-
[show abstract]
[hide abstract]
ABSTRACT: Cluster model: Large active-site models are used to investigate the selectivity of limonene epoxide hydrolase, both the wild type and mutants optimized through directed evolution. Good agreement is found between theory and the experimental data, thus demonstrating that the quantum chemical cluster approach can be a powerful tool in the field of asymmetric biocatalysis.
Angewandte Chemie International Edition 03/2013; · 13.45 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Quantum chemical calculations of active-site models of nitrous oxide reductase (N(2)OR) have been undertaken to elucidate the mechanism of N-O bond cleavage mediated by the supported tetranuclear Cu(4)S core (Cu(Z)) found in the enzymatic active site. Using either a minimal model previously employed by Gorelsky et al. (J. Am. Chem. Soc. 128:278-290, 2006) or a more extended model including key residue side chains in the active-site second shell, we found two distinct mechanisms. In the first model, N(2)O binds to the fully reduced Cu(Z) in a bent μ-(1,3)-O,N bridging fashion between the Cu(I) and Cu(IV) centers and subsequently extrudes N(2) while generating the corresponding bridged μ-oxo species. In the second model, substrate N(2)O binds loosely to one of the coppers of Cu(Z) in a terminal fashion, i.e., using only the oxygen atom; loss of N(2) generates the same μ-oxo copper core. The free energies of activation predicted for these two alternative pathways are sufficiently close to one another that theory does not provide decisive support for one over the other, posing an interesting problem with respect to experiments that might be designed to distinguish between the two. Effects of nearby residues and active-site water molecules are also explored.
European Journal of Biochemistry 03/2012; 17(5):687-98. · 3.42 Impact Factor
-
Gregory C Patton,
Pål Stenmark,
Deviprasad R Gollapalli,
Robin Sevastik,
Petri Kursula,
Susanne Flodin,
Herwig Schuler,
Colin T Swales,
Hans Eklund, Fahmi Himo,
Pär Nordlund,
Lizbeth Hedstrom
[show abstract]
[hide abstract]
ABSTRACT: Inosine monophosphate dehydrogenase (IMPDH) and guanosine monophosphate reductase (GMPR) belong to the same structural family, share a common set of catalytic residues and bind the same ligands. The structural and mechanistic features that determine reaction outcome in the IMPDH and GMPR family have not been identified. Here we show that the GMPR reaction uses the same intermediate E-XMP* as IMPDH, but in this reaction the intermediate reacts with ammonia instead of water. A single crystal structure of human GMPR type 2 with IMP and NADPH fortuitously captures three different states, each of which mimics a distinct step in the catalytic cycle of GMPR. The cofactor is found in two conformations: an 'in' conformation poised for hydride transfer and an 'out' conformation in which the cofactor is 6 Å from IMP. Mutagenesis along with substrate and cofactor analog experiments demonstrate that the out conformation is required for the deamination of GMP. Remarkably, the cofactor is part of the catalytic machinery that activates ammonia.
Nature Chemical Biology 12/2011; 7(12):950-8. · 14.69 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Density functional theory calculations are used to study the reaction mechanism and origins of C2 selectivity in a copper(I)-catalyzed amidation of indoles. It is shown that concerted metalation-deprotonation is not able to reproduce the observed regioselectivity. Instead, an unprecedented mechanism based on a four-center reductive elimination is proposed to be responsible for the reaction outcome. This mechanism has a lower reaction barrier and is able to reproduce the experimentally observed selectivity. A possible alternative mechanism involving a Cu(II) species instead of Cu(III) is presented, but it is shown that higher energy barriers are associated with this mechanism. An important technical detail is that addition of dispersion effects to the B3LYP results is necessary to reproduce the observed selectivity, although not important for the overall mechanistic proposal.
