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Computational Investigations of Biomolecular Systems and Comparison with Experiments in Various Environmental Conditions
KHABIRI, Morteza
Computational methods were used to study two different types of biological systems. The first study is related to the effect of three different organic solvents (formamide, acetone and isopropanol) on the structure and behavior of three globular proteins. These enzymes belong to the haloalkane dehalogenase family: DhaA, LinB, and DbjA. Moreover, the effect of mutation in the presence of DMSO was also investigated in two variants of DhaA; DhaA57 (L95V+A172V) and DhaA80 (Thr148Leu+Gly171Gln+Ala172Val+Cys176Phe). The simulation results showed that except for DhaA80, organic solvents entered the active site and influence its hydration. Not only the active site but also the enzyme?s hydration shell is influenced by organic molecules. The results showed that the water molecules are stripped out from the enzyme surfaces. It seems that the dual nature of organic molecules makes them favorable to solvate the enzymes. Radial Distribution Function (RDF) of the different parts of each organic molecule reveals that the behavior of each organic solvent in the vicinity of hydrophobic surfaces is similar to their behavior at the air-water interface. Structural analysis of root-mean-square-deviations (RMSD) and B-factors reveals that the flexibility of the enzymes decreased in the presence of most organic solvents, mainly in the CAP domain. Changes of other structural properties like radius of gyration and total solvent accessible surface areas are minimal. DbjA exists as a dimer and is more influenced by organic molecules. They penetrate to the amino acid network between monomers and influence their motion. The second study is the interaction of voltage-gated potassium channel Kv1.3 wild type and its mutants (Kv1.3_V388C, Kv1.3_V388C_H399T) with scorpion toxin (ChTX). Since there is no structure for Kv1.3, 94% sequence identity with Kv1.2 structure was used to make a homology model based on the Kv1.2 structure. MD structural analyses reveal that mutation of V388C changes the stability of selectivity filter by interrupting the amino acid network interactions behind the selectivity filter. The interaction of ChTX is also affected by the single mutant. ChTX is able to block wild type and double mutant channels but cannot occlude the pore entirely. Introducing the second point mutation H399T in the pore region reverts the structural changes back to the wild type. These results are entirely consistent with experimental results. Additionally, the binding energy of ChTX with the wild type mKv1.3 was investigated by the potential of mean force method, in the presence and absence of KCl solution. The results both in experiment and simulation show that, even though the unbinding process and dissociation rate is changing in the present of K+ ions, the binding energy is independent of K+ concentration. All together, the combination of computer simulations together with experiments provides new knowledge about channel-toxin interactions which could be helpful for drug design.
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