In a study published in JACS Au, Prof. ZHUANG Wei from Fujian Institute of Research on the Structure of Matter (FJIRSM) of the Chinese Academy of Sciences and Dr. HUANG Jing from Westlake University developed a novel unified OKE spectroscopic simulation via Drude/MPID (multipole and induced dipole) method.
Based on such consistent polarizable forcefield methods of solving the signal difference between the solubilized lysozyme-NAG3 ligand complex system and the ligand-free solution, the researchers accurately simulated the spectrum, and determined the contribution of the enzyme spectrum, water and ligand by decomposing the difference signal difference.
Further analysis indicated that the subtle fluctuation of the aromatic residues dominates the protein component in the difference spectra, which is a negative peak. Molecular details such as distances between the centers of these residues and dipole-dipole interaction energy were calculated to reveal the subtle spatial arrangement triggered by binding.
The water component is almost negligible for wildtype system because the bound ligand squeezes some hydration water originally inside the cavity out to the bulk. A new population of hydration water has been created around the part of ligand exposed to water and this inside-out dynamic is balanced.
The ligand signal itself contributed as an absolute positive peak compared with the pure protein solution. The total difference of the two systems results as undulating feature. From the decomposition, the action of binding alone indeed has reflection in the OKE spectrum.
However, the simulated D52S-Lz mutant difference signal results only show a strong negative peak. The water molecules are confined between the second ligand residue NAG-2 and the protein cavity wall near residues number 98-104 to a strong negative water component that domains the total signal, while the protein and ligand contributions are similar to wildtype case.
Besides, comparing the different spectrum signal with a hypothetical system with uncorrelated protein and ligand parts, the researchers discovered a significant response of possible protein-ligand activity binding in the OKE signal.
This study reveals the potential of THz OKE technology in the research on the picosecond structure dynamics of biomolecular systems and their biochemical correlation, as well as the possible important role of theoretical simulation.
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