The Journal of Organic Chemistry 11/2011; 76(22):9246-52. · 4.45 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Triapine (3-aminopyridine-2-carboxaldehyde thiosemicarbazone, 3-AP) is currently the most promising chemotherapeutic compound among the class of α-N-heterocyclic thiosemicarbazones. Here we report further insights into the mechanism(s) of anticancer drug activity and inhibition of mouse ribonucleotide reductase (RNR) by Triapine. In addition to the metal-free ligand, its iron(III), gallium(III), zinc(II) and copper(II) complexes were studied, aiming to correlate their cytotoxic activities with their effects on the diferric/tyrosyl radical center of the RNR enzyme in vitro. In this study we propose for the first time a potential specific binding pocket for Triapine on the surface of the mouse R2 RNR protein. In our mechanistic model, interaction with Triapine results in the labilization of the diferric center in the R2 protein. Subsequently the Triapine molecules act as iron chelators. In the absence of external reductants, and in presence of the mouse R2 RNR protein, catalytic amounts of the iron(III)-Triapine are reduced to the iron(II)-Triapine complex. In the presence of an external reductant (dithiothreitol), stoichiometric amounts of the potently reactive iron(II)-Triapine complex are formed. Formation of the iron(II)-Triapine complex, as the essential part of the reaction outcome, promotes further reactions with molecular oxygen, which give rise to reactive oxygen species (ROS) and thereby damage the RNR enzyme. Triapine affects the diferric center of the mouse R2 protein and, unlike hydroxyurea, is not a potent reductant, not likely to act directly on the tyrosyl radical.
Journal of inorganic biochemistry 07/2011; 105(11):1422-31. · 3.25 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The tungsten-dependent enzyme acetylene hydratase catalyzes the hydration of acetylene to acetaldehyde. Very recently, we proposed a reaction mechanism for this enzyme based on density functional calculations (Proc. Natl. Acad. Sci. U.S.A.2010, 107, 22523). The mechanism involves direct coordination of the substrate to the tungsten ion, followed by a nucleophilic attack by a water molecule concerted with a proton transfer to a second-shell aspartate, which then reprotonates the substrate. Here, we use the same methodology to investigate the factors involved in the control of the chemoselectivity of this enzyme. The hydration reactions of three representative compounds (propyne, ethylene, and acetonitrile) are investigated using a large model of the active site. The energy of substrate binding to the metal ion and the barrier for the following nucleophilic attack are used to rationalize the experimental observations. It is shown that all three compounds have higher barriers for hydration compared with acetylene. In addition, propyne is shown to have a larger binding energy, explaining its behavior as a competitive inhibitor. Taken together, the results provide further corroboration of our suggested mechanism for acetylene hydratase.Keywords: acetylene hydratase; enzyme mechanism; chemoselectivity; transition state; density functional theory
07/2011;
-
[show abstract]
[hide abstract]
ABSTRACT: Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus is a tungsten-dependent enzyme that catalyzes the oxidation of formaldehyde to formic acid. In the present study, quantum chemical calculations are used to elucidate the reaction mechanism of this enzyme. Several possible mechanistic scenarios are investigated with a large model of the active site designed on the basis of the X-ray crystal structure of the native enzyme. Based on the calculations, we propose a new mechanism in which the formaldehyde substrate binds directly to the tungsten ion. W(VI)=O then performs a nucleophilic attack on the formaldehyde carbon to form a tetrahedral intermediate. In the second step, which is calculated to be rate limiting, a proton is transferred to the second-shell Glu308 residue, coupled with a two-electron reduction of the tungsten ion. The calculated barriers for the mechanism are energetically very feasible and in relatively good agreement with experimental rate constants. Three other second-shell mechanisms, including one previously proposed based on experimental findings, are considered but ruled out because of their high barriers.
