Department of Chemistry, University of Kalyani, Kalyani, Nadia, West Bengal 741235, India.
Colloids Surf B Biointerfaces. 2009 Dec 1;74(2):468-76. doi: 10.1016/j.colsurfb.2009.07.019. Epub 2009 Jul 23.
Aminoacylation is a vital step in natural biosynthesis process of peptide and is the key step in correlating the realm of protein with the RNA world. Incorrect aminoacylation might lead to misacylation of d-amino acid in the tRNA which might cause synthesis of a hetero-peptide rather than natural homopeptide leading to the altered functionality of the peptide. However, the accuracy of this process is remarkable and leads to the attachment of the correct enantiomer of the amino acid with their cognate tRNA. Thus, the chiral discrimination is stringent. In the present work, we presented a combined ONIOM (ab initio/semi-empirical) study of the chiral discrimination in the first step of aminoacylation reaction based on a model of crystal structure of the oligomeric complex of histidyl-tRNA synthetase (HisRS) from Escherichia coli complexed with ATP and histidinol and histidyl-adenylate. The study reveals that the molecular mechanism of the chiral discrimination involves the amino acid, ATP as well as surrounding residues of the synthetase. Several factors are noted to be responsible for discrimination and explain the high level of stereospecificity of the process. The chirality of the amino acid of the substrate and its (principally) electrostatic interaction with the ATP is important for discrimination. The distance and orientational changes involved in the approach of the d-His towards the ATP is energetically unfavorable. The charge distributions on the His and ATP are important for the discrimination. Removal of the charges in the model drastically reduces the discrimination. Restricted nature of the mutual orientation within the cavity of the active site where the His and ATP are located during the change in orientation for the approach to form the adenylate makes the resultant interaction profile as different for l-His and d-His also influences chiral discrimination. The analysis of the transition state structure revealed that alteration of the chirality of the His destabilize the transition state by removing the favorable electrostatic interaction between the Glu-83 and NH(3)(+) group of the His substrate. The proximity of the surrounding residues as present in the active site of the synthetase with the His and ATP (the separation is of nanometer range) has influence of discrimination. The study provides a molecular mechanism of the retention of biological homochirality.
氨酰化是肽类天然生物合成过程中的一个重要步骤，也是将蛋白质领域与 RNA 世界联系起来的关键步骤。错误的氨酰化可能导致 tRNA 中 D-氨基酸的错误氨酰化，从而导致异肽的合成而不是天然同肽的合成，导致肽的功能改变。然而，这个过程的准确性是显著的，导致正确的氨基酸对与其互补的 tRNA 结合。因此，手性的区分是严格的。在本工作中，我们提出了一种基于大肠杆菌寡聚复合物晶体结构模型的组氨酸-tRNA 合成酶（HisRS）与 ATP 和组氨醇以及组氨酰-腺苷酸复合物的第一阶段氨酰化反应的 ONIOM（从头/半经验）联合研究，用于手性区分。研究表明，手性区分的分子机制涉及氨基酸、ATP 以及合成酶的周围残基。有几个因素被认为是区分的原因，并解释了该过程的高立体特异性。底物氨基酸的手性及其与 ATP 的（主要）静电相互作用对区分很重要。d-His 向 ATP 接近所涉及的距离和取向变化在能量上是不利的。His 和 ATP 上的电荷分布对区分很重要。模型中电荷的去除大大降低了区分度。活性位点空腔内 His 和 ATP 相互取向的受限性质在取向改变以形成腺苷酸时，使得相互作用的轮廓对于 l-His 和 d-His 也不同，这也影响手性区分。过渡态结构的分析表明，His 手性的改变通过去除 His 底物的 Glu-83 和 NH(3)(+) 基团之间有利的静电相互作用，使过渡态不稳定。合成酶活性位点中周围残基的接近（距离在纳米范围内）对区分有影响。该研究提供了生物同手性保留的分子机制。
