Department of Biophysics, Molecular Biology and Bioinformatics, 92, Acharya Prafulla Chandra Road, Kolkata 700009, India.
Comput Biol Chem. 2024 Feb;108:107978. doi: 10.1016/j.compbiolchem.2023.107978. Epub 2023 Nov 3.
Interactions between distantly placed amino acids in the primary chain (long-range) play a very crucial role in the formation and stabilization of the tertiary structure of a protein, while interactions between closely placed amino acids in the primary chain (short-range) mostly stabilize the secondary structures. Every protein needs to maintain marginal stability in order to perform its physiological functions in its native environment. The requirements for this stability in mesophilic and thermophilic proteins are different. Thermophilic proteins need to form more interactions as well as more stable interactions to survive in the extreme environment, they live in. Here, we aim to find out how the interacting amino acids in three-dimensional space are positioned in the primary chains in thermophilic and mesophilic. How does this arrangement help thermophiles to maintain their structural integrity at high temperatures? Working on a dataset of 1560 orthologous pairs we perceive that thermophiles are not only enriched with long-range interactions, they feature bigger connected clusters and higher network densities compared to their mesophilic orthologs, at higher interaction strengths between the amino acids. Moreover, we have observed the enrichment of different types of interactions at different secondary structural regions.
在一级链中（长程）相距较远的氨基酸之间的相互作用对于蛋白质三级结构的形成和稳定起着至关重要的作用，而一级链中（短程）相距较近的氨基酸之间的相互作用主要稳定二级结构。为了在其天然环境中执行生理功能，每种蛋白质都需要保持适度的稳定性。嗜温和嗜热蛋白对这种稳定性的要求不同。嗜热蛋白需要形成更多的相互作用以及更稳定的相互作用，以在其所处的极端环境中生存。在这里，我们旨在找出在三维空间中相互作用的氨基酸在嗜热和嗜温蛋白中的一级链中的定位方式。这种排列方式如何帮助嗜热菌在高温下保持其结构完整性？在对 1560 对直系同源物的数据集进行研究后，我们发现，与嗜温蛋白的直系同源物相比，嗜热蛋白不仅富含长程相互作用，而且在氨基酸之间的相互作用强度较高时，其连接的簇更大，网络密度更高。此外，我们还观察到在不同的二级结构区域存在不同类型的相互作用的富集。