Journal of inorganic biochemistry 07/2011; 105(7):927-36. · 3.25 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We report a new method for constructing the ABC ring system of strigolactones, in a single step from a simple linear precursor by acid-catalyzed double cyclization. The reaction proceeds with a high degree of stereochemical control, which can be qualitatively rationalized using DFT calculations. Our concise synthetic approach offers a new model for thinking about the (as yet) unknown chemistry that is employed in the biosynthetic pathways leading to this class of plant hormones.
Organic & Biomolecular Chemistry 06/2011; 9(15):5350-3. · 3.70 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: We present a systematic study of the decarboxylation step of the enzyme aspartate decarboxylase with the purpose of assessing the quantum chemical cluster approach for modeling this important class of decarboxylase enzymes. Active site models ranging in size from 27 to 220 atoms are designed, and the barrier and reaction energy of this step are evaluated. To model the enzyme surrounding, homogeneous polarizable medium techniques are used with several dielectric constants. The main conclusion is that when the active site model reaches a certain size, the solvation effects from the surroundings saturate. Similar results have previously been obtained from systematic studies of other classes of enzymes, suggesting that they are of a quite general nature.
J. Chem. Theory Comput. 04/2011; 7:1494-1501.
-
Wiley Interdisciplinary Reviews: Computational Molecular Science. 03/2011; 1(3):323 - 336.
-
[show abstract]
[hide abstract]
ABSTRACT: An unprecedented and highly diastereoselective 6-endo-trig cyclization of 2-alkenyl-1,3-dithiolanes has been developed yielding trans-decalins, an important scaffold present in numerous di- and triterpenes. The novelty of this 6-endo-trig cyclization stands in the stepwise mechanism involving 2-alkenyl-1,3-dithiolane, acting as a novel latent initiator. It is suggested that the thioketal opens temporarily under the influence of TMSOTf, triggering the cationic 6-endo-trig cyclization, and closes after C-C bond formation and diastereoselective protonation to terminate the process. DFT calculations confirm this mechanistic proposal and provide a rationale for the observed diastereoselectivity. The reaction tolerates a wide range of functionalities and nucleophilic partners within the substrate. We have also shown that the one-pot 6-endo-trig cyclization followed by in situ 1,3-dithiolane deprotection afford directly the corresponding ketone. This improvement allowed the achievement of the shortest total synthesis of triptophenolide and the shortest formal synthesis of triptolide.
The Journal of Organic Chemistry 03/2011; 76(9):3274-85. · 4.45 Impact Factor
-
Advanced Synthesis & Catalysis 02/2011; 353(2‐3):245 - 252. · 6.05 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The reaction mechanism of mycolic acid cyclopropane synthase is investigated using hybrid density functional theory. The direct methylation mechanism is examined with a large model of the active site constructed on the basis of the crystal structure of the native enzyme. The important active site residue Glu140 is modeled in both ionized and neutral forms. We demonstrate that the reaction starts via the transfer of a methyl to the substrate double bond, followed by the transfer of a proton from the methyl cation to the bicarbonate present in the active site. The first step is calculated to be rate-limiting, in agreement with experimental kinetic results. The protonation state of Glu140 has a rather weak influence on the reaction energetics. In addition to the natural reaction, a possible side reaction, namely a carbocation rearrangement, is also considered and is shown to have a low barrier. Finally, the energetics for the sulfur ylide proposal, which has already been ruled out, is also estimated, showing a large energetic penalty for ylide formation.
Biochemistry 02/2011; 50(9):1505-13. · 3.42 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Acetylene hydratase is a tungsten-dependent enzyme that catalyzes the nonredox hydration of acetylene to acetaldehyde. Density functional theory calculations are used to elucidate the reaction mechanism of this enzyme with a large model of the active site devised on the basis of the native X-ray crystal structure. Based on the calculations, we propose a new mechanism in which the acetylene substrate first displaces the W-coordinated water molecule, and then undergoes a nucleophilic attack by the water molecule assisted by an ionized Asp13 residue at the active site. This is followed by proton transfer from Asp13 to the newly formed vinyl anion intermediate. In the subsequent isomerization, Asp13 shuttles a proton from the hydroxyl group of the vinyl alcohol to the α-carbon. Asp13 is thus a key player in the mechanism, but also W is directly involved in the reaction by binding and activating acetylene and providing electrostatic stabilization to the transition states and intermediates. Several other mechanisms are also considered but the energetic barriers are found to be very high, ruling out these possibilities.
