Reaction mechanism of sarcosine oxidase elucidated using FMO and QM/MM methods

Physical Chemistry Chemical Physics
Monomeric sarcosine oxidase (MSOX) is a flavoprotein that oxidizes sarcosine to the corresponding imine product and is widely used in clinical diagnostics to test renal function. In the past decade, several experimental studies have been performed to elucidate the underlying mechanism of this oxidation reaction. However, the details of the molecular mechanism remain unknown. In this study, we theoretically examined three possible reaction mechanisms, namely, the single-electron transfer, hydride-transfer, and polar mechanisms, using the fragment molecular orbital (FMO) and mixed quantum mechanics/molecular mechanics (QM/MM) methods. We found that, of the three possible reaction pathways, the hydride-transfer one is the most energetically favorable. Significantly, the hydrogen is not transferred in the hydride state (H-) but in a hydrogen atom state (H.). Further, a single electron is simultaneously transferred from sarcosine to the flavin through their overlapping orbitals. Therefore,...  Read more

Prediction of luciferase inhibitors by high-performance MIEC-GBDT approach based on interaction energetic patterns

Physical Chemistry Chemical Physics
High-throughput screening (HTS) is widely applied in many fields ranging from drug discovery to clinical diagnostics and toxicity assessment. The firefly luciferase is commonly used as a reporter to monitor the effect of chemical compounds on the activity of a specific target or pathway in HTS. However, the false positive rate of luciferase-based HTS is relatively high because many artifacts or promiscuous compounds that have direct interaction with the luciferase reporter enzyme are usually identified as active compounds (hits). Therefore, it is necessary to develop a rapid screening method to identify these compounds that can inhibit the luciferase activity directly. In this study, a virtual screening (VS) classification model called MIEC-GBDT was developed to distinguish luciferase inhibitors from non-inhibitors. The molecular interaction energy components (MIECs) calculated by the Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition were used to...  Read more

In/out isomerism of cyclophanes: a theoretical account on 2,6,15-trithia-[34,10][7]metacyclophane and [34,10][7]metacyclophane, as well as their halogen substituted analogues

Physical Chemistry Chemical Physics
A detailed theoretical investigation of cyclophanes with a divergent set of methods, ranging from molecular mechanics through semiempirical to ab intio is presented. Cyclophanes have attracted interest over the years due to their unusual chemistry and increasing applications. There has been previous debate over the effects contributing to the greater stability of more crowded in isomers of certain cyclophanes and higher strain in the out isomer was the prevailing explanation. Application of EDA-NOCV and SAPT analysis has enabled us to distinguish between different effects controlling isomer stability and determine the significance of all effects involved. Our results show that, although strain has a large significance, orbital stabilization within the molecule from the aromatic electron density is crucial. Furthermore, we analysed halogen substituted cyclophanes in order to further understand these subtle effects.Read more

The mechanism of an asymmetric ring-opening reaction of epoxide with amine catalyzed by a metal–organic framework: insights from combined quantum mechanics and molecular mechanics calculations

Dalton Transactions
We applied QM/MM calculations to the asymmetric ring-opening reaction of cyclohexene oxide with aniline catalyzed by a two-dimensional metal–organic framework (MOF) that contains a Cu-paddlewheel (Cu-PDW) unit, aiming to elucidate the reaction mechanism and to identify the factors that determine the enantioselectivity of the reaction. Our QM/MM calculations show that the reaction consists of two major steps. In the first step, ring-opening of the epoxide moiety occurs that leads to an intermediate having an alkoxide ion, and the strong binding of the alkoxide to the Cu(II) center results in cleavage of one of the four coordination bonds of the copper with carboxylate ligands. In the second step of the reaction, there is a proton transfer from aniline to a distant site—i.e., the alkoxide oxygen atom—to form the β-amino alcohol product, and the carboxylate ligands of the Cu-PDW unit assist this process. The first ring-opening step was calculated as the...  Read more

Mechanistic insights into the catalytic reaction of ferulic acid decarboxylase from Aspergillus niger: a QM/MM study

