Search

Molecular dynamics (MD) simulations of a subtilisin-like serine protease VPR from the psychrophilic marine bacterium Vibrio sp. PA-44 and its mesophilic homologue, proteinase K (PRK), have been performed for 20 ns at four different temperatures (300, 373, 473, and 573 K). The comparative analyses of MD trajectories reveal that at almost all temperatures, VPR exhibits greater structural fluctuations/deviations, more unstable regular secondary structural elements, and higher global flexibility than PRK. Although these two proteases follow similar unfolding pathways at high temperatures, VPR initiates unfolding at a lower temperature and unfolds faster at the same high temperatures than PRK. These observations collectively indicate that VPR is less stable and more heat-labile than PRK. Analyses of the structural/geometrical properties reveal that, when compared to PRK, VPR has larger radius of gyration (Rg), less intramolecular contacts and hydrogen bonds (HBs), more protein-solvent HBs, and smaller burial of nonpolar area and larger exposure of polar area. These suggest that the increased flexibility of VPR would be most likely caused by its reduced intramolecular interactions and more favourable protein-solvent interactions arising from the larger exposure of the polar area, whereas the enhanced stability of PRK could be ascribed to its increased intramolecular interactions arising from the better optimized hydrophobicity. The factors responsible for the significant differences in local flexibility between these two proteases were also analyzed and ascertained. This study provides insights into molecular basis of thermostability of homologous serine proteases adapted to different temperatures.

Protein folding is a complex problem and involves a series of complicated processes. This problem was further divided into two main problems: (i) the thermodynamic question of how a native structur...

conditions is fundamental to describing their functions at molecular level. Sig-nificant advances in theory, experiment and simulation have been achieved (1), making it possible to solve the three mostly focused aspects of protein folding problems (2):(i) The thermodynamic question of how a native structure results from inter-atomic forces acting on an amino acid sequence - the folding code; (ii) The kinetic problem of how a native structure can fold so fast - the folding rate;(iii) The computational problem of how to predict the native structure of a protein from its amino acid sequence – the protein structure prediction. The views on protein folding have evolved from simple force-driven folding (3)