Simonson Thomas, Archontis Georgios, Karplus Martin
Laboratoire de Biologie et G'enomique Structurales (CNRS), IGBMC, 1 rue Laurent Fries, 67404 Illkirch-Strasbourg, France.
Acc Chem Res. 2002 Jun;35(6):430-7. doi: 10.1021/ar010030m.
In recent years, molecular dynamics simulations of biomolecular free energy differences have benefited from significant methodological advances and increased computer power. Applications to molecular recognition provide an understanding of the interactions involved that goes beyond, and is an important complement to, experimental studies. Poisson-Boltzmann electrostatic models provide a faster and simpler free energy method in cases where electrostatic interactions are important. We illustrate both molecular dynamics and Poisson-Boltzmann methods with a detailed study of amino acid recognition by aspartyl-tRNA synthetase, whose specificity is important for maintaining the integrity of the genetic code.
近年来，生物分子自由能差异的分子动力学模拟受益于重大的方法学进展和计算机能力的提升。分子识别方面的应用能够深入了解其中涉及的相互作用，这超越了实验研究，并且是对实验研究的重要补充。在静电相互作用起重要作用的情况下，泊松-玻尔兹曼静电模型提供了一种更快、更简便的自由能计算方法。我们通过对天冬氨酰-tRNA合成酶识别氨基酸的详细研究，阐述了分子动力学和泊松-玻尔兹曼方法，该酶的特异性对于维持遗传密码的完整性至关重要。
