Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions
The development of stable scaffolds that can tolerate environmental extremes has an immense potential for applications in industry and defense. Recently, we have engineered an eight-residue loop into the de novo designed Top7 protein, which specifically binds the glycoprotein CD4. The robust properties of the Top7, coupled with the ease in production, make it a robust scaffold to design novel functionalities for use under extreme environmental conditions. In the present work, a series of explicit-solvent molecular dynamics simulations are reported which investigates the effect of mutations and extreme conditions of temperature and pH on the structure, stability, and dynamics of the native and engineered Top7. These simulations indicate that i. The structural dynamics of the engineered and native Top7 in solution are equivalent under corresponding conditions of pH and temperature. Ensemble-averaged structures of the native and engineered Top7 maintain the overall tertiary structure pattern, albeit with loss of helical content when at low pH and high-temperature conditions. Mutations of residues E43A, D46A, E67A, E69A, EA81A along the ?-helices of the engineered Top7 did not lead to significant changes in the native fold under pH 2 and 400 K, suggesting that the helices can accommodate varying sequences. iii. The anti-parallel ?-sheet is the structural core responsible for the stability of the native and engineered Top7 and is well maintained under extreme pH and temperature conditions. These findings indicate that the insertion of an eight-residue loop into the structure of Top7 does not adversely affect the global fold or the structural stability of the Top7 scaffold.
- Research Organization:
- Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Lab. (EMSL)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC05-76RL01830
- OSTI ID:
- 990543
- Report Number(s):
- PNNL-SA-64137; 20895; TRN: US201020%%403
- Journal Information:
- Journal of Molecular Graphics and Modelling, 28(8):755-765, Vol. 28, Issue 8
- Country of Publication:
- United States
- Language:
- English
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