Department of Biotechnology, Indian Institute of Technology Madras, Chennai 600036, Tamilnadu, India.
Proteins. 2013 Apr;81(4):715-21. doi: 10.1002/prot.24232. Epub 2013 Jan 15.
The stability of thermophilic proteins has been viewed from different perspectives and there is yet no unified principle to understand this stability. It would be valuable to reveal the most important interactions for designing thermostable proteins for such applications as industrial protein engineering. In this work, we have systematically analyzed the importance of various interactions by computing different parameters such as surrounding hydrophobicity, inter-residue interactions, ion-pairs and hydrogen bonds. The importance of each interaction has been determined by its predicted relative contribution in thermophiles versus the same contribution in mesophilic homologues based on a dataset of 373 protein families. We predict that hydrophobic environment is the major factor for the stability of thermophilic proteins and found that 80% of thermophilic proteins analyzed showed higher hydrophobicity than their mesophilic counterparts. Ion pairs, hydrogen bonds, and interaction energy are also important and favored in 68%, 50%, and 62% of thermophilic proteins, respectively. Interestingly, thermophilic proteins with decreased hydrophobic environments display a greater number of hydrogen bonds and/or ion pairs. The systematic elimination of mesophilic proteins based on surrounding hydrophobicity, interaction energy, and ion pairs/hydrogen bonds, led to correctly identifying 95% of the thermophilic proteins in our analyses. Our analysis was also applied to another, more refined set of 102 thermophilic-mesophilic pairs, which again identified hydrophobicity as a dominant property in 71% of the thermophilic proteins. Further, the notion of surrounding hydrophobicity, which characterizes the hydrophobic behavior of residues in a protein environment, has been applied to the three-dimensional structures of elongation factor-Tu proteins and we found that the thermophilic proteins are enriched with a hydrophobic environment. The results obtained in this work highlight the importance of hydrophobicity as the dominating characteristic in the stability of thermophilic proteins, and we anticipate this will be useful in our attempts to engineering thermostable proteins.
嗜热蛋白的稳定性已从不同角度进行了研究，但目前还没有统一的原理来理解这种稳定性。揭示对于设计用于工业蛋白质工程等应用的耐热蛋白质最重要的相互作用将是有价值的。在这项工作中，我们通过计算各种参数，如周围疏水性、残基间相互作用、离子对和氢键，系统地分析了各种相互作用的重要性。每种相互作用的重要性是通过其在嗜热菌中的预测相对贡献与其在中温同系物中的相同贡献的比较来确定的，这是基于 373 个蛋白质家族的数据集。我们预测，疏水环境是嗜热蛋白稳定性的主要因素，并且发现分析的 80%的嗜热蛋白比其中温对应物具有更高的疏水性。离子对、氢键和相互作用能也分别在 68%、50%和 62%的嗜热蛋白中很重要且有利。有趣的是，具有降低的疏水环境的嗜热蛋白显示出更多的氢键和/或离子对。基于周围疏水性、相互作用能和离子对/氢键，对中温蛋白进行系统消除，正确识别了我们分析中 95%的嗜热蛋白。我们的分析还应用于另一组更精细的 102 个嗜热-中温对，再次在 71%的嗜热蛋白中鉴定出疏水性是主要特性。此外，周围疏水性的概念，它描述了蛋白质环境中残基的疏水性行为，已应用于延伸因子-Tu 蛋白质的三维结构，我们发现嗜热蛋白质富含疏水环境。这项工作的结果强调了疏水性作为嗜热蛋白稳定性的主要特征的重要性，我们期望这将有助于我们设计耐热蛋白质。