Proceedings of the National Academy of Sciences 12/2010; 107(52):22523-7. · 9.68 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Nuclease P1 is a trinuclear zinc enzyme that catalyzes the hydrolysis of single-stranded DNA and RNA. Density functional calculations are used to elucidate the reaction mechanism of this enzyme with a model of the active site designed on the basis of the X-ray crystal structure. 2-Tetrahydrofuranyl phosphate and methyl 2-tetrahydrofuranyl phosphate substrates are used to explore the phosphomonoesterase and phosphodiesterase activities of this enzyme, respectively. The calculations reveal that for both activities, a bridging hydroxide performs an in-line attack on the phosphorus center, resulting in inversion of the configuration. Simultaneously, the P-O bond is cleaved, and Zn2 stabilizes the negative charge of the leaving alkoxide anion and assists its departure. All three zinc ions, together with Arg48, provide electrostatic stabilization to the penta-coordinated transition state, thereby lowering the reaction barrier.
Inorganic Chemistry 08/2010; 49(15):6883-8. · 4.60 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The intramolecular aldol reaction of acyclic ketoaldehydes catalyzed by 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) is investigated using density functional theory calculations. Compared to the proline-catalyzed aldol reaction, the use of TBD provides a unique and unusual complete switch of product selectivity. Three mechanistic pathways are proposed and evaluated. The calculations provide new insights into the activation mode of bifunctional guanidine catalysts. In the favored mechanism, TBD first catalyzes the enolization of the substrate and then the C-C bond formation through two concerted proton transfers. In addition, the computationally predicted stereochemical outcome of the reaction is in agreement with the experimental findings.
The Journal of Organic Chemistry 07/2010; 75(14):4728-36. · 4.45 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Quantum chemical cluster models of enzyme active sites are today an important and powerful tool in the study of various aspects of enzymatic reactivity. This methodology has been applied to a wide spectrum of reactions and many important mechanistic problems have been solved. Herein, we report a systematic study of the reaction mechanism of the histone lysine methyltransferase (HKMT) SET7/9 enzyme, which catalyzes the methylation of the N-terminal histone tail of the chromatin structure. In this study, HKMT SET7/9 serves as a representative case to examine the modeling approach for the important class of methyl transfer enzymes. Active site models of different sizes are used to evaluate the methodology. In particular, the dependence of the calculated energies on the model size, the influence of the dielectric medium, and the particular choice of the dielectric constant are discussed. In addition, we examine the validity of some technical aspects, such as geometry optimization in solvent or with a large basis set, and the use of different density functional methods.
