A test of AMBER force fields in predicting the secondary structure of α-helical and β-hairpin peptides

Critical assessment of popular biomolecular force fields for molecular dynamics simulations of folding and enzymatic activity of main protease of coronavirus SARS-CoV-2

The main cysteine protease (Mpro) of coronavirus SARS-CoV-2 has become a promising target for computational development in anti-COVID-19 treatments. Here, we benchmarked the performance of six biomolecular molecular dynamics (MD) force fields (OPLS-AA, CHARMM27, CHARMM36, AMBER03, AMBER14SB and GROMOS G54A7) and three water models (TIP3P, TIP4P and SPC) for reproducing the native fold and the enzymatic activity of Mpro as monomeric and dimeric units. The MD sampling up to 1 μs suggested that the proper choice of the force fields and water models plays an essential role in reproducing the tertiary structure and the inter-residue distance between the catalytic dyad His41-Cys145. We found that while most benchmarked all-atom force fields reproduce well the native fold of Mpro, the CHARMM27/TIP3P and OPLS-AA/TIP4P setups revealed a good performance in reproducing the structure of the catalytic domain. In addition, these FF setups were also well-adopted for MD sampling of Mpro at the physiologic conditions by mimicking the presence of 100 mM NaCl and the elevated temperature of 310 K. Finally, both FFs were also performed well in reproducing the native fold of Mpro in a dimeric form. Therefore, comparing the preservation of the native fold of Mpro and the stability of its catalytic site architecture, our MD benchmarking suggests that the OPLS-AA/TIP4P and CHARMM27/TIP3P MD setups at the physiologic conditions may be well-suited for rapid in silico screening and developing broad-spectrum anti-coronaviral therapeutic agents.

Stable peptide-assembled nanozyme mimicking dual antifungal actions

Natural antimicrobial peptides (AMPs) and enzymes (AMEs) are promising non-antibiotic candidates against antimicrobial resistance but suffer from low efficiency and poor stability. Here, we develop peptide nanozymes which mimic the mode of action of AMPs and AMEs through de novo design and peptide assembly. Through modelling a minimal building block of IHIHICI is proposed by combining critical amino acids in AMPs and AMEs and hydrophobic isoleucine to conduct assembly. Experimental validations reveal that IHIHICI assemble into helical β-sheet nanotubes with acetate modulation and perform phospholipase C-like and peroxidase-like activities with Ni coordination, demonstrating high thermostability and resistance to enzymatic degradation. The assembled nanotubes demonstrate cascade antifungal actions including outer mannan docking, wall disruption, lipid peroxidation and subsequent ferroptotic death, synergistically killing >90% Candida albicans within 10 min on disinfection pad. These findings demonstrate an effective de novo design strategy for developing materials with multi-antimicrobial mode of actions.

Exploring α-synuclein stability under the external electrostatic fields: Effect of repeat unit

Parkinson's disease (PD) is a category of neurodegenerative disorders (ND) that currently lack comprehensive and definitive treatment strategies. The etiology of PD can be attributed to the presence and aggregation of a protein known as α-synuclein. Researchers have observed that the application of an external electrostatic field holds the potential to induce the separation of the fibrous structures into peptides. To comprehend this phenomenon, our investigation involved simulations conducted on the α-synuclein peptides through the application of Molecular Dynamics (MD) simulation techniques under the influence of a 0.1 V/nm electric field. The results obtained from the MD simulations revealed that in the presence of external electric field, the monomer and oligomeric forms of α-synuclein are experienced significant conformational changes which could prevent them from further aggregation. However, as the number of peptide units in the model system increases, forming trimers and tetramers, the stability against the electric field also increases. This enhanced stability in larger aggregates indicates a critical threshold in α-synuclein assembly where the electric field's effectiveness in disrupting the aggregation diminishes. Therefore, our findings suggest that early diagnosis and intervention could be crucial in preventing PD progression. When α-synuclein predominantly exists in its monomeric or dimeric form, applying even a lower electric field could effectively disrupt the initial aggregation process. Inhibition of α-synuclein fibril formation at early stages might serve as a viable solution to combat PD by halting the formation of more stable and pathogenic α-synuclein fibrils.

