Structural analysis of protein-ligand interactions using x-ray crystallography

Abstract

This research presents structural analysis of protein-ligand interactions using high-resolution X-ray diffraction. Four crystal structures were determined at Elettra Synchrotron Facility, Trieste, Italy, between September 2021 and August 2022: apo enzyme and three ligand-bound complexes. Diffraction data were collected at 100 K using wavelength 0.9793 Å, achieving resolutions from 1.47 to 1.82 Å. The apo enzyme refined to Rwork/Rfree of 0.172/0.198 at 1.47 Å. Electron density maps showed well-defined ligand positions with real-space correlation coefficients exceeding 0.91. Structural comparison identified conformational changes including 2.3 Å displacement of loop 178-192 and 47° rotation of Tyr156. Van der Waals interactions contributed -3.2 to -5.1 kcal/mol, electrostatics -2.1 to -4.2 kcal/mol, and hydrogen bonding -1.4 to -2.8 kcal/mol. Ligand C demonstrated highest binding affinity with 342 Ų hydrophobic contact surface and four direct hydrogen bonds.