Nunavath Hanumalal, Banoth Chandrasekhar, Talluri Venkateswar Rao, Bhukya Bhima
Department of Microbiology, Osmania University, Hyderabad - 500 007, India.
Professor TNA Innovation Center, VBTIPL, Sy. No.253/A, Jiblakpally, Pochampally - 508284, Nalgonda (Dist.), Telangana, India.
Bioinformation. 2016 Oct 10;12(6):318-323. doi: 10.6026/97320630012318. eCollection 2016.
The present study explains computational methods to design thermostable horseradish peroxidase enzyme using the crystal structure available from Protein Data Bank (PDB ID: 6ATJ). Multiple mutations were introduced to the original enzyme and developed a model by using Modeler9.14. After designing the model functional effect was confirmed in terms of protein ligand binding by molecular docking using Autodock 4.2. The implementation of modeling steps is demonstrated in the context of performing mutations for particular amino acid residue on the ligand pocket of the horseradish peroxidase, to derive the desired ligand binding properties. The docking investigation of modelled HRP with Quercetindihydroxide using Autodock 4.2 software that six amino acid residues, P139, H42, A31, L174, A38, and G169 are involved in hydrogen bonding. More importantly, it provides insight into understanding and properly interpreting the data produced by these methods. The 3D model was docked with Quercetindihydroxide (a known horseradish modulator) to understand molecular interactions at the active site region.
本研究阐述了利用蛋白质数据库（PDB ID：6ATJ）中可得的晶体结构来设计耐热辣根过氧化物酶的计算方法。对原始酶引入多个突变，并使用Modeler9.14开发了一个模型。在设计模型后，通过使用Autodock 4.2进行分子对接，从蛋白质-配体结合方面确认了功能效应。在对辣根过氧化物酶配体口袋上特定氨基酸残基进行突变的背景下，展示了建模步骤的实施，以获得所需的配体结合特性。使用Autodock 4.2软件对建模的辣根过氧化物酶与二氢槲皮素进行对接研究，结果表明六个氨基酸残基P139、H42、A31、L174、A38和G169参与氢键形成。更重要的是，它有助于深入理解和正确解释这些方法产生的数据。将三维模型与二氢槲皮素（一种已知的辣根调节剂）进行对接，以了解活性位点区域的分子相互作用。