Elucidating the Enzymatic Mechanism of Dihydrocoumarin Degradation: Insight into the Functional Evolution of Methyl-Parathion Hydrolase from QM/MM and MM MD Simulations

Methyl-parathion hydrolase (MPH), which evolved from dihydrocoumarin hydrolase, offers one of the most efficient enzymes for the hydrolysis of methyl-parathion. Interestingly, the substrate preference of MPH shifts from the methyl-parathion to the lactone dihydrocoumarin (DHC) after its mutation of five specific residues (R72L, L273F, L258H, T271I, and S193Δ, m5-MPH). Here, extensive QM/MM calculations and MM MD simulations have been used to delve into the structure-function relationship of MPH enzymes and plausible mechanisms for the chemical and nonchemical steps, including the transportation and binding of the substrate DHC to the active site, the hydrolysis reaction, and the product release. The results reveal that the five mutations remodel the active pocket and reposition DHC within the active site, leading to stronger enzyme-substrate interactions. The MM/GBSA-estimated binding free energies are about -20.7 kcal/mol for m5-MPH and -17.1 kcal/mol for wild-type MPH. Furthermore, this conformational adjustment of the protein may facilitate the chemical step of DHC hydrolysis and the product release, although there is a certain influence on the substrate transport. The hydrolytic reaction begins with the nucleophilic attack of the bridging OH- with the energy barriers of 22.0 and 18.0 kcal/mol for the wild-type and m5-MPH enzymes, respectively, which is rate-determining for the entire process. Unraveling these mechanistic intricacies may help in the understanding of the natural evolution of enzymes for diverse substrates and establish the enzyme structure-function relationship.

Potential Candidate Molecule of Photosystem II Inhibitor Herbicide-Brassicanate A Sulfoxide

Brassicanate A sulfoxide, a secondary metabolite of broccoli, exhibited the inhibition of weed growth, but its mechanism of action on weeds remains unclear. To elucidate the mechanism by which brassicanate A sulfoxide suppresses weeds, this study explores the interaction between brassicanate A sulfoxide and the photosystem II D1 protein through molecular docking and molecular dynamics simulations. This research demonstrates that brassicanate A sulfoxide interacts with the photosystem II D1 protein by forming hydrogen bonds with Phe-261 and His-214. The successful expression of the photosystem II D1 protein in an insect cell/baculovirus system validated the molecular docking and dynamics simulations. Biolayer interferometry experiments elucidated that the affinity constant of brassicanate A sulfoxide with photosystem II was 2.69 × 10-3 M, suggesting that brassicanate A sulfoxide can stably bind to the photosystem II D1 protein. The findings of this study contribute to the understanding of the mode of action of brassicanate A sulfoxide and also aid in the development of natural-product-based photosynthesis-inhibiting herbicides.

QM/MM and MM MD Simulations on Enzymatic Degradation of the Nerve Agent VR by Phosphotriesterase

