Structural and Energetic Determinants of Thermal Stability and Hierarchical Unfolding Pathways of Hyperthermophilic Proteins, Sac7d and Sso7d

Abstract

Identification of the structural and energetic determinants responsible for enhancing the stability of proteins is crucial. Hyperthermophilic proteins are naturally occurring proteins that exhibit high thermal stability and are good candidates for the investigation and understanding of structure-stability relationships. Sac7d from Sulfolobus acidocaldarius and Sso7d from Sulfolobus solfactaricus are two homologous hyperthermophilic proteins that were shown to be quite stable at high temperatures. Molecular dynamics simulations at the nanosecond time scale at different temperatures were performed to examine the factors affecting their stability. The three-dimensional structures of these proteins were observed to be similar to the experimental structure at 300 and 360 K but were found to undergo denaturation at 500 K. Both proteins exhibit similar unfolding pathways that correlates well with the calculated intermolecular interaction energies. The differential dynamic behaviors of these molecules at different temperatures were examined. Structural and energetic analysis of the contributions of salt bridges indicates a stabilizing effect at higher temperatures. However, the lifetimes of the salt bridges were found to be quite short, and several new salt bridges formed at 500 K supporting previous studies that the desolvation penalty due to the formation of salt bridges decreases at elevated temperatures. Hydrophobic interactions, which decrease with increase in temperature, were also found to be crucial in the stability of these proteins. Overall, the study shows that a balance among the salt bridge interactions, hydrophobic interactions, and solvent properties is primarily responsible for the high thermal stability of this class of proteins.

Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations

“…Several positively charged, surface residues at the interface rim form salt bridges with DNA and are involved in stabilizing the protein fold . Sac7d–DNA complexes are also stable during MD simulations at high temperatures (360 K) . Simulations on the Sac7d–DNA also indicate that partial DNA bending can occur even without residue intercalation at the target site .…”

Exploring the influence of hyperthermophilic protein Ssh10b on the stability and conformation of RNA by molecular dynamics simulation

“…[3,[45][46][47][48][49] There are numerous charged residues in Ssh10b, and they form salt bridges in each monomer, such as Glu36/Lys68, Glu54/Arg57, Asp63/Lys97, and Glu66/Arg95. The previous analysis found that the salt bridges of Ssh10b seems to be crucial in maintaining the 3D structures at elevated temperatures.…”

“…The previous analysis found that the salt bridges of Ssh10b seems to be crucial in maintaining the 3D structures at elevated temperatures. [49] Except for the salt bridges mentioned above in each monomer, we also monitored some salt bridges between monomer and monomer, such as Asp51/Arg86, Glu91/Arg71, Glu69/Arg71, Glu54/Arg86, Glu69/Arg95, and Glu91/Lys40 (Supporting Information Table S6). The salt bridges distributed in sheet-sheet, intrahelix and helix-sheet.…”

Atomistic details of the molecular recognition of DNA-RNA hybrid duplex by ribonuclease H enzyme

“…21,41,45,46 Briefly, the systems were subjected to a 500-step steepest decent (SD) minimization with harmonic restraints on heavy atoms of the protein and DNA-RNA hybrid together with the crystal Mg 2+ and water molecules. These minimized systems were then immersed in a pre-equilibrated water box and were made electrically neutral by adding sufficient number of ions.…”