Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations
Specific amino acid recognition by aspartyl-tRNA synthetase studied by free energy simulations
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DOI：
10.1006/jmbi.1997.1470
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发表时间：
1998-02-06
影响因子：
5.6
通讯作者：
Karplus, M
中科院分区：
文献类型：
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作者：
Archontis, G;Simonson, T;Karplus, M
氨酰-tRNA合成酶的特异性氨基酸结合对于遗传密码的正确翻译是必需的。为了深入了解特异性的起源，通过使用分子动力学和自由能模拟比较了带负电荷的底物天冬氨酸和中性类似物天冬酰胺与乙酰基-tRNA合成酶（AspRS）的结合。Asn-AspRS复合物的模拟表明，虽然Asn不能与Asp结合在相同的位置，但距离Asp位点1.5至2埃的几个可能的位置存在。通过炼金术自由能模拟，其中Asp逐渐突变成Asn与酶的复合物中的Asn，将这些位置中的三个中的Asn的结合自由能与Asp的结合自由能进行比较。为了正确地解释系统（包括散装溶剂）中的静电相互作用，使用了最近开发的混合方法，其中突变位点的区域被显微镜下处理，而远处的蛋白质和溶剂被连续静电处理。在蛋白质中进行了七次自由能模拟，在溶液中进行了两次。在蛋白质模拟的Asn端点处采样的各种Asn位置和方向产生非常相似的自由能差异。计算的Asp --> Asn自由能变化在溶液中为79.8（+/-1.5）kcal/mol，在与蛋白质的复合物中为95.1（+/-2.8）kcal/mol。因此，预测底物Asp比Asn更强地结合，结合自由能差为15.3 kcal/mol。这意味着AspRS与Asn的错误结合是极不可能的，并且不能解释遗传密码翻译中的任何错误。几乎所有的蛋白质贡献的天冬氨酸与天冬氨酸结合自由能的差异来自精氨酸和赖氨酸残基，氢键底物羧酸基团和天冬氨酸和谷氨酸，氢键这些;所有四个氨基酸残基是完全保守的AspRS。蛋白质有效地“溶剂化”的天冬氨酸侧链比水更强烈。分析模拟以确定Asn能够在结合口袋中产生的相互作用，以及AspRS和高度同源的AsnRS之间的哪些序列差异对于修饰氨基酸特异性是重要的。提出了AspRS的双重或三重突变，可以使其对Asn具有特异性，并得到突变体复合物的初步模拟的支持。(C)出版社：Academic Press Limited。
Specific amino acid binding by aminoacyl-tRNA synthetases is necessary for correct translation of the genetic code. To obtain insight into the origin of the specificity, the binding to aspartyl-tRNA synthetase (AspRS) of the negatively charged substrate aspartic acid and the neutral analogue asparagine was compared by use of molecular dynamics and free energy simulations. Simulations of the Asn-AspRS complex showed that although Asn cannot bind in the same position as Asp, several possible positions exist 1.5 to 2 Angstrom away from the Asp site. The binding free energy of Asn in three of these positions was compared to that of Asp through alchemical free energy simulations, in which Asp is gradually mutated into Asn in the complex with the enzyme. To correctly account for the electrostatic interactions in the system (including bulk solvent), a recently developed hybrid approach was used, in which the region of the mutation site is treated microscopically, whereas distant protein and solvent are treated by continuum electrostatics. Seven free energy simulations were performed in the protein and two in solution. The various Asn positions and orientations sampled at the Asn endpoints of the protein simulations yielded very similar free energy differences. The calculated Asp --> Asn free energy change is 79.8(+/-1.5) kcal/mol in solution and 95.1(+/-2.8) kcal/mol in the complex with the protein. Thus, the substrate Asp is predicted to bind much more strongly than Asn, with a binding free energy difference of 15.3 kcal/mol. This implies that erroneous binding of Asn by AspRS is highly improbable, and cannot account for any errors in the translation of the genetic code. Almost all of the protein contributions to the Asp versus Asn binding free energy difference arise from an arginine and a lysine residue that hydrogen bond to the substrate carboxylate group and an Asp and a Glu that hydrogen bond to these; all four amino acid residues are completely conserved in AspRSs. The protein effectively "solvates" the Asp side-chain more strongly than water does. The simulations were analyzed to determine the interactions that Asn is able to make in the binding pocket, and which sequence differences between AspRS and the highly homologous AsnRS are important for modifying the amino acid specificity. A double or triple mutation of AspRS that could make it specific for Asn was proposed, and supported by preliminary simulations of a mutant complex. (C) 1997 Academic Press Limited.