Physical Chemistry Chemical Physics
Ubiquinone plays a pivotal role in the aerobic cellular respiratory electron transport chain, whereas ferulic acid decarboxylase (FDC) is involved in the biosynthesis of ubiquinone precursor. Recently, the complete crystal structure of FDC (based on the co-expression of the A. niger fdc1 gene in E. coli with the associated ubix gene from E. coli) at high resolution was reported. Herein, the detailed catalytic non-oxidative decarboxylation mechanism of FDC has been investigated by a combined quantum mechanics/molecular mechanics (QM/MM) approach. Calculation results indicate that, after the 1,3-dipolar cycloaddition of the substrate and cofactor, the carboxylic group can readily split off from the adduct, and the overall energy barrier of the whole catalytic reaction is 23.5 kcal mol−1. According to the energy barrier analysis, the protonation step is rate-limiting. The conserved protonated Glu282 is suggested to be the...  Read more

Insights into the unprecedented epoxidation mechanism of fumitremorgin B endoperoxidase (FtmOx1) from Aspergillus fumigatus by QM/MM calculations

Physical Chemistry Chemical Physics
Fumitremorgin B endoperoxidase (FtmOx1) from Aspergillus fumigatus is the first reported α-ketoglutarate-dependent mononuclear non-haem iron enzyme that catalyzes the endoperoxide formation reaction, converting Fumitremorgin B to verruculogen. Experiments reveal that the molecular oxygen (O2) is incorporated into verruculogen without O–O bond scission, which differs from the currently known non-haem iron enzymes, but the mechanistic details are still unclear. In this paper, on the basis of the crystal structures of FtmOx1 in complex with either the co-substrate (α-ketoglutarate) or the substrate (fumitremorgin B), a ternary complex model of the enzyme-α-ketoglutarate-substrate has been constructed, and combined quantum mechanics and molecular mechanics (QM/MM) calculations have been performed to unravel the novel mechanism of FtmOx1. Our calculations indicate the quintet of the FeIVRead more

Pore modulation of metal–organic frameworks towards enhanced hydrothermal stability and acetylene uptake via incorporation of different functional brackets

Journal of Materials Chemistry A
Metal–organic frameworks (MOFs), as a class of adjustable porous crystalline materials, have received considerable attention in recent years. In this study, starting from an unstable MIL-88 type Co(II)-MOF as the prototype structure, two isoreticular stabilized MOFs with similar structural features but different water/thermal stabilities and acetylene sorption behaviors were prepared, which can be modulated by incorporating different functional brackets in the pores. MOF 1 equipped with open metal sites (OMSs) decomposed quickly in water solution, while the free N-donor functionalized MOF 2 could be stable in water with improved thermostability. The gas sorption study reveals that activated material 2 has a significantly enhanced acetylene uptake capacity with a lower Qst value than those of activated 1, showing a 79% increase (242 vs. 135...  Read more

Impact of Electronic Fluctuations and Their Description on the Exciton Dynamics in the Light-Harvesting Complex PE545

The Journal of Physical Chemistry B
Temperature-dependent fluctuations of both site energies and electronic couplings are known to affect the excitation energy transfer in light-harvesting complexes. Environment effects on such fluctuations as well as possible spatial correlations among them are investigated here in the PE545 complex from cryptophyte algae using ensemble-averaged wave packet dynamics to extract the exciton dynamics. This strategy directly uses the time-dependent fluctuations of the system Hamiltonian, as described by quantum mechanics/molecular mechanics calculations performed along a classical MD trajectory. Neither the fluctuations in the couplings nor spatial correlations including cross-correlations between site energies and couplings are found to be important in the exciton dynamics of the complex. This finding does not change if a polarizable embedding is used instead of its electrostatic counterpart. The impact of variations in spectral densities and screening of excitonic couplings based on the...  Read more

Theoretical Investigations on the Roles of Intramolecular Structure Distortion versus Irregular Intermolecular Packing in Optical Spectra of 6T Nanoparticles

