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首页> 外文期刊>Journal of Molecular Biology >Binding free energies and free energy components from molecular dynamicsand Poisson-Boltzmann calculations. Application to amino acid recognitionby aspartyl-tRNA synthetase
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Binding free energies and free energy components from molecular dynamicsand Poisson-Boltzmann calculations. Application to amino acid recognitionby aspartyl-tRNA synthetase

机译：结合分子动力学和Poisson-Boltzmann计算得出的结合自由能和自由能成分。天冬氨酰-tRNA合成酶在氨基酸识别中的应用

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摘要

Specific amino acid binding by aminoacyl-tRNA synthetases (aaRS) is necessary for correct translation of the genetic code. Engineering a modified specificity into aminoacyl-tRNA synthetases has been proposed as a means to incorporate artificial amino acid residues into proteins in vine. In a previous paper, the binding to aspartyl-tRNA synthetase of the substrate Asp and the analogue Asn were compared by molecular dynamics free energy simulations. Molecular dynamics combined with Poisson-Boltzmann free energy calculations represent a less expensive approach, suitable for examining multiple active site mutations in an engineering effort. Here, Poisson-Boltzmann free energy calculations for aspartyl-tRNA synthetase are first validated by their ability to reproduce selected molecular dynamics binding free energy differences, then used to examine the possibility of Asn binding to native and mutant aspartyl-tRNA synthetase. A component analysis of the Poisson-Boltzmann free energies is employed to identify specific interactions that determine the binding affinities. The combined use of molecular dynamics free energy simulations to study one binding process thoroughly, followed by molecular dynamics and Poisson-Boltzmann free energy calculations to study a series of related ligands or mutations is proposed as a paradigm for protein or ligand design.
机译：氨酰基-tRNA合成酶（aaRS）的特定氨基酸结合是正确翻译遗传密码所必需的。已经提出了将修饰的特异性工程改造成氨酰基-tRNA合成酶的方法，作为将人工氨基酸残基掺入葡萄中的蛋白质的手段。在先前的论文中，通过分子动力学自由能模拟比较了底物Asp和类似物Asn与天冬氨酰-tRNA合成酶的结合。分子动力学与Poisson-Boltzmann自由能计算相结合，代表了一种较便宜的方法，适用于在工程上检查多个活性位点突变。在这里，首先通过天冬氨酰-tRNA合成酶的泊松-玻尔兹曼自由能计算，通过其复制结合自由能差异的选定分子动力学的能力进行验证，然后用于检验Asn与天然和突变天冬氨酰-tRNA合成酶结合的可能性。使用泊松-玻尔兹曼自由能的成分分析来确定确定结合亲和力的特定相互作用。结合分子动力学自由能模拟来全面研究一个结合过程，然后结合分子动力学和Poisson-Boltzmann自由能计算来研究一系列相关配体或突变，被认为是蛋白质或配体设计的范例。

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