Muzammal, Shafaq
(2021)
Molecular interactions of protein-based materials with ionic liquids.
PhD thesis, University of Nottingham.
Abstract
Renewable polymer resources have attracted an increasing amount of attention predominantly due to two major reasons, firstly environmental concerns, and secondly the realisation that our petroleum resources are finite. Silks and keratin-based materials such as wool are rich in protein content and have an immense importance as a renewable raw material in textile industry. Processing of such complex biopolymers has been hindered by the extremely low solubility in conventional organic solvents. Room temperature ionic liquids (RTILs) have shown favourable solvation properties for these materials and open up a wide possible range for application by turning them into novel structures and composites. In this work, molecular interactions of ionic liquids (ILs) with a range of amino acids (AAs) and peptides selected as model compounds were investigated through molecular dynamic (MD) simulations. The aim was to explain the underlying molecular mechanisms observed in the macroscopic processes with biotechnological relevance, such as, the dissolution of biomaterials in ILs, application of ILs in the separation and purification of amino acid molecules and other bioprocesses involving the replacement of organic solvents with ILs.
Firstly, the effect of concentration ratio of ionic liquid (IL) to amino acid (AA) [IL:AA] at constant temperature (300K) was explored for lysine, arginine, aspartate, glutamate in pure 1-ethyl-3-methylimidazolium chloride [C2C1Im][Cl] IL. The amino acids were constructed in their charged side chains with zwitter-ionic backbone. The strength of interactions of IL ions with AA molecules was found to decrease with the increase in concentration ratio for all amino acids. The effect of concentration ratio, temperature and water addition on solute-solvent, solute-solute and solvent-solvent interactions were investigated for lysine and aspartate in pure, and water mixtures of [C2C1Im][Cl] and 1-ethyl-3-methylimidazolium acetate ([C2C1Im][CH3CO2]) ILs. The temperature increase (from 300K to 400K) was found to enhance the solute-solute interactions for both amino acids in [C2C1Im][Cl], whereas, the effect of temperature on solute interactions was substantially less in [C2C1Im][CH3CO2] IL. Water, in each case, was added in the simulation systems based on the ambient water level absorbed in the two ILs. Presence of water also caused a slight increase in the inter-amino acid interactions, and this impact was more prominent at a higher temperature of 400K.
Aromatic amino acids, histidine, tryptophan, phenyl-alanine and tyrosine were investigated in pure [C2C1Im][CH3CO2] IL at constant temperature. These amino acids were constructed with the zwitter-ionic backbone and the side chains in their neutral forms. The heterocyclic aromatics, histidine and tryptophan had a strong interaction with the IL cations above the plane, along with the strong interactions with IL anion in areas where hydrogen bonding might be expected. The non-aromatic, non-polar amino acid alanine was studied in the two above mentioned ILs and the temperature variation and addition of water in these systems were explored. Strong inter-amino acid interactions were identified at a lower temperature in comparison to polar amino acids and they increased at a higher temperature. Presence of ambient water levels were shown to break the solute-solute interactions. Acetate anions showed better solvation properties than chloride anions for all amino acids studied and the simulation results were verified against experimental findings. This consistency with experiment also validated the use of General Amber forcefield (GAFF) for studying small organic molecules in ionic liquids.
Two alanine based peptides, penta-alanine and deca-alanine, in addition to a peptide segment (ACE(leucine-aspargine-glycine-lysine-threonine-leucine-lysine-glycine)NME) from protein G in its non-standard form, were analysed for peptide-IL interactions in pure [C2C1Im][CH3CO2] IL and water. Secondary structures for all peptides studied were compared in two solvent media. It was observed that the organisational structuring of ionic liquid ions around the peptide residues was consistent with the single amino acid simulation results, however, the apparent strengths of interaction were found to be reduced and were affected by the position of the residue in the peptide. The current study provides a suitable framework for further development of macroscopic processes such as dissolution processes in ionic liquids.
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