Chemistry of Materials
It is of vital importance to theoretically understand unique nanoparticle size-tunable and excitation wavelength-dependent multiple optical properties in organic nanoparticles. In this work, we proposed a theoretical protocol to calculate the optical spectrum of the organic nanoparticles, which combines molecular dynamics (MD) simulation, the quantum mechanics/molecular mechanics (QM/MM) approach, and vibronic-coupled Frenkel exciton spectrum theory. By using the protocol, we explored the relationship between intramolecular structure distortion, irregular intermolecular packing, and optical spectra in α-sexithiophene nanoparticles. Two representative clusters cutting from the simulated amorphous nanoparticle were investigated and found to exhibit a blue shift for absorption and emission spectra compared to the solution, which is totally different from the blue-shifted absorption and red-shifted emission in crystal. For the cluster with distorted monomer and disordered packing, the...  Read more

Cleavage mechanism of the aliphatic C–C bond catalyzed by 2,4′-dihydroxyacetophenone dioxygenase from Alcaligenes sp. 4HAP: a QM/MM study

Catalysis Science & Technology
2,4′-Dihydroxyacetophenone dioxygenase (DAD) is a bacterial non-heme enzyme responsible for the oxygenative cleavage of the aliphatic C–C bond, which catalyzes the conversion of 2,4′-dihydroxyacetophenone to 4-hydroxybenzoic acid and formic acid. On the basis of the crystal structure and studies on two synthesized biomimetic model compounds, two possible reaction pathways that involve a dioxacyclic or alkylperoxo intermediate have been previously suggested. However, little is currently known about the mechanistic detail and the proposed intermediates have not been experimentally confirmed yet. To elucidate the reaction mechanism at the atomistic level, on the basis of the recently obtained crystal structure, the reactant enzyme–substrate complex has been constructed, and the reaction details have been studied using a quantum mechanics/molecular mechanics (QM/MM) approach. Our calculations reveal the triplet of the iron(III)-superoxide radical complex as the...  Read more

Atomic Adsorption on Nitrogenated Holey Graphene

The Journal of Physical Chemistry C
Two-dimensional (2D) crystals with C2N stoichiometry have recently been synthesized. This novel material, dubbed nitrogenated holey graphene (NHG), is a semiconductor unlike pristine graphene. For any novel material, it is fundamental to understand the behaviors of different adatoms on its surface, a process responsible for a rich phenomenology. In this work, we employed first-principles calculations and a hybrid quantum mechanics/molecular mechanics method to investigate the adsorption of H, B, and O on NHG sheets. The adsorption of H atoms could prove important for applications in hydrogen storage and gas sensors, whereas the adsorption of O in any new material is important to understand its oxidation process. Both N and B are common dopants in carbon-based systems, such as in BNC structures. We found that H and B prefer to adsorb on top of a nitrogen atom, whereas O prefers to adsorb on top of a carbon–carbon bond. The electronic structure of NHG also changes as a...  Read more

An Estimation of Hybrid Quantum Mechanical Molecular Mechanical Polarization Energies for Small Molecules Using Polarizable Force-Field Approaches

Journal of Chemical Theory and Computation
In this work, we report two polarizable molecular mechanics (polMM) force field models for estimating the polarization energy in hybrid quantum mechanical molecular mechanical (QM/MM) calculations. These two models, named the potential of atomic charges (PAC) and potential of atomic dipoles (PAD), are formulated from the ab initio quantum mechanical (QM) response kernels for the prediction of the QM density response to an external molecular mechanical (MM) environment (as described by external point charges). The PAC model is similar to fluctuating charge (FQ) models because the energy depends on external electrostatic potential values at QM atomic sites; the PAD energy depends on external electrostatic field values at QM atomic sites, resembling induced dipole (ID) models. To demonstrate their uses, we apply the PAC and PAD models to 12 small molecules, which are solvated by TIP3P water. The PAC model reproduces the QM/MM polarization energy with a R2 value...  Read more

