Questionable Math: From LEGOs to Ligands

Primary Author

William Hughes

Faculty Mentor

Dr. Lorenzo Brancaleon

Additional Mentor(s)

Omar Castillo

Abstract

Bovine β-Lactoglobulin (BLG) is a small globular protein (162 amino acid residues) which is the main component in milk and often used as a model protein. BLG has only two tryptophan residues (Trp-19 and Trp-61). Previous studies have shown the fluorescence capabilities of tryptophan (Trp-19) exclusively. BLG has different protein conformations depending on the acidity of the environment. We utilized a pdb (2BLG) that corresponds to the structural basis of the Tanford transition in alkaline environments (pH 8.2); as well as (3BLG) which represents the molecule in an acidic environment (pH 6.2). Our lab has previously worked with BLG and porphyrins (photosensitizers). We have demonstrated that upon irradiation, protein unfolding occurs through a mediated electron transfer mechanism that causes Trp-19 to form a derivative of kynurenine. However, since porphyrin and BLG binding is random, this study was aimed to ascertain the most likely energetic binding position of different porphyrins.

AutoDock was used to create molecular docking models between BLG and several different porphyrins, PPIX, MgPPIX, MnPPIX, FePPIX, ZnPPIX, and SnPPIX. Autodock utilizes the standard root mean square deviation calculation based atomic positions. Fluorescence spectroscopy experiments were used to evaluate the binding location of ligands relative to Trp-19 and whether any quenching occurs to which our computational modeling data was compared. Establishing the relative similarity between binding locations on 2BLG and 3BLG shows the effectiveness of these models in a range of pH environments.

Presentation

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