Multi-scale Modeling of Self-assembly - overview
Role of Solvation in (P, T) Stability of Proteins
Characterizing the delicate interplay of sequence, solvation, and thermodynamic conditions (temperature, pressure) is of fundamental importance for understanding protein function and for designing novel functional proteins. In collaboration with Matysiak group at UMD, we have been developing a coarse-grained model for solvated protein, which allows us to investigate the molecular underpinning of cold and pressure unfolding.
Surfactant Assembly at extreme conditions
Non-ionic surfactants can, at certain concentrations and thermodynamic conditions, aggregate into micelles due to their amphiphilic nature. Using a novel coarse-grained model of the solvated surfactant system, we investigate the molecular driving forces underlying the destabilization of micelles and the mechanism of micelle formation at different thermodynamic (P, T) conditions.
Solvent Quality Change Upon Mixing
Defining the solvent quality of mixtures has practical implication in understanding protein behavior in a crowded cellular environment. Using molecular dynamics simulations, we have found a counter-intuitive non-cosolvency of a protein-like polymer in a mixture of two good solvents (i.e. chemical denaturants, urea and GdmCl). The polymer collapses due to the “effective” long-range interaction between monomers mediated by urea clouds. Further analysis reveals a novel mechanism for the preferential adsorption of urea, which is not directly determined by the polymer-urea interactions. Instead, a complex interplay of polymer-solvent affinities and solvent-solvent interactions appear to be the driving force. These findings underline the importance of interactions between two solvent components in determining the solvent quality of the mixture.
1. Das, Payel, and Silvina Matysiak. "Direct characterization of hydrophobic hydration during cold and pressure denaturation." The Journal of Physical Chemistry B 116.18 (2012): 5342-5348.
2. Matysiak, Silvina, and Payel Das. "Effects of Sequence and Solvation on the Temperature-Pressure Conformational Landscape of Proteinlike Heteropolymers." Physical review letters 111.5 (2013): 058103.
3. Das, Payel, Zhen Xia, and Ruhong Zhou. "Collapse of a hydrophobic polymer in a mixture of denaturants." Langmuir 29.15 (2013): 4877-4882.