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

Heba A Alkhatabi1,2,3, Mohammad Alhashmi4,5, Hind Ali Alkhatabi6

  • 1Faculty of Applied Medical Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia.

Animals : an Open Access Journal From MDPI
|February 13, 2025
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Summary

Cytochrome c structural adaptations allow camels to survive extreme temperatures. Simulations reveal how flexibility and stability change with temperature, highlighting evolutionary strategies for harsh environments.

Keywords:
Camelus dromedarius (Arabian camel)Camelus ferus (wild Bactrian camel)cytochrome c stability and flexibilitythermal adaptation mechanismsthermal titration molecular dynamics (TTMD) simulation

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Area of Science:

  • Biochemistry
  • Structural Biology
  • Computational Biology

Background:

  • Cytochrome c is vital for cellular energy metabolism.
  • Species like camels (Camelus ferus and Camelus dromedarius) exhibit remarkable adaptations to extreme cold and hot environments, respectively.
  • Understanding the temperature-dependent properties of cytochrome c is key to explaining these adaptations.

Purpose of the Study:

  • To investigate the structural, thermodynamic, and dynamic properties of cytochrome c across a range of temperatures.
  • To elucidate the molecular mechanisms underlying cytochrome c's stability and flexibility in different thermal conditions.
  • To correlate these properties with the survival strategies of cold-adapted wild Bactrian camels and heat-adapted Arabian camels.

Main Methods:

  • Utilized Thermal Titration Molecular Dynamics (TTMD) simulations with GROMACS.
  • Performed simulations at multiple temperatures (245 K, 280 K, 303 K, 308 K, 320 K) for 100 nanoseconds each.
  • Analyzed Root Mean Square Deviation (RMSD), Root Mean Square Fluctuation (RMSF), Principal Component Analysis (PCA), and entropy.

Main Results:

  • Increased RMSD values at higher temperatures (0.4 nm at 320 K) indicate structural alterations.
  • Higher flexibility (0.3-0.4 nm RMSF) observed at 303 K and 320 K compared to lower temperatures (0.1-0.2 nm).
  • PCA revealed expanded conformational space at higher temperatures, while entropy analysis indicated diminished stability at 320 K.

Conclusions:

  • Cytochrome c exhibits distinct structural and dynamic adaptations to varying temperatures.
  • These adaptations are crucial for the cold stability in Camelus ferus and thermal resilience in Camelus dromedarius.
  • The study provides insights into evolutionary strategies enabling survival in extreme environments.