Flexibility of Catalytic Zinc Coordination in Thermolysin and HDAC8: A Born−Oppenheimer ab Initio QM/MM Molecular Dynamics Study

Abstract

AbstracsThe different coordination modes and fast ligand exchange of zinc coordination has been suggested to be one key catalytic feature of the zinc ion which makes it an invaluable metal in biological catalysis. However, partly due to the well known difficulties for zinc to be characterized by spectroscopy methods, evidence for dynamic nature of the catalytic zinc coordination has so far mainly been indirect. In this work, Born-Oppenheimer ab initio QM/MM molecular dynamics simulation has been employed, which allows for a first-principle description of the dynamics of the metal active site while properly including effects of the heterogeneous and fluctuating protein environment. Our simulations have provided direct evidence regarding inherent flexibility of the catalytic zinc coordination shell in Thermolysin (TLN) and Histone Deacetylase 8 (HDAC8). We have observed different coordination modes and fast ligand exchange during the picosecond's timescale. For TLN, the coordination of the carboxylate group of Glu166 to Zinc is found to continuously change between monodentate and bidentate manner dynamically; while for HDAC8, the flexibility mainly comes from the coordination to a non-amino-acid ligand. Such distinct dynamics in the zinc coordination shell between two enzymes suggests that the catalytic role of Zinc in TLN and HDAC8 is likely to be different in spite of the fact that both catalyze the hydrolysis of amide bond. Meanwhile, considering that such Born-Oppenheimer ab initio QM/MM MD simulations are very much desired but are widely considered to be too computationally expensive to be feasible, our current study demonstrates the viability and powerfulness of this state-of-the-art approach in simulating metalloenzymes.Zinc is relatively abundant in biological materials. Approximately 10% of the total human proteome have been identified to bind with zinc in vivo from a bioinformatics investigation1 and they play very crucial roles in all forms of life2 -6 . For mononuclear zinc enzymes, a typical metal coordination environment contains three amino acid side chain ligands (His, Glu, Asp and Cys) and one/two small molecule(s). 3, 7 , 8 The flexibility of zinc coordination, which allows different coordination modes and fast ligand exchange, has been suggested to be one key catalytic feature of the zinc ion which makes it an invaluable metal in biological catalysis.9 However, partly due to the well known difficulties for zinc to be characterized by spectroscopy methods 10,11 , evidence for dynamic nature of the catalytic zinc coordination has so far mainly In order to provide deep insights into the dynamics and flexibility of the zinc catalytic site, which would be essential in characterizing their catalytic mechanisms and rational design of novel inhibitors for zinc enzymes, we have carried out DFT QM/MM Born-Oppenheimer molecular dynamics (BOMD) simulations on TLN and HDAC8. Although semi-empirical QM/MM BOMD simulations of some zinc-dependent enzymes have been carried out 29-32, one main concern is the acc...

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