title: High temperature and pressure influence the interdomain orientation of Nip7 proteins from P. abyssi and P. furiosus: MD simulations.
abstract: Interactions between protein domains and their position and movement relative to each other are essential for the stability and normal functioning of a protein molecule. Features of the movement of domains may define the mechanism of enzymatic reactions. Therefore, the description of this motion is an important task in the analysis of the structures and functions of multidomain proteins. In the current work, we investigated the influence of pressure and temperature on changes in the movement of the two domains of the protein Nip7, expressed by deep-water (Pyrococcus abyssi) and shallow-water (Pyrococcus furiosus) archaea. The results of the present study show that the interdomain interfaces of the Nip7 proteins of P. abyssi and P. furiosus are formed by stable hydrophobic interactions. It was shown that high pressure and high temperature significantly changed the orientation of domains in Nip7 proteins which perhaps was connected with functional features of these domains. It was found that increasing the pressure significantly changed the angle of rotation of these domains, to a greater extent in the shallow-water protein, while an increase in temperature slightly reduced the angle of rotation of these domains. Moreover, the results suggest that the type of motion of the domains under study is similar to shear motion.
authors.affiliation: a Systems Biology Department , Institute of Cytology and Genetics SB RAS , Prospekt Lavrentyeva 10, Novosibirsk 630090 , Russia.|c Department of Biophysics , University of Texas Southwestern Medical Center , Dallas , TX , USA.
authors.forename: Kirill E
authors.identifier: 0000-0002-7982-4242
authors.initials: KE
authors.lastname: Medvedev
authors.affiliation: a Systems Biology Department , Institute of Cytology and Genetics SB RAS , Prospekt Lavrentyeva 10, Novosibirsk 630090 , Russia.|b Chair of Informational Biology , Novosibirsk State University , Pirogova str. 2, Novosibirsk 630090 , Russia.
authors.forename: Nikolay A
authors.initials: NA
authors.lastname: Kolchanov
authors.affiliation: a Systems Biology Department , Institute of Cytology and Genetics SB RAS , Prospekt Lavrentyeva 10, Novosibirsk 630090 , Russia.|b Chair of Informational Biology , Novosibirsk State University , Pirogova str. 2, Novosibirsk 630090 , Russia.
authors.forename: Dmitry A
authors.initials: DA
authors.lastname: Afonnikov
mesh_terms: D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites / Q000235:genetics; D006358:Hot Temperature; D006860:Hydrogen Bonding; D057927:Hydrophobic and Hydrophilic Interactions; D056004:Molecular Dynamics Simulation; D009038:Motion; D011312:Pressure; D000072417:Protein Domains; D043903:Pyrococcus abyssi / Q000235:genetics / Q000378:metabolism*; D020027:Pyrococcus furiosus / Q000235:genetics / Q000378:metabolism*; D013045:Species Specificity
chemical_list: D019843:Archaeal Proteins
keywords: Nip7 protein; adaptation; domain motions; high temperature; interdomain interface