V-type nerve agents are hardly degraded by phosphotriesterase (PTE). Interestingly, the PTE variant of BHR-73MNW can effectively improve the hydrolytic efficiency of VR, especially for its Sp-enantiomer. Here, the whole enzymatic degradation of both Sp and Rp enantiomers of VR by the wild-type PTE and its variant BHR-73MNW was investigated by quantum mechanics/molecular mechanics (QM/MM) calculations and MM molecular dynamics simulations. Present results indicate that the degradation of VR can be initiated by the nucleophilic attack of the bridging OH- and the zinc-bound water molecule. The QM/MM-predicted energy barriers for the hydrolytic process of Sp-VR are 19.8 kcal mol-1 by the variant with water as a nucleophile and 22.0 kcal mol-1 by the wild-type PTE with OH- as a nucleophile, and corresponding degraded products are bound to the dinuclear metal site in monodentate and bidentate coordination modes, respectively. The variant effectively increases the volume of the large pocket, allowing more water molecules to enter the active pocket and resulting in the improvement of the degradation efficiency of Sp-VR. The hydrolysis of Rp-VR is triggered only by the hydroxide with an energy span of 20.6 kcal mol-1 for the wild-type PTE and 20.7 kcal mol-1 for the variant BHR-73-MNW PTE. Such mechanistic insights into the stereoselective degradation of VR by PTE and the role of water may inspire further studies to improve the catalytic efficiency of PTE toward the detoxification of nerve agents.

Accelerated Molecular Dynamics for Peptide Folding: Benchmarking Different Combinations of Force Fields and Explicit Solvent Models

Accelerated molecular dynamics (aMD) protocols were assessed on predicting the secondary structure of eight peptides, of which two are helical, three are β-hairpins, and three are disordered. Protocols consisted of combinations of three force fields (ff99SB, ff14SB, ff19SB) and two explicit solvation models (TIP3P and OPC), and were evaluated in two independent aMD simulations, one starting from an extended conformation, the other starting from a misfolded conformation. The results of these analyses indicate that all three combinations performed well on helical peptides. As for β-hairpins, ff19SB performed well with both solvation methods, with a slight preference for the TIP3P solvation model, even though performance was dependent on both peptide sequence and initial conformation. The ff19SB/OPC combination had the best performance on intrinsically disordered peptides. In general, ff14SB/TIP3P suffered the strongest helical bias.

Turning thermostability of Aspergillus terreus (R)-selective transaminase At-ATA by synthetic shuffling

As versatile and green biocatalysts for the asymmetric amination of ketones, the insufficient thermostability of transaminases always limits its broad application in the pharmaceutical and fine chemical industries. Here, synthetic shuffling technology was used to enhance stability of (R)-selective transaminase from Aspergillus terreus. The results showed that 30 out of 5000 mutants had improved thermostability by color-based screening method, among which mutants with residual enzyme activity higher than 50% at 45 °C for 10 min were selected for further analysis. Especially, the half-inactivation temperature (T₅₀¹⁰), half-life (t_1/2), and melting temperature (T_m) of the best mutant M14 (M280C-H210N-M150C-F115L) were 13.7 °C, 165.8 min, and 13.9 °C higher than that of the wild type (WT), respectively. M14 also exhibited a significant biocatalytic efficiency toward acetophenone and 1-acetylnaphthalene, the yield of which were 265.6% and 117.5% higher than WT, respectively. Based on molecular dynamics simulation, improved catalytic efficiency of M14 could be attributed to its increased hydrogen bonds interaction around the mutation sites. Additionally, the introduction of disulfide bond combined with above mutations has a synergistic effect on the improved protein thermostability.

Energetics of a protein disorder-order transition in small molecule recognition

Many proteins recognise other proteins via mechanisms that involve the folding of intrinsically disordered regions upon complex formation. Here we investigate how the selectivity of a drug-like small molecule arises from its modulation of a protein disorder-to-order transition. Binding of the compound AM-7209 has been reported to confer order upon an intrinsically disordered ‘lid’ region of the oncoprotein MDM2. Calorimetric measurements revealed that truncation of the lid region of MDM2 increases the apparent dissociation constant of AM-7209 250-fold. By contrast, lid truncation has little effect on the binding of the ligand Nutlin-3a. Insights into these differential binding energetics were obtained via a complete thermodynamic analysis that featured adaptive absolute alchemical free energy of binding calculations with enhanced-sampling molecular dynamics simulations. The simulations reveal that in apo MDM2 the ordered lid state is energetically disfavoured. AM-7209, but not Nutlin-3a, shows a significant energetic preference for ordered lid conformations, thus shifting the balance towards ordering of the lid in the AM-7209/MDM2 complex. The methodology reported herein should facilitate broader targeting of intrinsically disordered regions in medicinal chemistry.

