Seminars Archive

Solvation structure and dynamics of biomolecules in non-aqueous media

Abstract
Non-aqueous media become one of the options in bio-catalysis as addition of co-solvent can influence the enzymatic activity, stability and structure of biomolecules. Solvation of biomolecules in non-aqueous media can be used in pharmaceutical industries, therefore a detailed understanding of the micro-solvation environment at the molecular level is needed to be studied both experimentally and theoretically. Understanding the role of solvents such as organic solvents, ionic liquids (ILs) and deep eutectic solvents (DESs) at molecular level on biomolecules such as proteins, enzymes, DNA and RNA bring valuable information on the activation/deactivation and stability of them. In this respect the interaction of ions and biomolecules was studied for first time systemically by Hofmeister therefor understanding the effect of more complicated systems such as organic solvents and ionic liquids on the structure of biomolecules is crucial for their future applications. In this contribution, classical molecular dynamics (MD) simulations as a computational tool has been used to study solvation structure and dynamics of biomolecules in aqueous solutions of organic solvents and ionic liquids. Simulation results showed that organic molecules and cations of ionic liquids have special influence and interaction at the surface of biomolecules which influence the stability and activity of biomolecules. Also we have studied the interaction of different ionic liquids in different concentrations with formate dehydrogenases enzyme both experimentally and theoretically which revealed that in low concentrations of some ionic liquids the activity of enzyme can be enhanced while some other ionic liquids with different anions such as acetate can decrease the activity of enzyme.[3] Moreover, we have studied the interaction of ionic liquids with natural biopolymers such as cellulose by means of classical molecular dynamics (MD) simulations. MD simulations revealed that the interplay between hydrogen bonds between anions of ionic liquids and hydroxyl groups of cellulose play a key role on dissolution of cellulose in ionic liquids. Last but not least the interaction of different ionic liquids in different concentration on stability, structure and dynamics of DNA have been studied by means of MD simulations.
References [1] Khabiri M., Minofar B., Brezovský J., Damborský J., Ettrich R.; Interaction of Organic Solvents with Protein Structures at Protein Solvent Interface J. Mol. Model. (2013) 19: 4701.
[2] Štepankova, V. , Khabiri, M. , Brezovsky, J. , Pavelka, A. , Sykora, J. , Amaro, M. , Minofar, B. , Prokop, Z. , Hof, M. , Ettrich, R. , Chaloupkova, R. and Damborsky, J. (2013), Expansion of Access Tunnels and Active‐Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents. ChemBioChem, 14: 890-897.
[3] D'Oronzo, E. , Secundo, F. , Minofar, B. , Kulik, N. , Pometun, A. A. and Tishkov, V. I., Activation/Inactivation Role of Ionic Liquids on Formate Dehydrogenase from Pseudomonas sp. 101 and Its Mutated Thermostable Form. ChemCatChem 2018, 10, 3247.