Structure Of Biomolecules Through Molecular Dynamics Simulations

Abstract

Proteins are complex biological macromolecules performing a great variety of functions in the living systems. In order to get insight into the atomic structures and the time evolution of proteins, besides experimental techniques, mathematical and computational modeling approaches can be also used. Nowadays, Molecular Dynamics (MD) simulations constitute a powerful technique for understanding the physical basis of the structure of proteins, since via MD simulations someone can obtain information about proteins at the microscopic level and express it in macroscopic properties. In the current work, we present a detailed simulation approach concerning the modeling of two proteins in the native state, through all-atom Molecular Dynamics simulations under specific (physiological) conditions. The homodimeric Rop protein, that is a paradigm of a canonical 4-a-helical bundle, and its loopless mutation (RM6) are studied in aqueous solution. Their structural, conformational properties, as well as their hydrogen bond network, are characterized in atomic detail. Our findings reveal that both Rop and RM6 proteins have stable native states. The stability of the secondary conformation can be attributed to the formation of hydrogen bonds. The calculation of the root mean square deviation (RMSD) verifies that the system is in an equilibrated structure, validating at the same time, our model. Furthermore, the stereochemical quality of our protein models is demonstrated through the calculation of the Ramachandran plot. Finally, the thermal stability of RM6 protein is studied, and the results show that it is a hyperthermostable protein.