Modeling Group II Chaperonin “Heat Shock” Protein Structure: pH and temperature dependency Piyasi Ghosh1,2 Vivek Govind Kumar1,3 Mahmoud Moradi3 Ruben Michael Ceballos1,2,4 University of Arkansas, Cell and Molecular Biology Program University of Arkansas, Department of Biological Sciences University of Arkansas, Department of Chemistry and Biochemistry Arkansas Center for Space and Planetary Sciences Program

Abstract

Group II chaperonins or “heat shock proteins” (HSPs) are expressed in hyperthermophilic archaea of the family Sulfolobaceae. Three chaperonins designated as HSPα, HSPβ, and HSPγ have been reported and serve as subunits in the formation of nonameric double-ring (18-mer) complexes. HSP complexes in nature function to protect cellular proteins (e.g., enzymes) during thermal shock and, perhaps, other stressors such as pH flux. HSPα and HSPβ are stoichiometrically favored in HSP complex formation, whereas the HSPγ subunit is more rarely found as a constituent subunit. In vitro, HSPα homomers, HSPβ homomers, and HSPα/HSPβ heteromers will form in the presence of ATP and divalent cations (e.g., Mg++). HSP complexes feature a central pore that leads to an internal cavity. Pore openings are found at both apical and basal extremities of the 18-mer complex. It has been suggested that HSPs have “opened” and “closed” states. Whether the pore is “opened” or “closed” is a function of conformational changes in the individual HSP subunits that lead to subunit rearrangements in the complex. Since the thermotolerant nature and protective function of HSP complexes is likely based on the ability of the system to open and close, it is of interest to understand the changes in subunit ultra-structure that mediate switching between to these two conformational states. In this study, molecular dynamics simulations were conducted test the relative stability of HSPα versus HSPβ and to determine how HSPα and HSPβ tertiary structure may be impacted by temperature and pH. SWISS-MODEL and PyMOL were used to generate the 3-D HSP structures. CHARMM-GUI solution builder was used to solvate the modeled structures in a “water box” as an energy minimization step prior to running simulations, which were performed in Nanoscale Molecular Dynamics (NAMD). Output was later visualized using Visual Molecular Dynamics (VMD). We demonstrate that HSP a-helical structures change conformation as pH drops from neutral to acidic. Our data suggest that changes in subunit structure under thermal shock lead to changes in pore diameter; however, it is unclear if pH flux influences opening and closing of the HSP complex pore. These results demonstrate a plausible biophysical mechanism by which group II chaperonin complexes change conformation while serving client proteins.