Role of Urea–Aromatic Stacking Interactions in Stabilizing the Aromatic Residues of the Protein in Urea-Induced Denatured State
| Autor: | U. Deva Priyakumar, Siddharth Goyal, Koushik Kasavajhala, Aditya Chattopadhyay |
|---|---|
| Rok vydání: | 2017 |
| Předmět: |
Protein Denaturation
Protein Folding Stacking Molecular Dynamics Simulation 010402 general chemistry 01 natural sciences Biochemistry Catalysis Residue (chemistry) chemistry.chemical_compound Colloid and Surface Chemistry Protein stability 0103 physical sciences Urea Organic chemistry 010304 chemical physics Protein Stability Proteins Reproducibility of Results General Chemistry 0104 chemical sciences Solvent Folding (chemistry) chemistry Intramolecular force Biophysics Thermodynamics Protein folding |
| Zdroj: | Journal of the American Chemical Society. 139:14931-14946 |
| ISSN: | 1520-5126 0002-7863 |
| DOI: | 10.1021/jacs.7b05463 |
| Popis: | A delicate balance of different types of intramolecular interactions makes the folded states of proteins marginally more stable than the unfolded states. Experiments use thermal, chemical, or mechanical stress to perturb the folding equilibrium for examining protein stability and the protein folding process. Elucidation of the mechanism by which chemical denaturants unfold proteins is crucial; this study explores the nature of urea-aromatic interactions relevant in urea-assisted protein denaturation. Free energy profiles corresponding to the unfolding of Trp-cage miniprotein in the presence and absence of urea at three different temperatures demonstrate the distortion of the hydrophobic core to be a crucial step. Exposure of the Trp6 residue to the solvent is found to be favored in the presence of urea. Previous experiments showed that urea has a high affinity for aromatic groups of proteins. We show here that this is due to the remarkable ability of urea to form stacking and NH-π interactions with aromatic groups of proteins. Urea-nucleobase stacking interactions have been shown to be crucial in urea-assisted RNA unfolding. Examination of these interactions using microsecond-long unrestrained simulations shows that urea-aromatic stacking interactions are stabilizing and long lasting. Further MD simulations, thermodynamic integration, and quantum mechanical calculations on aromatic model systems reveal that such interactions are possible for all the aromatic amino acid side-chains. Finally, we validate the ubiquitous nature of urea-aromatic stacking interactions by analyzing experimental structures of urea transporters and proteins crystallized in the presence of urea or urea derivatives. |
| Databáze: | OpenAIRE |
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