Computational analysis of protein conformational heterogeneity

Abstract

In this paper, we applied the molecular dynamics (MD) simulations and used thermolysin as the system to study the overall protein dynamics and side chain dihedral angles across the Arrhenius break. Simulations were performed at a high temperature of 36 °C which is above the previously observed Arrhenius break, and the lower temperature of 20 °C which is below the Arrhenius break. We observed different protein dynamics and conformational heterogeneity of side chain dihedral angles of thermolysin at the two temperatures. Our results indicated that certain regions of thermolysin have a higher level of fluctuation at lower temperature. A temperature dependent dihedral angles were also observed at the two temperatures. The changes observed in the protein indicated key areas of temperature sensitivity within the protein.

Communicated by Ramaswamy H. Sarma

Keywords:

• Protein conformational heterogeneity
• molecular dynamics simulation
• temperature dependent protein dynamics
• thermolysin

Acknowledgements

Computational facilities of the Computational Molecular Engineering Lab and the ViCAR Center at North Carolina A & T State University.

Disclosure statement

No potential conflict of interest was reported by the authors.