Biomolecular Design and Receptor-Ligand Interaction of a Potential Industrial Biocatalsyt: A Thermostable Thermolysin-Phosphoethanolamine-Ca2+ Protein Complex

Abstract

Protein structures are prone to modification based on the fundamental rules of design and function. Calculations of free binding energies (DG) of chemical molecules (effectors) that bind to proteins are important in molecular signaling processes and catalytic mechanisms of certain key enzymes. These calculations can be obtained via in silico and theoretical approaches. A series of 48 pockets were identified in thermolysin (KEI) and the four biggest pockets were selected for their suitable sites for modification. Application of molecular docking on phosphoethanolamine (PSE) and 1,10-phenanthroline (PHN) that act as intermediate ligands in the designated protein complex showed favorable final docked energy at different pockets (-8.49 to -4.80 kcal/mol). Analysis on docking of a divalent metal ion (Ca²⁺) to ligand (PSE) produced a final docked energy of -4.15 kcal/mol within acceptable distance (1.5 Ã… £ M ≤ 3.0 Ã…). It was found that the thermolysin-phosphoetanolamine-Ca²⁺ represented the putative protein complex of semisynthetic metalloprotease. Combinatorial modeling methods were applied in order to determine the best metalloenzyme complex. The identification of the potential protein pocket was conducted using CASTp. Selected ligands and metal ions were docked into each pocket using AutoDock 3.05. Analyses on their docking energy, non-covalent interaction as well as their geometry were conducted in order to determine the best metalloenzyme complex. This complex displayed the lowest docking energy with the additional Ca²⁺ suitably docked. It was hypothesized that metal ions can add new functionality to proteins and catalyze some of the challenging biological reactions, particularly in the pharmaceutical and fine chemicals industries.