Thermophilic Rnase And Its Cognate Protein Molecular Dynamics Simulation Study

Protein from thermophilic organisms and their mesophilic homologues attract people because of their unique characters. Generally, they are very similar in sequences, structures and functions. But they are very different in thermostability and acid-resistant etc. It is an interest subject that what lead the differences. There is no unifying accepted theory though some research have been performed to determine the cause of different behave between them.A number of recent studies have challenged the theory that the hyperthermostability of proteins from thermophilic organisms have originated from their conformational rigidity. We add to the evidence, studying a pair of homologous ribonuclease HI enzymes, one thermophilic from Thermus thermophilus and the other mesophilic from Escherichia coli, by molecular dynamics simulations in explicit water solution. Each protein was subjected to three 5 ns independent simulations at both 310 K and 340 K. The simulations reproduced the respective stability or instability of the enzymes at corresponding temperatures. Even though only simulations of the mesophilic enzyme at the higher temperature show significant instability of the native structure, simulations of the thermophilic enzyme showed larger overall positional fluctuations at both temperatures as compared to the mesophilic enzyme. When respective local segments on the two proteins are compared, their relative flexibility seems to change with temperature differently for different segments. Principle component analysis of the positional covariance matrices showed that the conformational spaces two proteins...