Elucidating the Bacterial Membrane Disruption Mechanism of Human α-Defensin 5: A Theoretical Study

The Journal of Physical Chemistry B
Human α-defensin 5 (HD5) is a broad-spectrum antibacterial peptide produced by small intestinal Paneth cells. Despite considerable experimental evidence for the correlation between bacterial membrane destruction and the antibacterial activity of HD5, its membrane disruption mechanism remains unclear. Using all-atom molecular dynamics simulations and molecular mechanics Poisson–Boltzmann surface area analysis, we demonstrate the membrane disruption mechanism of HD5 based on the intrinsic binding of HD5 to Gram-negative (GN) bacterial inner membrane. It was found that both monomer and dimer forms of HD5 bind to the surface of the GN membrane rather than embedding in the hydrophobic core region of the bilayer. Regardless of the form of HD5, the peptide orientated itself similarly on the membrane surface with an inward-pointing electric dipole moment and an outward-pointing hydrophobic dipole moment. We investigated its possible membrane disruption mechanisms and determined that...  Read more

Quantifying the Risks of Asparagine Deamidation and Aspartate Isomerization in Biopharmaceuticals by Computing Reaction Free-Energy Surfaces

The Journal of Physical Chemistry B
Early identification of asparagine deamidation and aspartate isomerization degradation sites can facilitate the successful development of biopharmaceuticals. Several knowledge-based models have been proposed to assess these degradation risks. In this study, we propose a physics-based approach to identify the degradation sites on the basis of the free-energy barriers along the prechemical conformational step and the chemical reaction pathway. These contributions are estimated from classical and quantum mechanics/molecular mechanics molecular dynamics simulations. The computed barriers are compared to those for reference reactions in water within GNG and GDG sequence motifs in peptides (which demonstrate the highest degradation rates). Two major factors decreasing the degradation rates relative to the reference reactions are steric hindrance toward accessing reactive conformations and replacement of water by less polar side chains in the solvation shell of transition states. Among the...  Read more

Theoretical studies on FGFR isoform selectivity of FGFR1/FGFR4 inhibitors by molecular dynamics simulations and free energy calculations

Physical Chemistry Chemical Physics
The activation and overexpression of fibroblast growth factor receptors (FGFRs) are highly correlated with a variety of cancers. Most small molecule inhibitors of FGFRs selectively target FGFR1-3, but not FGFR4. Hence, designing highly selective inhibitors towards FGFR4 remains a great challenge because FGFR4 and FGFR1 have a high sequence identity. Recently, two small molecule inhibitors of FGFRs, ponatinib and AZD4547, have attracted huge attention. Ponatinib, a type II inhibitor, has high affinity towards FGFR1/4 isoforms, but AZD4547, a type I inhibitor of FGFR1, displays much reduced inhibition toward FGFR4. In this study, conventional molecular dynamics (MD) simulations, molecular mechanics/generalized Born surface area (MM/GBSA) free energy calculations and umbrella sampling (US) simulations were carried out to reveal the principle of the binding preference of ponatinib and AZD4547 towards FGFR4/FGFR1. The results provided by MM/GBSA illustrate that ponatinib has similar...  Read more

Computational Study of the Catalytic Mechanism of the Cruzain Cysteine Protease

ACS Catalysis
Cysteine proteases of the papain family are involved in many diseases, making them attractive targets for developing drugs. In this paper, different catalytic mechanisms of cruzain cysteine protease have been studied on the basis of molecular dynamics simulations within hybrid quantum mechanics/molecular mechanics potentials. The obtained free energy surfaces have allowed characterizing every single step along the mechanisms. The results confirm that the full process can be divided into an acylation and a deacylation stage, but important differences with respect to previous studies can be deduced from our calculations. Thus, our calculations suggest that the acylation stage takes place in a stepwise mechanism where a proton from a conserved His159 is transferred first to the N1 atom of the peptide and, after a transient intermediate is located, the Cys25 attacks the carbonyl carbon atom. The stabilization of the activated Cys25 is achieved by an effect of the local environment through...  Read more

