采用系统生物学的综合方法,通过突变分析和分子动力学模拟来挑战目标蛋白的功能。
An integrative approach using systems biology, mutational analysis with molecular dynamics simulation to challenge the functionality of a target protein.
机构信息
Computational Biophysics Laboratory, Department of Molecular Biology and Biotechnology, Tezpur University, Tezpur, Assam, India.
出版信息
Chem Biol Drug Des. 2019 Jun;93(6):1050-1060. doi: 10.1111/cbdd.13502. Epub 2019 Mar 20.
Visceral leishmaniasis affects millions of people worldwide in areas where Leishmania donovani is endemic. The protozoan species serves a greater threat as it has gradually evolved drug resistance whereby requiring newer approaches to treat the infection. State-of-art techniques are mostly directed toward finding better targets extracted from the available proteome data. In light of recent computational advancements, we ascertain and validate one such target, adenylosuccinate lyase (ADSL) by implementation of in-silico methods which led to the identification of critical amino acid residues that affects its functional attributes. Our target selection was based on comprehensive topological analysis of a knowledge-based protein-protein interaction network. Subsequently, mutations were incorporated and the dynamic behavior of mutated and native proteins was traced using MD simulations for a total time span of 600 ns. Comparative analysis of the native and mutated structures exhibited perceptible changes in the ligand-bound catalytic region with respect to time. The unfavorable changes in the orientations of specific catalytic residues, His118 and His196, induced by generated mutations reduce the enzyme specificity. In summary, this integrative approach is able to select a target against pathogen, identify crucial residues, and challenge its functionality through the selected mutations.
内脏利什曼病影响全球许多地方的人,在那里利什曼原虫是地方性的。原生动物物种构成更大的威胁,因为它已经逐渐进化出药物抗性,因此需要新的方法来治疗感染。最先进的技术主要针对从现有蛋白质组数据中提取更好的目标。鉴于最近的计算进展,我们通过实施计算方法来确定和验证这样的一个目标,即腺嘌呤核苷酸琥珀酸裂解酶(ADSL),这导致了确定影响其功能属性的关键氨基酸残基。我们的目标选择是基于基于知识的蛋白质-蛋白质相互作用网络的全面拓扑分析。随后,对突变体进行了突变,并通过 MD 模拟追踪突变体和天然蛋白质的动态行为,总时间跨度为 600ns。天然和突变体结构的比较分析表明,配体结合催化区域的时间发生了明显变化。突变产生的特定催化残基 His118 和 His196 的取向的不利变化降低了酶的特异性。总之,这种综合方法能够选择针对病原体的靶标,识别关键残基,并通过选定的突变挑战其功能。