虚拟查,以检测 fenylalanine 类似物与 fenylalanyl-tRNA 合成酶的结合
Pin Wang1, Nagarajan Vaidehi, David A Tirrell
1Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
Journal of the American Chemical Society
|November 28, 2002
概括
这项研究介绍了HierDock,这是一种计算方法,可以预测 fenylalanine 类似物与 fenylalanyl-tRNA 合成酶 (PheRS) 的结合程度. 这种工具有助于虚拟选氨基酸类似物,节省了蛋白质工程研究的时间和资源.
科学领域:
- 生物化学 生物化学
- 计算生物学 计算生物学
- 蛋白质工程是指蛋白质工程.
背景情况:
- 对于蛋白质工程而言,研究非自然氨基酸至关重要,但实验性昂贵.
- 氨-tRNA合成酶 (PheRS) 在将氨类似物纳入蛋白质中发挥着关键作用.
研究的目的:
- 开发和验证一个计算协议,HierDock,用于预测PheRS.Penylalanine类型的结合能.
- 评估HierDock在确定适合蛋白质生物合成的氨基酸类型中的实用性.
主要方法:
- 使用了Thermus thermophilus PheRS. 的晶体结构.
- 采用HierDock计算协议来预测氨酸类型的结合点和能量.
- 与大肠杆菌的实验转化活动相关的预测结合能.
主要成果:
- HierDock准确地预测了氨 (Phe) 的结合部位,距离实验确定部位的1.1 Å以内.
- 使用HierDock计算的结合能量与大肠杆菌中的Phe类似物的转化活动有很强的相关性.
- HierDock确定了p-基氨酸和3-基氨酸是PheRS的有希望的基质,与实验结果一致.
结论:
- HierDock协议提供了一种可靠的计算方法,用于预测氨基酸模拟-PheRS相互作用.
- HierDock可以显著帮助氨基酸类型的虚拟选,减少实验成本和时间.
- 这种计算工具有可能加速发现用于蛋白质工程的新型氨基酸类似物.
相关概念视频
Transfer RNA Synthesis
One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
tRNA Activation
Aminoacyl-tRNA synthetases are present in both eukaryotes and bacteria. Though eukaryotes have 20 different aminoacyl-tRNA synthetases to couple to 20 amino acids, many bacteria do not have genes for all of these aminoacyl-tRNA synthetases. Despite this, they still use all 20 amino acids to synthesize their proteins. For instance, some bacteria do not have the gene encoding the enzyme that couples glutamine with its partner tRNA. In these organisms, one enzyme adds glutamic acid to all of the...
Improving Translational Accuracy
Base complementarity between the three base pairs of mRNA codon and the tRNA anticodon is not a failsafe mechanism. Inaccuracies can range from a single mismatch to no correct base pairing at all. The free energy difference between the correct and nearly correct base pairs can be as small as 3 kcal/ mol. With complementarity being the only proofreading step, the estimated error frequency would be one wrong amino acid in every 100 amino acids incorporated. However, error frequencies observed in...
Allosteric Proteins-ATCase
Binding sites linkages can regulate a protein's function. For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Transfer RNA Synthesis
One of the unique features of tRNA is the presence of modified bases. In some tRNAs, modified bases account for nearly 20% of the total bases in the molecule. Altogether, these unusual bases protect the tRNA from enzymatic degradation by RNases.
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...
Each of these chemical modifications is carried by a specific enzyme, post-transcription. All of these enzymes have unique base and site-specificity. Methylation, the most common chemical modification, is carried by at least nine different enzymes, with...


