A Dynamic Hydrophobic Core and Surface Salt Bridges Thermostabilize a Designed Three-Helix Bundle
| Autor: | Gabriel Gouvêa Slade, Catrina Nguyen, Ronaldo Junio de Oliveira, Jennifer T. Young, Michelle E. McCully |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2019 |
| Předmět: |
Protein Conformation
alpha-Helical Entropy Movement Static Electricity Biophysics Molecular Dynamics Simulation 03 medical and health sciences Molecular dynamics 0302 clinical medicine Protein structure Static electricity Amino Acid Sequence 030304 developmental biology Thermostability Helix bundle 0303 health sciences Chemistry Hydrogen bond Protein Stability Temperature Proteins Hydrogen Bonding Articles Directed evolution Fusion protein Crystallography Hydrophobic and Hydrophilic Interactions Monte Carlo Method 030217 neurology & neurosurgery |
| Zdroj: | Biophysical Journal |
| ISSN: | 1542-0086 0006-3495 |
| Popis: | Thermostable proteins are advantageous in industrial applications, as pharmaceuticals or biosensors, and as templates for directed evolution. As protein-design methodologies improve, bioengineers are able to design proteins to perform a desired function. Although many rationally designed proteins end up being thermostable, how to intentionally design de novo, thermostable proteins is less clear. UVF is a de novo-designed protein based on the backbone structure of the Engrailed homeodomain (EnHD) and is highly thermostable (Tm > 99°C vs. 52°C for EnHD). Although most proteins generally have polar amino acids on their surfaces and hydrophobic amino acids buried in their cores, protein engineers followed this rule exactly when designing UVF. To investigate the contributions of the fully hydrophobic core versus the fully polar surface to UVF's thermostability, we built two hybrid, chimeric proteins combining the sets of buried and surface residues from UVF and EnHD. Here, we determined a structural, dynamic, and thermodynamic explanation for UVF's thermostability by performing 4 μs of all-atom, explicit-solvent molecular dynamics simulations at 25 and 100°C, Tanford-Kirkwood solvent accessibility Monte Carlo electrostatic calculations, and a thermodynamic analysis of 40 temperature runs by the weighted-histogram analysis method of heavy-atom, structure-based models of UVF, EnHD, and both chimeric proteins. Our models showed that UVF was highly dynamic because of its fully hydrophobic core, leading to a smaller loss of entropy upon folding. The charged residues on its surface made favorable electrostatic interactions that contributed enthalpically to its thermostability. In the chimeric proteins, both the hydrophobic core and charged surface independently imparted thermostability. |
| Databáze: | OpenAIRE |
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