A comparative study of galactose oxidase and active site analogs based on QM/MM Car-Parrinello simulations

A parallel study of the radical copper enzyme galactose oxidase (GOase) and a low mol. wt. analog of the active site was performed with dynamic d. functional and mixed quantum-classical calcns. This combined approach enables a direct comparison of the properties of the biomimetic and the natural systems throughout the course of the catalytic reaction. In both cases, five essential forms of the catalytic cycle have been investigated: the resting state in its semi-reduced (catalytically inactive) and its oxidized (catalytically active) form, Asemi and Aox, resp.; a protonated intermediate B; the transition state for the rate-detg. hydrogen abstraction step C, and its product D. For A and B the electronic properties of the biomimetic compd. are qual. very similar to the ones of the natural target. However, in agreement with the exptl. obsd. difference in catalytic activity, the calcd. activation energy for the hydrogen abstraction step is distinctly lower for GOase (16 kcal/mol) than for the mimetic compd. (21 kcal/mol). The enzymic transition state is stabilized by a delocalization of the unpaired spin d. over the sulfur-modified equatorial tyrosine Tyr272, an effect that for geometric reasons is essentially absent in the biomimetic compd. Further differences between the mimic and its natural target concern the structure of the product of the abstraction step, which is characterized by a weakly coordinated aldehyde complex for the latter and a tightly bound linear complex for the former. [on SciFinder (R)]

Drug resistance in HIV-1 protease: flexibility-assisted mechanism of compensatory mutations

Paolo Carloni, Ursula Röthlisberger

The emergence of drug-resistant variants is a serious side effect assocd. with acquired immune deficiency syndrome therapies based on inhibition of human immunodeficiency virus type 1 protease (HIV-1 PR). In these variants, compensatory mutations, usually located far from the active site, are able to affect the enzymic activity via mol. mechanisms that have been related to differences in the conformational flexibility, although the detailed mechanistic aspects have not been clarified so far. Here, we perform multinanosecond mol. dynamics simulations on L63P HIV-1 PR, corresponding to the wild type, and one of its most frequently occurring compensatory mutations, M46I, complexed with the substrate and an enzymic intermediate. The quality of the calcns. is established by comparison with the available NMR data. Our calcns. indicate that the dynamical fluctuations of the mutated enzyme differ from those in the wild type. These differences in the dynamic properties of the adducts with the substrate and with the gem-diol intermediate might be directly related to variations in the enzymic activity and therefore offer an explanation of the obsd. changes in catalytic rate between wild type and mutated enzyme. We anticipate that this "flexibility-assisted" mechanism might be effective in the vast majority of compensatory mutations, which do not change the electrostatic properties of the enzyme. [on SciFinder (R)]

2002

Understanding the Effect of Magnesium Ion Concentration on the Catalytic Activity of Ribonuclease H through Computation: Does a Third Metal Binding Site Modulate Endonuclease Catalysis?

Matteo Dal Peraro

Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase superfamily and hydrolyzes the phosphodiester linkage on the RNA strand of a DNA/RNA hybrid duplex. Due to its activity in HIV reverse transcription, it represents a promising target for anti-HIV drug design. While crystallographic data have located two ions in the catalytic site, there is ongoing debate concerning just how many metal ions bound at the active site are optimal for catalysis. Indeed, experiments have shown a dependency of the catalytic activity on the Mg2+ concentration. Moreover, in RNase H, the glutamate residue E188 has been shown to be essential for full enzymatic activation, regardless of the Mg2+ concentration. The catalytic center is known to contain two Mg2+ ions, and E188 is not one of the primary metal ligands. Herein, classical molecular dynamics (MD) simulations are employed to study the metal-ligand coordination in RNase H at different concentration of Mg2+. Importantly, the presence of a third Mg2+ ion, bound to the second-shell ligand E188, is a persistent feature of the MD simulations. Free energy calculations have identified two distinct conformations, depending on the concentration of Mg2+. At standard concentration, a third Mg2+ is found in the catalytic pocket, but it does not perturb the optimal RNase H active conformation. However, at higher concentration, the third Mg2+ ion heavily perturbs the nucleophilic water and thereby influences the catalytic efficiency of RNase H. In addition, the E188A mutant shows no ability to engage additional Mg2+ ions near the catalytic pocket. This finding likely explains the decrease in catalytic activity of E188A and also supports the key role of E188 in localizing the third Mg2+ ion at the active site. Glutamate residues are commonly found surrounding the metal center in the endonuclease family, which suggests that this structural motif may be an important feature to enhance catalytic activity. The present MD calculations support the hypothesis that RNase H can accommodate three divalent metal ions in its catalytic pocket and provide an in-depth understanding of their dynamic role for catalysis.

2010

Molecular Engineering of Electrode Surfaces for Electrocatalysis

Patrick Eduard Alexa

Electrocatalysts play an important part on the route towards environmental friendly energy sources. They support modern technologies like fuel cells to move further away from the utilization of fossil fuels and the resulting CO2 emission into our atmosphere. The main principle of such energy conversion technologies is to store chemical energy within chemical bonds and to release it as electric energy to fulfill the energy demand of today's society. However energy conversion chemistry in such technologies requires catalysts in order to be effective by providing an alternative reaction pathway that lowers activation energies and maximizes the energy output. Providing suitable catalyst surfaces requires a fundamental knowledge of the interaction of reactants and reaction intermediates with the catalyst surfaces. This concern is addressed in this thesis by fabricating specifically tailored molecular components on metal surfaces, which act as organic/inorganic hybrid electrodes for various energy conversion reactions in electrocatalysis. Characterizing the electrode surface is crucial in order to identify active sites of the catalyst. The molecular structure is investigated by surface sensitive techniques, such as STM and XPS in combination with a home-build transfer system, which enables electrode fabrication in UHV and electrocatalytic experiments in a liquid environment. A detailed characterization of organic polymer components on electrode surfaces is obtained by combining experimental data with MD simulations. The morphology of polymer networks can be successfully mimicked and depending on the chemical composition and the structure, spatial correlations on short length scales are reported. Hybrid electrodes with organic polymer co-catalysts reveal an increased catalytic activity for the HER by providing suitable docking sites that act as catalytic active sites. Reactants and reaction intermediates are stabilized via hydrogen bonding, which results in a higher catalytic turnover. The specific designed structure of the organic co-catalyst helps to identify a fraction of the reaction mechanism and highlights the importance of molecular components in electrocatalysis. The utilization of organic units on electrocatalysts provides also an excellent opportunity in order to use single metal atoms as catalysts. Engineering large pi-systems has no significant impact on the ORR activity, while the distance between active sites and the underlying electrode are crucial for enhancing the catalytic activity. A significant factor in using molecular components in electrocatalysis is the stability of the organics. Using electrografting allows to design organic/inorganic hybrid electrodes with covalent bonds between the molecular component and the metal substrate. Attaching empty porphyrin molecules to substrates introduces a powerful technique in molecular engineering, since empty porphyrin cycles can be metallized with various metal centers that can act as electrocatalysts for different electrochemical reactions. In summary, this thesis provides multiple engineering aspects, which are useful in designing molecular components on metal electrodes for energy conversion. Such hybrid catalyst surfaces are capable of improving the catalytic activity and allow to study the mechanism of catalytic reactions. Implementing organic components provides new routes for tailoring novel materials, which deliver new insight into the complex field of electrocatalysis.