Molecular dynamics and density functional theory studies of substrate binding and catalysis of human brain aspartoacylase

Zhang, Chenghua; Gao, Jieying; Chen, Zeqin; Yang, Xue

doi:10.1016/j.jmgm.2010.02.005

Cited by 10 publications

(6 citation statements)

References 40 publications

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“…By all means we cannot confirm the conclusion from the papers of Zhang et al , that the ES → TS1 → I1 stage is responsible for the observed reaction kinetics. Analysis of the energy diagram in Figure shows that other stages beyond the nucleophilic attack of water should be also taken into consideration.…”

Section: Discussioncontrasting

confidence: 88%

“…From the theoretical side, Zhang et al reported the results of computational simulations of the initial stages of this reaction. , The authors performed the density functional theory (DFT) calculations for a small cluster composed of a few molecular groups at the active site and computed the potential energy barrier of 34 kcal/mol for the nucleophilic attack of the catalytic water molecule . Later, the quantum mechanics/molecular mechanics (QM/MM) based calculations were performed to map the minimum-energy pathway using the semiempirical version of DFT, the self-consistent charge-density functional tight-binding (SCC-DFTB) model, to estimate potentials in the QM region.…”

Section: Introductionmentioning

confidence: 99%

“…12,13 The authors performed the density functional theory (DFT) calculations for a small cluster composed of a few molecular groups at the active site and computed the potential energy barrier of 34 kcal/mol for the nucleophilic attack of the catalytic water molecule. 12 Later, 13 the quantum mechanics/ molecular mechanics (QM/MM) based calculations were performed to map the minimum-energy pathway using the semiempirical version of DFT, the self-consistent charge-density functional tight-binding (SCC-DFTB) model, to estimate potentials in the QM region. The reaction pathway was modeled from the ES complex to the first intermediate and then to a system composed of the protonated acetic acid and the doubly charged (2−) L-aspartate with a neutral amine group, but not the true product species as indicated in the right-hand side of Scheme 1.…”

Section: ■ Introductionmentioning

confidence: 99%

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Modeling the Complete Catalytic Cycle of Aspartoacylase

et al. 2016

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The complete catalytic cycle of aspartoacylase (ASPA), a zinc-dependent enzyme responsible for cleavage of N-acetyl-l-aspartate, is characterized by the methods of molecular modeling. The reaction energy profile connecting the enzyme-substrate (ES) and the enzyme-product (EP) complexes is constructed by the quantum mechanics/molecular mechanics (QM/MM) method assisted by the molecular dynamics (MD) simulations with the QM/MM potentials. Starting from the crystal structure of ASPA complexed with the intermediate analogue, the minimum-energy geometry configurations and the corresponding transition states are located. The stages of substrate binding to the enzyme active site and release of the products are modeled by MD calculations with the replica-exchange umbrella sampling technique. It is shown that the first reaction steps, nucleophilic attack of a zinc-bound nucleophilic water molecule at the carbonyl carbon and the amide bond cleavage, are consistent with the glutamate-assisted mechanism hypothesized for the zinc-dependent hydrolases. The stages of formation of the products, acetate and l-aspartate, and regeneration of the enzyme are characterized for the first time. The constructed free energy diagram from the reactants to the products suggests that the enzyme regeneration, but not the nucleophilic attack of the catalytic water molecule, corresponds to the rate-determining stage of the full catalytic cycle of ASPA.

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Section: Discussioncontrasting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Section: ■ Introductionmentioning

confidence: 99%

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Modeling the Complete Catalytic Cycle of Aspartoacylase

et al. 2016

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“…The semiempirical AM1/d-PhoT and SCC-DFTBPR single point recalculations using the QM/MM BLYP geometries provided PES profiles that were significantly different from those calculated by DFT and ab initio methods. The semiempirical Hamiltonians have been parametrized for reaction with phosphates , and extensively used to decipher reaction mechanisms catalyzed by proteins and RNA enzymes. ,,− The AM1/d-PhoT method has previously been used in QM/MM studies of ribozyme catalysis. ,, Both the AM1/d-PhoT and SCC-DFTBPR PESs favor a sequential reaction pathway, in which proton transfer precedes the nucleophilic attack step (Figure D,E). Proton transfer is realized with the A-1(O2′)···G+1(P) distance greater than ∼2.6 Å and is well separated from the nucleophilic attack step.…”

