Theoretical studies of cyclic adenosine monophosphate dependent protein kinase: native enzyme and ground-state and transition-state analogues

Metal Fluorides as Analogues for Studies on Phosphoryl Transfer Enzymes

The 1994 structure of a transition-state analogue with AlF₄^- and GDP complexed to G1α, a small G protein, heralded a new field of research into the structure and mechanism of enzymes that manipulate the transfer of phosphoryl (PO₃^- ) groups. The number of enzyme structures in the PDB containing metal fluorides (MF_x ) as ligands that imitate either a phosphoryl or a phosphate group was 357 at the end of 2016. They fall into three distinct geometrical classes: 1) Tetrahedral complexes based on BeF₃^- that mimic ground-state phosphates; 2) octahedral complexes, primarily based on AlF₄^- , which mimic "in-line" anionic transition states for phosphoryl transfer; and 3) trigonal bipyramidal complexes, represented by MgF₃^- and putative AlF₃⁰ moieties, which mimic the geometry of the transition state. The interpretation of these structures provides a deeper mechanistic understanding into the behavior and manipulation of phosphate monoesters in molecular biology. This Review provides a comprehensive overview of these structures, their uses, and their computational development.

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes

The phosphoryl group, PO₃^-, is the dynamic structural unit in the biological chemistry of phosphorus. Its transfer from a donor to an acceptor atom, with oxygen much more prevalent than nitrogen, carbon, or sulfur, is at the core of a great majority of enzyme-catalyzed reactions involving phosphate esters, anhydrides, amidates, and phosphorothioates. The serendipitous discovery that the phosphoryl group could be labeled by "nuclear mutation," by substitution of PO₃^- by MgF₃^- or AlF₄^-, has underpinned the application of metal fluoride (MF _x ) complexes to mimic transition states for enzymatic phosphoryl transfer reactions, with sufficient stability for experimental analysis. Protein crystallography in the solid state and ¹⁹F NMR in solution have enabled direct observation of ternary and quaternary protein complexes embracing MF _x transition state models with precision. These studies have underpinned a radically new mechanistic approach to enzyme catalysis for a huge range of phosphoryl transfer processes, as varied as kinases, phosphatases, phosphomutases, and phosphohydrolases. The results, without exception, have endorsed trigonal bipyramidal geometry (tbp) for concerted, "in-line" stereochemistry of phosphoryl transfer. QM computations have established the validity of tbp MF _x complexes as reliable models for true transition states, delivering similar bond lengths, coordination to essential metal ions, and virtually identical hydrogen bond networks. The emergence of protein control of reactant orbital overlap between bond-forming species within enzyme transition states is a new challenging theme for wider exploration.

Synthesis, structure and reactivity of a terminal magnesium fluoride compound, [TpBut,Me]MgF: hydrogen bonding, halogen bonding and C-F bond formation

The bulky tris(3-tert-butyl-5-pyrazolyl)hydroborato ligand, [TpBut,Me], has been employed to obtain the first structurally characterized example of a molecular magnesium compound that features a terminal fluoride ligand, namely [TpBut,Me]MgF, via the reaction of [TpBut,Me]MgMe with Me3SnF. The chloride, bromide and iodide complexes, [TpBut,Me]MgX (X = Cl, Br, I), can also be obtained by an analogous method using Me3SnX. The molecular structures of the complete series of halide derivatives, [TpBut,Me]MgX (X = F, Cl, Br, I) have been determined by X-ray diffraction. In each case, the Mg-X bond lengths are shorter than the sum of the covalent radii, thereby indicating that there is a significant ionic component to the bonding, in agreement with density functional theory calculations. The fluoride ligand of [TpBut,Me]MgF undergoes halide exchange with Me3SiX (X = Cl, Br, I) to afford [TpBut,Me]MgX and Me3SiF. The other halide derivatives [TpBut,Me]MgX undergo similar exchange reactions, but the thermodynamic driving forces are much smaller than those involving fluoride transfer, a manifestation of the often discussed silaphilicity of fluorine. In accord with the highly polarized Mg-F bond, the fluoride ligand of [TpBut,Me]MgF is capable of serving as a hydrogen bond and halogen bond acceptor, such that it forms adducts with indole and C6F5I. [TpBut,Me]MgF also reacts with Ph3CCl to afford Ph3CF, thereby demonstrating that [TpBut,Me]MgF may be used to form C-F bonds.

A Theoretical Study of Phosphoryl Transfers of Tyrosyl-DNA Phosphodiesterase I (Tdp1) and the Possibility of a "Dead-End" Phosphohistidine Intermediate

Tyrosyl-DNA phosphodiesterase I (Tdp1) is a DNA repair enzyme conserved across eukaryotes that catalyzes the hydrolysis of the phosphodiester bond between the tyrosine residue of topoisomerase I and the 3'-phosphate of DNA. Atomic level details of the mechanism of Tdp1 are proposed and analyzed using a fully quantum mechanical, geometrically constrained model. The structural basis for the computational model is the vanadate-inhibited crystal structure of human Tdp1 (hTdp1, Protein Data Bank entry 1RFF ). Density functional theory computations are used to acquire thermodynamic and kinetic data along the catalytic pathway, including the phosphoryl transfer and subsequent hydrolysis. Located transition states and intermediates along the reaction coordinate suggest an associative phosphoryl transfer mechanism with five-coordinate phosphorane intermediates. Similar to both theoretical and experimental results for phospholipase D, the proposed mechanism for hTdp1 also includes the thermodynamically favorable possibility of a four-coordinate phosphohistidine "dead-end" product.