@article {155540, title = {Ionic Liquid-Induced Modulation of Ubiquitin Stability: The Dominant Role of Hydrophobic Interactions.}, journal = {Langmuir}, volume = {41}, year = {2025}, month = {2025 Mar 11}, pages = {5823-5837}, abstract = {

Despite the widespread use of imidazolium-based ionic liquids (ILs) in biotechnology, pharmaceuticals, and green chemistry, their detailed interactions with proteins, particularly affecting structural stability, remain poorly understood. This study examines the effects of ILs on ubiquitin, a thermodynamically robust protein with a β-grasp structure. We found that IL-induced destabilization follows a consistent order with previous findings: [BMIM] \> [BMPyr] \> [EMIM] for cations and [BF] \> [MeSO] \> [Cl] for anions. Through pH and ionic strength-dependent studies, we observed that hydrophobic interactions predominantly influence the stability of positively charged ubiquitin, with electrostatic interactions playing a secondary role. NMR studies identified residues impacted by [BMIM][BF]; however, site-directed mutagenesis of these residues showed minimal changes in destabilization, suggesting a global effect. This led us to conduct a broader empirical analysis, incorporating solvent-accessible surface area evaluations, which confirmed that hydrophobic residues are the primary drivers of stability alterations in ubiquitin, with charged residues playing a minimal role. Additionally, single-molecule force spectroscopy results indicate that imidazolium ILs lower the unfolding barrier without altering the transition state structure, offering insights into protein folding dynamics. ILs appear to modulate the stability landscape of proteins by energetically and kinetically favoring the unfolded state over the folded state. These insights offer potential strategies for the selective tuning of protein stability, which could be exploited to modulate protein-protein or protein-substrate interactions in various applications of ILs.

}, keywords = {Hydrogen-Ion Concentration, Hydrophobic and Hydrophilic Interactions, Imidazoles, Ionic Liquids, Protein Stability, Thermodynamics, Ubiquitin}, issn = {1520-5827}, doi = {10.1021/acs.langmuir.4c03886}, url = {https://pubmed.ncbi.nlm.nih.gov/40065704/}, author = {Shrivastava, Aditya and Kamma, Harika and Das, Ranabir and Ainavarapu, Sri Rama Koti} } @article {102046, title = {Rational Design of Protein-Specific Folding Modifiers.}, journal = {J Am Chem Soc}, year = {2021}, month = {2021 Nov 01}, abstract = {

Protein-folding can go wrong and , with significant consequences for the living organism and the pharmaceutical industry, respectively. Here we propose a design principle for small-peptide-based protein-specific folding modifiers. The principle is based on constructing a "xenonucleus", which is a prefolded peptide that mimics the folding nucleus of a protein. Using stopped-flow kinetics, NMR spectroscopy, F{\"o}rster resonance energy transfer, single-molecule force measurements, and molecular dynamics simulations, we demonstrate that a xenonucleus can make the refolding of ubiquitin faster by 33 {\textpm} 5\%, while variants of the same peptide have little or no effect. Our approach provides a novel method for constructing specific, genetically encodable folding catalysts for suitable proteins that have a well-defined contiguous folding nucleus.

}, issn = {1520-5126}, doi = {10.1021/jacs.1c09611}, author = {Das, Anirban and Yadav, Anju and Gupta, Mona and R, Purushotham and Terse, Vishram L and Vishvakarma, Vicky and Singh, Sameer and Nandi, Tathagata and Banerjee, Arkadeep and Mandal, Kalyaneswar and Gosavi, Shachi and Das, Ranabir and Ainavarapu, Sri Rama Koti and Maiti, Sudipta} }