Revisiting structural organization of proteins at high temperature from a network perspective

• Published in: Computational biology and chemistry 2024-02, Vol.108, p.107978-107978, Article 107978
• Main Authors: Hait, Suman, Kundu, Sudip
• Format: Article
• Language: English
• Subjects: Amino Acids - chemistry; Bacterial Proteins - chemistry; Coulombic interaction; network density; protein contact network; Protein Structure, Secondary; Protein thermostability; Proteins - chemistry; Temperature; Van der Waals interaction
• ISSN: 1476-9271; 1476-928X
• DOI: 10.1016/j.compbiolchem.2023.107978

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. [Display omitted] •Protein contact network helps in understanding thermal stability.•Diverse thermo-meso orthologs reveal distinguishable differences in network properties.•Thermophilic Van der Waals LRNs feature larger connected components.•Thermophilic proteins exhibit denser Van der Waals LRNs.•Coulombic SRNs display higher attractive ̶ repulsive interactions in thermophilic.