Bahar I, Jernigan R L
Molecular Structure Section, Laboratory of Experimental and Computational Biology, Division of Basic Sciences, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5677, USA.
Biochemistry. 1999 Mar 23;38(12):3478-90. doi: 10.1021/bi982697v.
Tryptophan synthase (TRPS), with linearly arrayed subunits alphabetabetaalpha, catalyzes the last two reactions in the biosynthesis of L-tryptophan. The two reactions take place in the respective alpha- and beta-subunits of the enzyme, and the intermediate product, indole, is transferred from the alpha- to the beta-site through a 25 A long hydrophobic tunnel. The occurrence of a unique ligand-mediated long-range cooperativity for substrate channeling, and a quest to understand the mechanism of allosteric control and coordination in metabolic cycles, have motivated many experimental studies on the structure and catalytic activity of the TRPS alpha2beta2 complex and its mutants. The dynamics of these complexes are analyzed here using a simple but rigorous theoretical approach, the Gaussian network model. Both wild-type and mutant structures, in the unliganded and various liganded forms, are considered. The substrate binding site in the beta-subunit is found to be closely coupled to a group of hinge residues (beta77-beta89 and beta376-beta379) near the beta-beta interface. These residues simultaneously control the anticorrelated motion of the two beta-subunits, and the opening or closing of the hydrophobic tunnel. The latter process is achieved by the large amplitude fluctuations of the so-called COMM domain in the same subunit. Intersubunit communications are strengthened in the presence of external aldimines bound to the beta-site. The motions of the COMM core residues are coordinated with those of the alpha-beta hinge residues beta174-beta179 on the interfacial helix betaH6 at the entrance of the hydrophobic tunnel. And the motions of betaH6 are coupled, via helix betaH1 and alphaL6, to those of the loop alphaL2 that includes the alpha-subunit catalytically active residue Asp60. Overall, our analysis sheds light on the molecular machinery underlying subunit communication, and identifies the residues playing a key role in the cooperative transmission of conformational motions across the two reaction sites.
色氨酸合成酶（TRPS）由αβαβ线性排列的亚基组成，催化L - 色氨酸生物合成中的最后两个反应。这两个反应分别在酶的α和β亚基中进行，中间产物吲哚通过一条25埃长的疏水通道从α位点转移到β位点。底物通道化过程中独特的配体介导的长程协同作用的存在，以及对代谢循环中变构控制和协调机制的探索，推动了许多关于TRPS α2β2复合物及其突变体的结构和催化活性的实验研究。本文使用一种简单而严谨的理论方法——高斯网络模型，对这些复合物的动力学进行了分析。研究考虑了野生型和突变体结构，包括未结合配体和各种结合配体的形式。发现β亚基中的底物结合位点与β - β界面附近的一组铰链残基（β77 - β89和β376 - β379）紧密耦合。这些残基同时控制两个β亚基的反相关运动以及疏水通道的打开或关闭。后一过程是通过同一亚基中所谓COMM结构域的大幅度波动实现的。在与β位点结合的外部醛亚胺存在的情况下，亚基间的通信得到加强。COMM核心残基的运动与疏水通道入口处界面螺旋βH6上的α - β铰链残基β174 - β179的运动相协调。并且βH6的运动通过螺旋βH1和αL6与包含α亚基催化活性残基Asp60的环αL2的运动相耦合。总体而言，我们的分析揭示了亚基通信背后的分子机制，并确定了在两个反应位点之间构象运动的协同传递中起关键作用的残基。