Section: Resultsmentioning

confidence: 99%

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

Mlýnský

Banáš

Šponer

et al. 2014

J. Chem. Theory Comput.

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We have analyzed the capability of state-of-the-art multiscale computational approaches to provide atomic-resolution electronic structure insights into possible catalytic scenarios of the hairpin ribozyme by evaluating potential and free energy surfaces of the reactions by various hybrid QM/MM methods. The hairpin ribozyme is a unique catalytic RNA that achieves rate acceleration similar to other small self-cleaving ribozymes but without direct metal ion participation. Guanine 8 (G8) and adenine 38 (A38) have been identified as the catalytically essential nucleobases. However, their exact catalytic roles are still being investigated. In line with the available experimental data, we considered two reaction scenarios involving protonated A38H(+) as a general acid which is further assisted by either canonical G8 or deprotonated G8(-) forms. We used the spin-component scaled Møller-Plesset (SCS-MP2) method at the complete basis set limit as the reference method. The semiempirical AM1/d-PhoT and SCC-DFTBPR methods provided acceptable activation barriers with respect to the SCS-MP2 data but predicted significantly different reaction pathways. DFT functionals (BLYP and MPW1K) yielded the same reaction pathway as the SCS-MP2 method. The activation barriers were slightly underestimated by the GGA BLYP functional, although with accuracy comparable to the semiempirical methods. The SCS-MP2 method and hybrid MPW1K functional gave activation barriers that were closest to those derived from experimentally measured rate constants.

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“…Results of few experimental studies of hAsp, ,− as well as results of previous computational simulations − form a basis of our consideration. Two papers , reported the estimated parameters of the Michaelis–Menten kinetics.…”

Section: Introductionmentioning

confidence: 99%

Three Faces of N-Acetylaspartate: Activator, Substrate, and Inhibitor of Human Aspartoacylase

et al. 2017

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Hydrolysis of N-acetylaspartate (NAA), one of the most concentrated metabolites in brain, catalyzed by human aspartoacylase (hAsp) shows a remarkable dependence of the reaction rate on substrate concentration. At low NAA concentrations, sigmoidal shape of kinetic curve is observed, followed by typical rate growth of the enzyme-catalyzed reaction, whereas at high NAA concentrations self-inhibition takes place. We show that this rate dependence is consistent with a molecular model, in which N-acetylaspartate appears to have three faces in the enzyme reaction, acting as activator at low concentrations, substrate at moderate concentrations, and inhibitor at high concentrations. To support this conclusion we identify binding sites of NAA at the hAsp dimer including those on the protein surface (activating sites) and at the dimer interface (inhibiting site). Using the Markov state model approach we demonstrate that population of either activating or inhibiting site shifts the equilibrium between the hAsp dimer conformations with the open and closed gates leading to the enzyme active site buried inside the protein. These conclusions are in accord with the calculated values of binding constants of NAA at the hAsp dimer, indicating that the activating site with a higher affinity to NAA should be occupied first, whereas the inhibiting site with a lower affinity to NAA should be occupied later. Application of the dynamical network analysis shows that communication pathways between the regulatory sites (activating or inhibiting) and the gates to the active site do not interfere. These considerations allow us to develop a kinetic mechanism and to derive the equation for the reaction rate covering the entire NAA concentration range. Perfect agreement between theoretical and experimental kinetic data provides strong support to the proposed catalytic model.

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Molecular dynamics and density functional theory studies of substrate binding and catalysis of human brain aspartoacylase

Cited by 10 publications

References 40 publications

Modeling the Complete Catalytic Cycle of Aspartoacylase

Modeling the Complete Catalytic Cycle of Aspartoacylase

Comparison of ab Initio, DFT, and Semiempirical QM/MM Approaches for Description of Catalytic Mechanism of Hairpin Ribozyme

Three Faces of N-Acetylaspartate: Activator, Substrate, and Inhibitor of Human Aspartoacylase

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