The O2-Evolving Complex of Photosystem II: Recent Insights from Quantum Mechanics/Molecular Mechanics (QM/MM), Extended X-ray Absorption Fine Structure (EXAFS), and Femtosecond X-ray Crystallography Data

Accounts of Chemical Research
When PSII in the S1 state is exposed to light, the S1 state is advanced to the higher oxidation states and eventually binds substrate water molecules. Identifying the substrate waters is of paramount importance for establishing the water-oxidation mechanism but is complicated by a large number of spectroscopically similar waters. Water analogues can, therefore, be helpful because they serve as spectroscopic markers that help to track the motion of the substrate waters. Due to a close structural and electronic similarity to water, ammonia has been of particular interest. We review three competing hypotheses on substrate water/ammonia binding and compile theoretical and experimental evidence to support them. Binding of ammonia as a sixth ligand to Mn4 during the S1 → S2 transition seems to satisfy most of the criteria, especially the most compelling recent EPR data on D1-D61A mutated PSII. Such a binding mode suggests delivery of water from...  Read more

Protonation-Dependent Structural Heterogeneity in the Chromophore Binding Site of Cyanobacterial Phytochrome Cph1

The Journal of Physical Chemistry B
Phytochromes are biological red/far-red light sensors found in many organisms. Photoisomerization of the linear methine-bridged tetrapyrrole triggers transient proton translocation events in the chromophore binding pocket (CBP) leading to major conformational changes of the protein matrix that are in turn associated with signaling. By combining pH-dependent resonance Raman and UV–visible absorption spectroscopy, we analyzed protonation-dependent equilibria in the CBP of Cph1 involving the proposed Pr-I and Pr-II substates that prevail below and above pH 7.5, respectively. The protonation pattern and vibrational properties of these states were further characterized by means of hybrid quantum mechanics/molecular mechanics calculations. From this combined experimental–theoretical study, we were able to identify His260 as the key residue controlling pH-dependent equilibria. This residue is not only responsible for the conformational heterogeneity of CBP in the Pr state of prokaryotic...  Read more

Hierarchical transfer of chiral information from the molecular to the mesoscopic scale by Langmuir–Blodgett deposition of tetrasteroid-porphyrins

New Journal of Chemistry
Chiral mesoscopic structures were obtained by Langmuir–Blodgett (LB) deposition of two tetrasteroid-porphyrins differing by the number of hydroxy groups functionalizing the steroid rings. The morphology of the porphyrin aggregates was characterized by spectroscopy (UV-Vis absorption, steady-state fluorescence, circular dichroism) and microscopy (fluorescence, scanning electrons, atomic force) techniques. Molecular Mechanics calculations were also carried out to analyze the hierarchical self-assembly process leading to the propagation of the structural properties of the tetrasteroid-porphyrin building blocks to the mesoscopic scale of the imaged chiral architectures. It has been found that, while the transfer of chiral information from the molecular to the nanoscale is determined by the winding of the tetrasteroid chains functionalizing the porphyrin scaffold, the morphology of the mesoscopic aggregates (rods or twisted ribbons) is determined by the amphiphilic (rods) or hydrophobic...  Read more

Mechanistic Models of Chemical Exchange Induced Relaxation in Protein NMR

Journal of the American Chemical Society
Long-lived conformational states and their interconversion rates critically determine protein function and regulation. When these states have distinct chemical shifts, the measurement of relaxation by NMR may provide us with useful information about their structure, kinetics, and thermodynamics at atomic resolution. However, as these experimental data are sensitive to many structural and dynamic effects, their interpretation with phenomenological models is challenging, even if only a few metastable states are involved. Consequently, approximations and simplifications must often be used which increase the risk of missing important microscopic features hidden in the data. Here, we show how molecular dynamics simulations analyzed through Markov state models and the related hidden Markov state models may be used to establish mechanistic models that provide a microscopic interpretation of NMR relaxation data. Using ubiquitin and BPTI as examples, we demonstrate how the approach allows us...  Read more