Important role of hydrophobic interactions in high-pressure adaptation of proteins

Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species

Background

The identification of the mechanisms of adaptation of protein structures to extreme environmental conditions is a challenging task of structural biology. We performed molecular dynamics (MD) simulations of the Nip7 protein involved in RNA processing from the shallow-water (P. furiosus) and the deep-water (P. abyssi) marine hyperthermophylic archaea at different temperatures (300 and 373 K) and pressures (0.1, 50 and 100 MPa). The aim was to disclose similarities and differences between the deep- and shallow-sea protein models at different temperatures and pressures.

Results

The current results demonstrate that the 3D models of the two proteins at all the examined values of pressures and temperatures are compact, stable and similar to the known crystal structure of the P. abyssi Nip7. The structural deviations and fluctuations in the polypeptide chain during the MD simulations were the most pronounced in the loop regions, their magnitude being larger for the C-terminal domain in both proteins. A number of highly mobile segments the protein globule presumably involved in protein-protein interactions were identified. Regions of the polypeptide chain with significant difference in conformational dynamics between the deep- and shallow-water proteins were identified.

Conclusions

The results of our analysis demonstrated that in the examined ranges of temperatures and pressures, increase in temperature has a stronger effect on change in the dynamic properties of the protein globule than the increase in pressure. The conformational changes of both the deep- and shallow-sea protein models under increasing temperature and pressure are non-uniform. Our current results indicate that amino acid substitutions between shallow- and deep-water proteins only slightly affect overall stability of two proteins. Rather, they may affect the interactions of the Nip7 protein with its protein or RNA partners.

Evolution of general transcription factors

Three genes GTF2IRD1, GTF2I, and GTF2IRD2, which encode members of the GTF2I (or TFII-I) family of so-called general transcription factors, were discovered and studied during the last two decades. Chromosome location and similarity of exon-intron structures suggest that the family evolved by duplications. The initial duplication of ancestral proto-GTF2IRD1 gene likely occurred in early vertebrates prior to origin of cartilaginous fish and led to formation of GTF2I (>450 MYA), which was later lost in bony fish but successfully evolved in the land vertebrates. The second duplication event, which created GTF2IRD2, occurred prior to major radiation events of eutherian mammalian evolution (>100 MYA). During recent steps of primate evolution there was another duplication which led to formation of GTF2IRD2B (<4 MYA). Two latest duplications were coupled with inversions. Genes belonging to the family have several highly conservative repeats which are implicated in DNA binding. Phylogenetic analysis of the repeats revealed a pattern of intragenic duplications, deletions and substitutions which led to diversification of the genes and proteins. Distribution of statistically rare atypical substitutions (p ≤ 0.01) sheds some light on structural differentiation of repeats and hence evolution of the genes. The atypical substitutions are often located on secondary structures joining α-helices and affect 3D arrangement of the protein globule. Such substitutions are commonly traced at the early stages of evolution in Tetrapoda, Amniota, and Mammalia.