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醛缩酶结合3-磷酸甘油醛脱氢酶的布朗动力学模拟及底物通道化的可能性

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

作者信息

Ouporov I V, Knull H R, Huber A, Thomasson K A

机构信息

Department of Chemistry, University of North Dakota, Grand Forks 58202-9024, USA.

出版信息

Biophys J. 2001 Jun;80(6):2527-35. doi: 10.1016/S0006-3495(01)76224-8.

Abstract

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.

摘要

布朗动力学(BD)模拟测试了底物3-磷酸甘油醛(GAP)在果糖-1,6-二磷酸醛缩酶(醛缩酶)和3-磷酸甘油醛脱氢酶(GAPDH)之间传递时的通道化情况。首先,BD模拟确定了醛缩酶和GAPDH之间的有利复合物;GAPDH的两个相邻亚基与醛缩酶的两个亚基形成盐桥。这些分子间接触在酶之间提供了强大的静电相互作用。其次,BD模拟了GAP从A或D醛缩酶亚基的活性位点移出并进入GAPDH的四个活性位点中的任何一个。转移效率由到达GAPDH任何活性位点的BD轨迹的相对数量确定。基于成功轨迹的持续时间计算转移时间的分布函数。将GAP从溶液结合到醛缩酶/GAPDH复合物的BD模拟与通道化模拟进行了比较。与GAP从溶液结合到GAPDH时的1.3%相比,GAP在醛缩酶/GAPDH复合物内的转移效率为2%至3%。与从溶液中结合相比,GAP在醛缩酶和GAPDH之间更倾向于通道化。然而,这种倾向还不足以被视为这些蛋白质之间通道化的理论证据。

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