Molecular dynamics study of high pressure influence on the structure of Nip7 protein from deep-sea and shallow-water archaea
Pressure is an important environmental factor for living organisms. Most of them live at atmospheric pressure of 0,1 MPa. At high pressure the functioning of a number of important cellular systems such as replication, transcription, translation and protein synthesis and transport of substances through the membrane is disrupted. This results in cell malfunction and death. However, there exist organisms, piezophiles, which are able to live and proliferate at pressures about one thousand times more than atmospheric, for example, at the bottom of the Mariana Trench (~ 100 MPa). The study of adaptation mechanisms of these organisms to high pressure environment will allow to identify the factors that provide resistance of living systems to extreme conditions. Their proteins can be used in biotechnology. One of the damaging factors at high pressures is the destabilization of proteins performing important functions. It was experimentally shown that high pressure destabilizes the structure of proteins and their complexes. Protein complexes tend to dissociate at pressures of about 200 MPa. The pressure of 500 MPa induce partial denaturation of proteins. The pressure of 1 GPa result in complete unfolding of protein chain. It is believed that the main factor of such instability is the penetration of solvent molecules into the hydrophobic core of the protein. Studies of the mechanisms of protein stability at high pressures are of great importance. Recently, computer simulations of protein dynamics were implemented to tackle this problem. This field of research is becoming increasingly important as molecular dynamics provides a detailed picture of the biomolecular processes in solution. It allows to receive the distribution of the thermal properties of molecules and analyze the ensemble of conformations of the proteins. We study the structures of archaeal proteins Nip7 from Pyrococcus species from shallow hydrothermal vents (Pyrococcus furiosus, the depth of habitat is about 100 m) and deep-sea pezofiles (Pyrococcus abyssi, the depth habitat is about 2200 m) at different pressures. Nip7 protein participates in ribosomal biogenesis and is involved in the processing of 27S pre-rRNA and the formation of 60S ribosomal subunits. We compared computer models of three-dimensional structures of Nip7 proteins from P. abyssi and P. furiosus at pressures ranging from 0,1 MPa to 200MPa. It was shown that the deformation of the structure Nip7 shallow P. furiosus is larger than for the deep-sea P. abyssi. P. furiosus protein had larger structural deformation of the RNA-binding site at high pressure. Moreover, analysis of computer models of Nip7 proteins from P. abyssi and P. furiosus demonstrated that with the increasing pressure the solvent-accessible surface area decreases. This area is smaller for models Nip7 P. abyssi and its relative change is less than that from P. furiosus. Obtained results are consistent with the hypothesis about the importance of protein interaction with the solvent while the pressure increases.