Hybrid Potentials for Large Molecular Systems

Determination of the structure form of the fourth ligand of zinc in Acutolysin A using combined quantum mechanical and molecular mechanical simulation

Acutolysin A, which is isolated from the snake venom of Agkistrodon acutus, is a member of the SVMPs subfamily of the metzincin family, and it is a snake venom zinc metalloproteinase possessing only one catalytic domain. The catalytic zinc ion, in the active site, is coordinated in a tetrahedral manner with three imidazole nitrogen atoms of histidine and one oxygen atom. It is uncertain whether this oxygen atom is a water molecule or a hydroxide ion just from the three-dimensional X-ray crystal structure. The identity of the fourth ligand of zinc is theoretically determined for the first time by performing both combined quantum mechanical and molecular mechanical (QM/MM) simulation and high-level quantum mechanical calculations. All of the results obtained indicate that the fourth ligand in the active site of the reported X-ray crystal structure is a water molecule rather than a hydroxide anion. On the basis of these theoretical results, we note that the experimental observed pH dependence of the proteolytic and hemorrhagic activity of Acutolysin A can be attributed to the deprotonation of the zinc-bound water to yield a better nucleophile, the hydroxide ion. Structural analyses revealed structural details useful for the understanding of acutolysin catalytic mechanism.

Lennard-Jones parameters for the combined QM/MM method using the B3LYP/6-31G*/AMBER potential

A combined DFT quantum mechanical and AMBER molecular mechanical potential (QM/MM) is presented for use in molecular modeling and molecular simulations of large biological systems. In our approach we evaluate Lennard-Jones parameters describing the interaction between the quantum mechanical (QM) part of a system, which is described at the B3LYP/6-31+G* level of theory, and the molecular mechanical (MM) part of the system, described by the AMBER force field. The Lennard-Jones parameters for this potential are obtained by calculating hydrogen bond energies and hydrogen bond geometries for a large set of bimolecular systems, in which one hydrogen bond monomer is described quantum mechanically and the other is treated molecular mechanically. We have investigated more than 100 different bimolecular systems, finding very good agreement between hydrogen bond energies and geometries obtained from the combined QM/MM calculations and results obtained at the QM level of theory, especially with respect to geometry. Therefore, based on the Lennard-Jones parameters obtained in our study, we anticipate that the B3LYP/6-31+G*/AMBER potential will be a precise tool to explore intermolecular interactions inside a protein environment.

A quantum chemical study of the reaction mechanism of acetyl-coenzyme a synthase

Recent experimental and theoretical studies have focused on the mechanism of the A-cluster active site of acetyl-CoA synthase that produces acetyl-CoA from a methyl group, carbon monoxide, and CoA. Several proposals have been made concerning the redox states of the (Ni-Ni) bimetallic center and the iron-sulfur cluster connected to one of the metals. Using hybrid density functional theory, we have investigated putative intermediate states from the catalytic cycle. Among our conclusions are the following: (i) the zerovalent state proposed for the proximal metal is unlikely if the charge on the iron-sulfur cluster is +2; (ii) a mononuclear mechanism in which both CO and CH(3) bind the proximal nickel is favored over the binuclear mechanism in which CO and CH(3) bind the proximal and distal nickel ions, respectively; (iii) the formation of a disulfide bond in the active site could provide the two electrons necessary for the reaction but only if methylation occurs simultaneously; and (iv) the crystallographic closed form of the active site needs to open to accommodate ligands in the equatorial site.

