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Brownian dynamics simulations of aldolase binding glyceraldehyde 3-phosphate dehydrogenase and the possibility of substrate channeling.

机译:醛缩酶结合甘油醛3-磷酸脱氢酶的布朗动力学模拟和底物通道的可能性。

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摘要

Brownian dynamics (BD) simulations test for channeling of the substrate, glyceraldehyde 3-phosphate (GAP), as it passes between the enzymes fructose-1,6-bisphosphate aldolase (aldolase) and glyceraldehyde 3-phosphate dehydrogenase (GAPDH). First, BD simulations determined the favorable complexes between aldolase and GAPDH; two adjacent subunits of GAPDH form salt bridges with two subunits of aldolase. These intermolecular contacts provide a strong electrostatic interaction between the enzymes. Second, BD simulates GAP moving out of the active site of the A or D aldolase subunit and entering any of the four active sites of GAPDH. The efficiency of transfer is determined as the relative number of BD trajectories that reached any active site of GAPDH. The distribution functions of the transfer time were calculated based on the duration of successful trajectories. BD simulations of the GAP binding from solution to aldolase/GAPDH complex were compared to the channeling simulations. The efficiency of transfer of GAP within an aldolase/GAPDH complex was 2 to 3% compared to 1.3% when GAP was binding to GAPDH from solution. There is a preference for GAP channeling between aldolase and GAPDH when compared to binding from solution. However, this preference is not large enough to be considered as a theoretical proof of channeling between these proteins.
机译:布朗动力学(BD)模拟测试了底物3-磷酸甘油醛(GAP)的通道,该底物在1,6-双磷酸果糖醛缩酶(aldolase)和3-磷酸甘油醛脱氢酶(GAPDH)之间通过。首先,BD模拟确定了醛缩酶与GAPDH之间有利的配合物; GAPDH的两个相邻亚基与醛缩酶的两个亚基形成盐桥。这些分子间的接触在酶之间提供了强大的静电相互作用。其次,BD模拟GAP移出A或D醛缩酶亚基的活性位点并进入GAPDH的四个活性位点中的任何一个。转移的效率取决于到达GAPDH任何活性位点的BD轨迹的相对数量。传输时间的分布函数是根据成功轨迹的持续时间计算的。从溶液到醛缩酶/ GAPDH复合物的GAP结合的BD模拟与通道模拟进行了比较。醛缩酶/ GAPDH复合物中GAP的转移效率为2%至3%,而当GAP与溶液中的GAPDH结合时,GAP的转移效率为1.3%。与来自溶液的结合相比,醛缩酶和GAPDH之间的GAP通道是优选的。但是,这种偏爱还不够大,不足以被视为这些蛋白之间通道的理论证据。

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