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J Mol Graph Model. 2008 Aug;27(1):88-94. doi: 10.1016/j.jmgm.2008.03.002. Epub 2008 Mar 16.

Temperature-induced unfolding pathway of a type III antifreeze protein: insight from molecular dynamics simulation.

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  • 1Bioinformatics Centre, Bose Institute, Kolkata, India.


Molecular dynamics simulations of the temperature-induced unfolding reaction of a cold-adapted type III antifreeze protein (AFPIII) from the Antarctic eelpout Lycodichthys dearborni have been carried out for 10 ns each at five different temperatures. While the overall character and order of events in the unfolding process are well conserved across temperatures, there are substantial differences in the timescales over which these events take place. Plots of backbone root mean square deviation (RMSD) against radius of gyration (Rg) serve as phase space trajectories. These plots also indicate that the protein unfolds without many detectable intermediates suggestive of two-state unfolding kinetics. The transition state structures are identified from essential dynamics, which utilizes a principal component analysis (PCA) on the atomic fluctuations throughout the simulation. Overall, the transition state resembles an expanded native state with the loss of the three 3(10) helices and disrupted C-terminal region. Our study provides insight into the structure-stability relationship of AFPIII, which may help to engineer AFPs with increased thermal stability that is more desirable than natural AFPs for some industrial and biomedical purposes.

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