In Silico Analysis of Temperature-Induced Structural, Stability, and Flexibility Modulations in Camel Cytochrome c

Abstract

Cytochrome c is a critical protein in energy metabolism, and its structural adaptations to different temperatures play a key role in enabling species like the wild Bactrian camel (Camelus ferus) and the Arabian camel (Camelus dromedarius) to thrive in their respective cold and hot environments. This study investigates the structural, thermodynamic, and dynamic properties of cytochrome c at different temperatures. Thermal Titration Molecular Dynamics (TTMD) simulations, which involve analyzing protein behaviour across a range of temperatures, were carried out using GROMACS, with each simulation running for 100 nanoseconds, at 245 K, 280 K, 303 K, 308 K, and 320 K, to evaluate stability and flexibility. Structural alterations were indicated by an increase in root mean square deviations (RMSDs) to 0.4 nm at 320 K, as opposed to lower RMSD values (0.1–0.2 nm) at 245 K and 280 K. Root mean square fluctuation (RMSF) analyses revealed modest flexibility at 245 K and 280 K (0.1–0.2 nm) but considerable flexibility (0.3–0.4 nm) at 303 K and 320 K. Principal component analysis (PCA) found that the formational space was constrained at lower temperatures but expanded at higher temperatures. Entropy peaked at 280 K (13,816 J/mol) and then fell substantially at 320 K (451.765 J/mol), indicating diminished stability. These findings highlight cytochrome c adaptations for cold stability in Camelus ferus and thermal resilience in Camelus dromedarius, showing evolutionary strategies for harsh conditions.

Keywords

• <i>Camelus ferus</i> (wild <i>Bactrian camel</i>)
• <i>Camelus dromedarius</i> (<i>Arabian camel</i>)
• thermal adaptation mechanisms
• cytochrome c stability and flexibility
• thermal titration molecular dynamics (TTMD) simulation