Dependence of Transition State Structure on Substrate: The Intrinsic C-13 Kinetic Isotope Effect Is Different for Physiological and Slow Substrates of the Ornithine Decarboxylase Reaction Because of Different Hydrogen Bonding Structures

Ornithine decarboxylase is the first and the rate-controlling enzyme in polyamine biosynthesis; it decarboxylates l-ornithine to form the diamine putrescine. We present calculations performed using a combined quantum mechanical and molecular mechanical (QM/MM) method with the AM1 semiempirical Hamiltonian for the wild-type ornithine decarboxylase reaction with ornithine (the physiological substrate) and lysine (a "slow" substrate) and for mutant E274A with ornithine substrate. The dynamical method is variational transition state theory with quantized vibrations. We employ a single reaction coordinate equal to the carbon-carbon distance of the dissociating bond, and we find a large difference between the intrinsic kinetic isotope effect for the physiological substrate, which equals 1.04, and that for the slow substrate, which equals 1.06. This shows that, contrary to a commonly accepted assumption, kinetic isotope effects on slow substrates are not always good models of intrinsic kinetic isotope effects on physiological substrates. Furthermore, analysis of free-energy-based samples of transition state structures shows that the differences in kinetic isotope effects may be traced to different numbers of hydrogen bonds at the different transition states of the different reactions.

Balancing kinetic and thermodynamic control: the mechanism of carbocation cyclization by squalene cyclase

Molecular dynamics simulations with a combined quantum mechanical and molecular mechanical (QM/MM) potential have been carried out to investigate the squalene-to-hopene carbocation cyclization mechanism in squalene-hopene cyclase (SHC). The present study is based on free energy simulations by constructing the free energy surface for the cyclization steps along the reaction pathway. The picture that emerges for the carbocation cyclization cascade is a delicate balance of thermodynamic and kinetic control that ultimately favors the formation of the final hopanoids carbon skeleton. A key finding is that the five- to six-membered ring expansion process is not a viable reaction pathway for either C- or D-ring formation in the cyclization reaction. The only significant intermediate is the A/B-bicyclic cyclohexyl cation (III), from which two asynchronous concerted reaction pathways lead to, respectively, the 6,6,6,5-tetracyclic carbon skeleton and the 6,6,6,6,5-pentacyclic hopanoids. Experimentally, these two products are observed to have 1% and 99% yields, respectively, in the wild-type enzyme. We conclude that the product distribution in the wild-type enzyme is dictated by kinetic control of these two reaction pathways.

Reaction mechanism of the HGXPRTase from Plasmodium falciparum: a hybrid potential quantum mechanical/molecular mechanical study

Parasites lack the ability to synthesize purines de novo. Instead, they use an enzyme, hypoxanthine-guanine-xanthine phosphoribosyltransferase (HGXPRTase), to salvage host purine and to construct their own nucleotides. In this paper, we investigate the reaction mechanism of the HGXPRTase from Plasmodium falciparum using free-energy simulations and a hybrid potential QM/MM description of the enzyme. The possibility of both dissociative and associative nucleophilic substitutions is discussed, as contradictory hypotheses have been postulated on the basis of crystallographic data and kinetic isotope effect experiments. The preferred pathway is predicted to be stepwise with a rapid proton transfer from the hypoxanthine to the protein followed by a rate-limiting glycosyl transfer. This latter step has a D(N)A(N) mechanism with a transition state in which the pyrophosphate leaving group is more closely bound than the attacking hypoxanthine nucleophile. The energy barrier is comparable to the experimentally observed one.

Density functional calculations for modeling the active site of nickel-iron hydrogenases. 2. Predictions for the unready and ready States and the corresponding activation processes

ZORA relativistic DFT calculations are presented which aim to model the geometric and electronic structure of the active site of NiFe hydrogenases in its EPR-active oxidized states Ni-A (unready state) and Ni-B (ready state). Starting coordinates are taken from the X-ray structure of a mutant of Desulfovibrio fructosovorans hydrogenase refined at 1.81 A resolution. Nine possible candidates for Ni-A and Ni-B are analyzed in terms of their geometric and electronic structure. Comparison of calculated geometric and magnetic resonance parameters with available experimental data indicates that both oxidized states have a micro-hydroxo bridge between the two metal centers. The different electronic structures of both forms can be explained by a modification of a terminal cysteine in Ni-B, best modeled by protonation of the sulfur atom. A possible mechanism for the activation of both oxidized forms is presented.