Yuemin Liu

QM/MM (ONIOM) study of glycerol binding and hydrogen abstraction by the coenzyme B12-independent dehydratase.

Glycerol binding and the radical-initiated hydrogen transfer by the coenzyme B(12)-independent glycerol dehydratase from Clostridium butyricum were investigated by using quantum mechanical/molecular mechanical (QM/MM) calculations based on the high-resolution crystal structure (PDB code: 1r9d). Our QM/MM calculations of enzyme catalysis considered the electrostatic coupling between the quantum-mechanical and molecular-mechanical subsystems and two alternative mechanisms. In addition to performing QM/MM calculations in the enzyme, we evaluated energetics along the same reaction pathway in aqueous solution modeled by the polarized dielectric and in the virtual enzyme site that included full steric component from the enzyme residues described by molecular mechanics but lacked the electrostatic contribution of these residues. In this way, we established significant enzyme catalytic effect with respect to reference reactions in both an aqueous solution and a nonpolar cavity. Structurally, four hydrogen bonds formed between glycerol and H164, S282, E435, and D447 anchor glycerol for hydrogen abstraction by thiyl radical on C433. These hydrogen-bond partners orient glycerol molecule to facilitate the formation of the transition state for hydrogen abstraction from carbon C1. This reaction then proceeds with the activation free energy of 6.3 kcal/mol and the reaction free energy of 6.1 kcal/mol. The polarization effects imposed by these hydrogen bonds represent a predominant contribution to a 7.5 kcal/mol enzyme catalytic effect. These results demonstrate the importance of electrostatic catalysis and hydrogen-bonding in enzyme-catalyzed radical reactions and advance our understanding of the catalytic mechanism of B(12)-independent glycerol dehydratases.

CH···π Interactions Do Not Contribute to Hydrogen Transfer Catalysis by Glycerol Dehydratase

The role of the nonbonded CH···π interaction in the hydrogen abstraction from glycerol by the coenzyme B(12)-independent glycerol dehydratase (GDH) was examined using the QM/MM (ONIOM), MP2, and CCSD(T) methods. The studied CH···π interaction included the hydrogen atom of the -C(2)H(OH)- group of the glycerol substrate and the tyrosine-339 residue of the dehydratase. A contribution of this interaction to the stabilization of the transition state for the transfer of a hydrogen atom from the adjacent terminal C(1)H(2)(OH) group to cysteine 433 was determined by ab initio HF, MP2, and CCSD(T) calculations with the aug-cc-pvDZ basis set for the corresponding methane/benzene, methanol/phenol, and glycerol radical/phenol subsystems. The calculated CH···π distance, defined as the distance between the H atom and the center of the phenol ring, shortened from 2.62 to 2.52 Å upon going from the ground- to the transition-state of the GDH-catalyzed reaction. However, this shortening was not accompanied by the expected lowering of the CH···π interaction free energy. Instead, this interaction remained weak (about -1 kcal/mol) along the entire reaction coordinate. Additionally, the mutual orientation of the CH group and the phenol ring did not change significantly during the reaction. These results suggest that the phenol group of the tyrosine-339 does not contribute to lowering the activation barrier in the enzyme, but do not exclude the possibility that tyrosine 339 facilitates proper orientation of glycerol for the electrostatic catalysis, or inhibits side-reactions of the reactive glycerol radical intermediate.

The diversity and molecular modelling analysis of B 12-dependent and B 12-independent glycerol dehydratases

To broaden our knowledge on the diversity of glycerol dehydratases, comprehensive sequence and molecular modelling analyses of these enzymes were performed. Our sequence analysis showed that B 12-dependent and B 12-independent glycerol dehydratases are not related, suggesting that they evolved from different ancestors. Second, our study demonstrated that a gene fusion event occurred between α and β subunits of B 12-dependent glycerol dehydratases in several bacteria during enzyme evolution. In addition, our sequence and molecular modelling analyses revealed more B 12-independent glycerol dehydratases including hypothetical proteins. Furthermore, we found that some microorganisms contain both B 12-dependent and B 12-independent glycerol dehydratases in their genomes.

Synthesis, structure, thermal, magnetic properties and quantum mechanical calculations of bridged [bis(di(2-methylpyridyl)amine)-(μ2-1,2-bis(4-pyridyl)ethane)-tetraperchlorato-dicopper(II)] dihydrate complex

The title compound [Cu2(DPA)2(μ-bpe)(ClO4)4]·2H2O, I where DPA = di(2-methylpyridyl)amine and bpe = 1,2-bis(4-pyridyl)ethane was studied by single crystal X-ray crystallography at different temperatures, spectroscopic methods, differential scanning calorimetry (DSC) and by magnetic susceptibility methods. DSC studies were recorded between 125 K and 647 K and magnetic studies between 2 K and 300 K. The X-ray diffraction studies were carried out at 293, 200, 150 and 100 K. Cooling the crystal from 293 K to 100 K produces a significant change in cell constants but no change in space group. X-ray and DSC studies revealed that significant phase transitions occur at temperatures between 200 K and 100 K that are described herein. The X-ray studies revealed a thermally-induced case of polymorphism whereby the cell volume triples on going from 293 to 100 K. This transition was reversible even though there is a marked hysteresis in the process. The major structural change between 200 K and 100 K is due to the displacement of the central bpe pyridyl rings relative to the plane defining CuN1N2N3 and the bending angle Cu–N1–C3. This transitional phase change was indirectly supported by quantum mechanical calculations which indicated the absence of significant π–π stacking interaction between the central bpe pyridyl rings forming the two parallel dinuclear species. This was attributed to the long 8.28 A distances between the two indicated moieties. Lack of energetic and spatial constraints justified the pyridyl ring displacement along the N–C3 axis. The temperature dependence of the magnetic behavior of I was that of a simple paramagnet down to 2 K. The complex revealed a very weak to non-existent magnetic coupling between the Cu(II) centers (J = −0.34 cm−1).