Molecular simulations and biophysical measurements elucidate why the ligand AM-7209 orders a disordered region of the protein MDM2 on binding. This work expands strategies available to medicinal chemists for targeting disordered proteins.

Heterologous expression, characterization and evolution prediction of a diaphorase from Geobacillus sp. Y4.1MC1

β-hydroxybutyric acid is the most sensitive indicator in ketoacidosis detection, and accounts for nearly 78% of the ketone bodies. Diaphorase is commonly used to detect the β-hydroxybutyric acid in clinical diagnosis. However, the extraction of diaphorase from animal myocardium is complex and low-yield, which is not convenient for large-scale production. In this study, a diaphorase from Geobacillus sp. Y4.1MC1 was efficiently heterologous expressed and purified in E. coli with a yield of 110 mg/L culture. The optimal temperature and pH of this recombinant diaphorase (rDIA) were 55 °C and 6.5, respectively. It was proved that rDIA was a dual acid- and thermo-stable enzyme, and which showed much more accurate detection of β-hydroxybutyric acid than the commercial enzyme. Additionally, we also investigated the molecular interaction of rDIA with the substrate, and the conformation transition in different pH values by using homology modeling and molecular dynamics simulation. The results showed that 141-161 domain of rDIA played important role in the structure changes and conformations transmission at different pH values. Moreover, it was predicted that F105W, F105R, and M186R mutants were able to improve the binding affinity of rDIA, and A2Y, P35F, Q36D, N210L, F211Y mutants were benefit for the stability of rDIA.

Degradation of pesticides diazinon and diazoxon by phosphotriesterase: insight into divergent mechanisms from QM/MM and MD simulations

Enzymatic hydrolysis by phosphotriesterase (PTE) is one of the most effective ways of degrading organophosphorus pesticides, but the catalytic efficiency depends on the structural features of substrates. Here the enzymatic degradation of diazinon (DIN) and diazoxon (DON), characterized by PS and PO, respectively, have been investigated by QM/MM calculations and MM MD simulations. Our calculations demonstrate that the hydrolysis of DON (with PO) is inevitably initiated by the nucleophilic attack of the bridging-OH^- on the phosphorus center, while for DIN (with PS), we proposed a new degradation mechanism, initiated by the nucleophilic attack of the Zn_α-bound water molecule, for its low-energy pathway. For both DIN and DON, the hydrolytic reaction is predicted to be the rate-limiting step, with energy barriers of 18.5 and 17.7 kcal mol^-1, respectively. The transportation of substrates to the active site, the release of the leaving group and the degraded product are generally verified to be favorable by MD simulations via umbrella sampling, both thermodynamically and dynamically. The side-chain residues Phe132, Leu271 and Tyr309 play the gate-switching role to manipulate substrate delivery and product release. In comparison with the DON-enzyme system, the degraded product of DIN is more easily released from the active site. These new findings will contribute to the comprehensive understanding of the enzymatic degradation of toxic organophosphorus compounds by PTE.

QM/MM and MM MD simulations on decontamination of the V-type nerve agent VX by phosphotriesterase: Toward a comprehensive understanding of steroselectivity and activity

Due to deadly toxicity and high environmental stability of the nerve agent VX, an efficient decontamination approach is desperately needed in tackling its severe threat to human secu-rity. The enzymatic...