Journal of Computational Chemistry 06/2010; 31(8):1707-14. · 4.58 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The mechanistic details of the hydrogenation of molecular oxygen by the 18e amino-hydride Cp*IrH(TsDPEN) (1H(H)) complex to give Cp*Ir(TsDPEN-H) (1) and 1 equiv of H(2)O were investigated by means of hybrid density functional calculations (B3LYP). To comprehensively describe the overall catalytic cycle of the hydrogenation of dioxygen using H(2) catalyzed by the Ir complex 1, the potential energy surfaces for the hydrogenation process of both the catalyst 1 and the corresponding unsaturated iridium(III) amine cation ([1H](+)) were explored at the same level of theory. The results of our computations, in agreement with experimental findings, confirm that the addition of H(2) to the 16e diamido complexes 1 is favorable but is slow and is accelerated by the presence of Bronsted acids, such as HOTf, which convert 1 into the corresponding amine cation [1H](+). By deprotonation of the subsequently hydrogenated [1H(H(2))](+) complex the amine hydride catalyst 1H(H) is generated, which is able to reduce molecular oxygen. Calculations corroborate that the O(2) reduction goes through formation of an intermediate iridium hydroperoxo complex that reacts with 1H(H) to eliminate water, restore 1, and restart the catalytic cycle. From the outcomes of our computational analysis it results that the slow step of the overall O(2) hydrogenation process is the O(2) insertion into the Ir-H bond, and the highest calculated barrier along this pathway to give the hydroperoxo product shows a good agreement with the experimentally estimated value. As a consequence, unreacted 1H(H) approaches 1H(OOH) to give 1H(OH) and water according to the experimentally observed second-order kinetics with respect to [1H(H)]. Calculations were carried out to explore the possibility that H(2)O(2) is released from the hydroperoxo intermediate together with catalyst 1, and the subsequent water elimination reaction occurs by reduction of produced H(2)O(2) with 1H(H) to regenerate catalyst 1. Preliminary results concerning the O(2) reduction in acidic conditions show that the reaction proceeds by intermediate production of H(2)O(2), which reacts with 1H(H) to eliminate water, restore [1H](+), and restart the catalytic cycle. The energetics of the process appear to be definitely more favorable with respect the analogous pathways in neutral conditions.
Journal of the American Chemical Society 03/2010; 132(12):4178-90. · 9.91 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: Phosphatidylcholine-preferring phospholipase C is a trinuclear zinc-dependent phosphodiesterase, catalyzing the hydrolysis of choline phospholipids. In the present study, density functional theory is used to investigate the reaction mechanism of this enzyme. Two possible mechanistic scenarios were considered with a model of the active site designed on the basis of the high resolution X-ray crystal structure of the native enzyme. The calculations show that a Zn1 and Zn3 bridging hydroxide rather than a Zn1 coordinated water molecule performs the nucleophilic attack on the phosphorus center. Simultaneously, Zn2 activates a water molecule to protonate the leaving group. In the following step, the newly generated Zn2 bound hydroxide makes the reverse attack, resulting in the regeneration of the bridging hydroxide. The first step is calculated to be rate-limiting with a barrier of 17.3 kcal/mol, in good agreement with experimental kinetic studies. The zinc ions are suggested to orient the substrate for nucleophilic attack and provide electrostatic stabilization to the dianionic penta-coordinated trigonal bipyramidal transition states, thereby lowering the barrier.
The Journal of Physical Chemistry B 02/2010; 114(7):2533-40. · 3.70 Impact Factor
-
[show abstract]
[hide abstract]
ABSTRACT: The reaction mechanism of the dinuclear zinc enzyme human renal dipeptidase is investigated using hybrid density functional theory. This enzyme catalyzes the hydrolysis of dipeptides and beta-lactam antibiotics. Two different protonation states in which the important active site residue Asp288 is either neutral or ionized were considered. In both cases, the bridging hydroxide is shown to be capable of performing the nucleophilic attack on the substrate carbonyl carbon from its bridging position, resulting in the formation of a tetrahedral intermediate. This step is followed by protonation of the dipeptide nitrogen, coupled with C-N bond cleavage. The calculations establish that both cases have quite feasible energy barriers. When the Asp288 is neutral, the hydrolytic reaction occurs with a large exothermicity. However, the reaction becomes very close to thermoneutral with an ionized Asp288. The two zinc ions are shown to play different roles in the reaction. Zn1 binds the amino group of the substrate, and Zn2 interacts with the carboxylate group of the substrate, helping in orienting it for the nucleophilic attack. In addition, Zn2 stabilizes the oxyanion of the tetrahedral intermediate, thereby facilitating the nucleophilic attack.
Journal of inorganic biochemistry 10/2009; 104(1):37-46. · 3.25 Impact Factor
