白质中具有重要的功能，包括腺苷酸激酶（AK），它经历与底物结合相结合的化学限速结构域运动。由于嗜中温菌和嗜热菌在重要的功能运动上经常不同，我们比较了AKmeso和AKthermo的粗粒度模拟，以及设计用于相互转换动力学的几种脯氨酸和甘氨酸突变变体。正如预期的那样，相对于AKmeso， AKthermo的域运动和局部展开运动都减少了。在AKthermo中，这两种类型的运动都可以通过加热或改变铰链脯氨酸来部分地转向更灵活的AKmeso。然而，只有高度柔韧性的甘氨酸突变才能产生像AKmeso那样的运动。因此，限制速率的全局转变可能取决于LID和NMP域中铰链灵活性和稳定性的组合。最后，这种诱变框架可以为其他蛋白质的柔韧性和变构的合理设计提供信息，从而设计出新的生物控制系统。
Dynamic properties are functionally important in many proteins, including the enzyme adenylate kinase (AK), for which the open/closed transition limits the rate of catalytic turnover. Here, we compare our previously published coarse-grained (double-well Gō) simulation of mesophilic AK from E. coli (AKmeso) to simulations of thermophilic AK from Aquifex aeolicus (AKthermo). In AKthermo, as with AKmeso, the LID domain prefers to close before the NMP domain in the presence of ligand, but LID rigid-body flexibility in the open (O) ensemble decreases significantly. Backbone foldedness in O and/or transition state (TS) ensembles increases significantly relative to AKmeso in some interdomain backbone hinges and within LID. In contact space, the TS of AKthermo has fewer contacts at the CORE-LID interface but a stronger contact network surrounding the CORE-NMP interface than the TS of AKmeso. A “heated” simulation of AKthermo at 375K slightly increases LID rigid-body flexibility in accordance with the “corresponding states” hypothesis. Furthermore, while computational mutation of 7 prolines in AKthermo to their AKmeso counterparts produces similar small perturbations, mutation of these sites, especially positions 8 and 155, to glycine is required to achieve LID rigid-body flexibility and hinge flexibilities comparable to AKmeso. Mutating the 7 sites to proline in AKmeso reduces some hinges' flexibilities, especially hinge 2, but does not reduce LID rigid-body flexibility, suggesting that these two types of motion are decoupled in AKmeso. In conclusion, our results suggest that hinge flexibility and global functional motions alike are correlated with but not exclusively determined by the hinge residues. This mutational framework can inform the rational design of functionally important flexibility and allostery in other proteins toward engineering novel biochemical pathways. Dynamic properties are functionally important in many proteins, including the enzyme adenylate kinase (AK), which undergoes chemically rate-limiting domain motions coupled to substrate binding. Since mesophiles and thermophiles often differ in functionally important motions, we compare coarse-grained simulations of AKmeso and AKthermo as well as several proline and glycine mutational variants designed to interconvert the dynamics. As might be expected, both domain motions and local unfolding motions are reduced in AKthermo relative to AKmeso. In AKthermo, both of these types of motions can be partially shifted toward more flexible AKmeso by heating or by mutating hinge prolines. However, only mutation to highly flexible glycine produces motions like those of AKmeso. Thus, the rate-limiting global transition likely depends on a combination of hinge flexibility and stability within the LID and NMP domains. Finally, this mutagenic framework can inform the rational design of flexibility and allostery in other proteins toward engineering novel biological control systems.
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DOI：
10.1007/s00249-008-0332-x
发表时间：
2008-09-01
影响因子：
2
作者：
Hajdu, Istvan;Bothe, Csaba;Zavodszky, Peter
通讯作者：
Zavodszky, Peter
影响因子：
2.9
作者：
Formaneck, Mark S.;Ma, Liang;Cui, Qiang
通讯作者：
Cui, Qiang
DOI：
10.1073/pnas.0408098102
发表时间：
2005-05-10
影响因子：
11.1
作者：
Best, RB;Hummer, G
通讯作者：
Hummer, G
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
5.6
作者：
Beckstein O;Denning EJ;Perilla JR;Woolf TB
通讯作者：
Woolf TB