Co-solvent effects on biomolecules, hydrophobes and water structure:
Recently, room temperature ionic liquids (ILs) have been shown to counteract the deleterious effect of urea on proteins. Using atomistic molecular dynamics we show that a ternary mix- ture containing a particular 20 ammonium-based IL, triethylammonium acetate (TEAA), and urea (in The folding/unfolding equilibrium of proteins in an aqueous medium can be altered by adding small organic molecules generally termed as co-solvents. Denaturants such as urea are instrumental in the unfolding of proteins while protecting osmolytes favor the folded ensemble (1 : 5 molar ratio) helps a small 15- residue S-peptide analog regain most of its native structure, whereas a binary aqueous mixture containing a large amount of urea alone completely distorts it. Our simulations show that the denaturant urea directly interacts with the peptide backbone in the binary mixture while for the ternary mixture both urea as well as the IL are preferentially excluded from the peptide surface. Similar observation for Choline chloride and we have analyzed the phenomenon in detailed, focusing on the hydrogen bond and rotational dynamics of choline chloride.
Relevant Publications:
1. Osmolyte-induced Conformational Stabilization of a Hydrophobic Polymer - Pooja Nanavare, Soham Sarkar, Abhijit Bijay Jena, and Rajarshi Chakrabarti Phys. Chem. Chem. Phys. xx, xxxx (2024).
2. Dynamics of a Methane Hydrophobe in Aqueous Choline Chloride Solution: Insights from Molecular Dynamics Simulations - Pooja Nanavare, Ligesh Theyancheri, Soham Sarkar and Rajarshi Chakrabarti, Chem. Phys. Impact 6, 100223 (2023).
3. Structure and Orientation of Water and Choline Chloride Molecules Around a Methane Hydrophobe: A Computer Simulation Study - Pooja Nanavare, Asha Rani Choudhury, Soham Sarkar, Atanu Maity and Rajarshi Chakrabarti ChemPhysChem 23, e202200446 (2022). (Special Collection Issue: Theoretical Chemistry Symposium 2021). This article has appeared as a Cover Feature of the Journal.
4. In silico Elucidation of Molecular Picture of Water-Choline Chloride Mixture - Soham Sarkar, Atanu Maity and Rajarshi Chakrabarti, J. Phys. Chem. B, 125, 13212 (2021).
5. Microscopic Structural Features of Water in Aqueous-Reline Mixture of varying Compositions - Soham Sarkar, Atanu Maity and Rajarshi Chakrabarti, Phys. Chem. Chem. Phys. 23, 3779 (2021).
6. Choline chloride as a nano-crowder protects HP-36 from urea-induced denaturation: Insights from Solvent Dynamics and Protein-Solvent interaction - Atanu Maity, Soham Sarkar, Ligesh Theeyancheri and Rajarshi Chakrabarti, ChemPhysChem 21, 552 (2020).
7. Ammonium-based stabilizers effectively counteract the Urea-conferred denaturation in a small protein: Insights from molecular dynamics simulations - Soham Sarkar, Soumadwip Ghosh and Rajarshi Chakrabarti, RSC Adv. 7, 52888 (2017).
8. Can ammonium-based room temperature ionic liquid counteract the urea-induced denaturation of a small peptide? - Soumadwip Ghosh, Souvik Dey, Mahendra Patel and Rajarshi Chakrabarti, Phys. Chem. Chem. Phys. 19, 7772 (2017). (This article has been featured in an online themed collection: New Frontiers in Indian Research).