Conformational Change of H64 and Substrate Transportation: Insight Into a Full Picture of Enzymatic Hydration of CO2 by Carbonic Anhydrase

The enzymatic hydration of CO₂ into HCO₃ ^- by carbonic anhydrase (CA) is highly efficient and environment-friendly measure for CO₂ sequestration. Here extensive MM MD and QM/MM MD simulations were used to explore the whole enzymatic process, and a full picture of the enzymatic hydration of CO₂ by CA was achieved. Prior to CO₂ hydration, the proton transfer from the water molecule (WT1) to H64 is the rate-limiting step with the free energy barrier of 10.4 kcal/mol, which leads to the ready state with the Zn-bound OH^-. The nucleophilic attack of OH^- on CO₂ produces HCO₃ ^- with the free energy barrier of 4.4 kcal/mol and the free energy release of about 8.0 kcal/mol. Q92 as the key residue manipulates both CO₂ transportation to the active site and release of HCO₃ ^-. The unprotonated H64 in CA prefers in an inward orientation, while the outward conformation is favorable energetically for its protonated counterpart. The conformational transition of H64 between inward and outward correlates with its protonation state, which is mediated by the proton transfer and the product release. The whole enzymatic cycle has the free energy span of 10.4 kcal/mol for the initial proton transfer step and the free energy change of -6.5 kcal/mol. The mechanistic details provide a comprehensive understanding of the entire reversible conversion of CO₂ into bicarbonate and roles of key residues in chemical and nonchemical steps for the enzymatic hydration of CO₂.

Adaptive Markov state model estimation using short reseeding trajectories

In the last decade, advances in molecular dynamics (MD) and Markov State Model (MSM) methodologies have made possible accurate and efficient estimation of kinetic rates and reactive pathways for complex biomolecular dynamics occurring on slow time scales. A promising approach to enhanced sampling of MSMs is to use "adaptive" methods, in which new MD trajectories are "seeded" preferentially from previously identified states. Here, we investigate the performance of various MSM estimators applied to reseeding trajectory data, for both a simple 1D free energy landscape and mini-protein folding MSMs of WW domain and NTL9(1-39). Our results reveal the practical challenges of reseeding simulations and suggest a simple way to reweight seeding trajectory data to better estimate both thermodynamic and kinetic quantities.

Insight Into the Binding Mechanism of p53/pDIQ-MDMX/MDM2 With the Interaction Entropy Method

The study of the p53-MDMX/MDM2 binding sites is a research hotspot for tumor drug design. The inhibition of p53-targeted MDMX/MDM2 has become an effective approach in anti-tumor drug development. In this paper, a theoretically rigorous and computationally accurate method, namely, the interaction entropy (IE) method, combined with the polarized protein-specific charge (PPC) force field, is used to explore the difference in the binding mechanism between p53-MDMX and p53-MDM2. The interaction of a 12mer peptide inhibitor (pDIQ), which is similar to p53 in structure, with MDMX/MDM2 is also studied. The results demonstrate that p53/pDIQ with MDM2 generates a stronger interaction than with MDMX. Compared to p53, pDIQ has larger binding free energies with MDMX and MDM2. According to the calculated binding free energies, the differences in the binding free energy among the four complexes that are obtained from the combination of PPC and IE are more consistent with the experimental values than with the results from the combination of the non-polarizable AMBER force field and IE. In addition, according to the decomposition of the binding free energy, the van der Waals (vdW) interactions are the main driving force for the binding of the four complexes. They are also the main source of the weaker binding affinity of p53/pDIQ-MDMX relative to p53/pDIQ-MDM2. Compared with p53-MDMX/MDM2, according to the analysis of the residue decomposition, the predicated total residue contributions are higher in pDIQ-MDMX/MDM2 than in p53-MDMX/MDM2, which explains why pDIQ has higher binding affinity than p53 with MDMX/MDM2. The current study provides theoretical guidance for understanding the binding mechanisms and designing a potent dual inhibitor that is targeted to MDMX/MDM2.

Probing the functional conformations of an atypical proline-rich fusion peptide

Simulations confirm a propensity for extended and solvent exposed conformations of the p15 fusion peptide capable of membrane targeting.