title: Molecular dynamics simulations of the Nip7 proteins from the marine deep- and shallow-water Pyrococcus species.
abstract: 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.
authors.affiliation: Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. albatros@bionet.nsc.ru.
authors.forename: Kirill E
authors.initials: KE
authors.lastname: Medvedev
authors.affiliation: Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. alemasov@bionet.nsc.ru.
authors.forename: Nikolay A
authors.initials: NA
authors.lastname: Alemasov
authors.affiliation: Institute of Chemical Biology and Fundamental Medicine SB RAS, Prospekt Lavrentyeva 8, Novosibirsk, 630090, Russia. ynvorob@niboch.nsc.ru.
authors.forename: Yuri N
authors.initials: YN
authors.lastname: Vorobjev
authors.affiliation: Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. boldyrev@nsu.ru.|Institute of Solid Chemistry and Mechanochemistry, SB RAS, Novosibirsk, 630090, Russia. boldyrev@nsu.ru.
authors.forename: Elena V
authors.initials: EV
authors.lastname: Boldyreva
authors.affiliation: Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. kol@bionet.nsc.ru.|Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. kol@bionet.nsc.ru.|NRC Kurchatov Institute, 1, Akademika Kurchatova pl., Moscow, 123182, Russia. kol@bionet.nsc.ru.
authors.forename: Nikolay A
authors.initials: NA
authors.lastname: Kolchanov
authors.affiliation: Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia. ada@bionet.nsc.ru.|Novosibirsk State University, Pirogova str. 2, Novosibirsk, 630090, Russia. ada@bionet.nsc.ru.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Afonnikov
mesh_terms: D000222:Adaptation, Physiological; D019943:Amino Acid Substitution; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001274:Atmospheric Pressure; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D056004:Molecular Dynamics Simulation; D009687:Nuclear Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D055550:Protein Stability; D017433:Protein Structure, Secondary; D019711:Pyrococcus / Q000145:classification / Q000502:physiology*; D012492:Salts / Q000378:metabolism; D012623:Seawater / Q000382:microbiology; D013696:Temperature
chemical_list: D019843:Archaeal Proteins; D009687:Nuclear Proteins; D012492:Salts