Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.

In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO226-234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.

In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like (3CLpro) protease can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.14 Å resolution crystal structure of 3CLpro C145S bound to NEMO 226-235 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro- NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for in the pathology of COVID-19.

Protein Molecular Dynamics Simulations with Approximate QM: What Can We Learn?

Classical force fields are essential for computer simulations of proteins and are typically parameterized to reproduce secondary and tertiary structure of isolated proteins. However, while protein-protein interactions are ubiquitous in nature, they are not considered in parameterization efforts and are far less understood than isolated proteins. A better characterization of intermolecular interactions is widely recognized as a key to revolutionizing drug and therapeutic developments with high-throughput computational screening. Urgently needed is a critical assessment of the performance of modern protein force fields against first-principles electronic structure methods and experiments. In a daring step toward this goal, we here describe a comparison of peptide folding dynamics as predicted by a molecular mechanics force field on the one hand and by an approximate electronic structure quantum mechanical (QM) method based on density-functional tight-binding (DFTB) on the other. We further compare the dynamics from straightforward DFTB simulations with a near-linear scaling version of DFTB for massively parallel computation based on the fragment molecular orbital (FMO-DFTB) method. We illustrate differences between the phenomenology of the folding dynamics from these three methods for a small model peptide, as well as charge polarization and dynamic fluctuations, point out possible correlations and implications for force field developers, and discuss the lessons learned that might become applicable to future predictive high-throughput computer screening for personalized neoantigen cancer therapy.

The Fragment Molecular Orbital Method Based on Long-Range Corrected Density-Functional Tight-Binding.

The presently available linear scaling approaches to density-functional tight-binding (DFTB) based on the fragment molecular orbital (FMO) method are severely impacted by the problem of artificial charge transfer due to the self-interaction error (SIE), which hampers the simulation of zwitterionic systems such as biopolymers or ionic liquids. Here we report an extension of FMO-DFTB where we included a long-range corrected (LC) functional designed to mitigate the DFTB SIE, called the FMO-LC-DFTB method, resulting in a robust method which succeeds in simulating zwitterionic systems. Both energy and analytic gradient are developed for the gas phase and the polarizable continuum model of solvation. The scaling of FMO-LC-DFTB with system size N is shown to be almost linear, O( N1.13-1.28), and its numerical accuracy is established for a variety of representative systems including neutral and charged polypeptides. It is shown that pair interaction energies between fragments for two mini-proteins are in excellent agreement with results from long-range corrected density functional theory. The new method was employed in long time scale (1 ns) molecular dynamics simulations of the tryptophan cage protein (PDB: 1L2Y ) in the gas phase for four different protonation states and in stochastic global minimum structure searches for 1-ethyl-3-methylimidazolium nitrate ionic liquid clusters containing up to 2300 atoms.

Light-Emitting Covalent Organic Frameworks: Fluorescence Improving via Pinpoint Surgery and Selective Switch-On Sensing of Anions.

Covalent organic frameworks (COFs) offer ordered π structures that are useful for developing light-emitting materials. However, most COFs are weak in luminescence. Here we report the conversion of less emissive COFs into light-emitting materials via a pinpoint surgery on the pore walls. Deprotonation of the N-H bond to form an anionic nitrogen species in the hydrazone linkage can eliminate the nitrogen-related fluorescence quenching pathway. The resulting COF enhances the fluorescence in a linear proportion to the progress of deprotonation, achieving a 3.8-fold improved emission. This pinpoint N-H cleavage on the pore walls can be driven only by the fluoride anion while other halogen anions, including chloride, bromide, and iodide, remain inactive, enabling the selective fluorescence switch-on sensing of the fluoride anion at a ppb level.

Quantum chemical replica-exchange umbrella sampling molecular dynamics simulations reveal the formation mechanism of iron phthalocyanine from iron and phthalonitrile.

Phthalocyanine (Pc) and its metal complexes (MPcs) have been used industrially since their discovery in the early 20th century. The phthalonitrile (PN) method is a well-known synthesis method in which Pc or MPc can be afforded by heating a mixture of PN and metal powders over 280 °C with only moderate yield. However, the formation mechanism of the phthalocyanines and the intermediate stages of this seemingly simple reaction have yet to be fully understood. To study this mechanism computationally, we carried out quantum chemical molecular dynamics (MD) simulations based on the density-functional tight-binding (DFTB) method, applying the replica-exchange umbrella sampling (REUS) method, starting from four PN molecules and one iron atom. The DFTB-REUS-MD simulations successfully yielded FePc, and a metastable structure very similar to FePc but with a reactive nitrene unit was also identified that might explain the incomplete conversion of the reactants into FePc. Analysis of the MD trajectories reveals a three-step FePc formation mechanism for the PN method.

Simulations of the synthesis of boron-nitride nanostructures in a hot, high pressure gas volume.

We performed nanosecond timescale computer simulations of clusterization and agglomeration processes of boron nitride (BN) nanostructures in hot, high pressure gas, starting from eleven different atomic and molecular precursor systems containing boron, nitrogen and hydrogen at various temperatures from 1500 to 6000 K. The synthesized BN nanostructures self-assemble in the form of cages, flakes, and tubes as well as amorphous structures. The simulations facilitate the analysis of chemical dynamics and we are able to predict the optimal conditions concerning temperature and chemical precursor composition for controlling the synthesis process in a high temperature gas volume, at high pressure. We identify the optimal precursor/temperature choices that lead to the nanostructures of highest quality with the highest rate of synthesis, using a novel parameter of the quality of the synthesis (PQS). Two distinct mechanisms of BN nanotube growth were found, neither of them based on the root-growth process. The simulations were performed using quantum-classical molecular dynamics (QCMD) based on the density-functional tight-binding (DFTB) quantum mechanics in conjunction with a divide-and-conquer (DC) linear scaling algorithm, as implemented in the DC-DFTB-K code, enabling the study of systems as large as 1300 atoms in canonical NVT ensembles for 1 ns time.

Cryptic bioactivity capacitated by synthetic hybrid plant peptides.

Evolution often diversifies a peptide hormone family into multiple subfamilies, which exert distinct activities by exclusive interaction with specific receptors. Here we show that systematic swapping of pre-existing variation in a subfamily of plant CLE peptide hormones leads to a synthetic bifunctional peptide that exerts activities beyond the original subfamily by interacting with multiple receptors. This approach provides new insights into the complexity and specificity of peptide signalling.

Self-assembly of endohedral metallofullerenes: a decisive role of cooling gas and metal-carbon bonding.

The endohedral metallofullerene (EMF) self-assembly process in Sc/carbon vapor in the presence and absence of an inert cooling gas (helium) is systematically investigated using quantum chemical molecular dynamics simulations. It is revealed that the presence of He atoms accelerates the formation of pentagons and hexagons and reduces the size of the self-assembled carbon cages in comparison with analogous He-free simulations. As a result, the Sc/C/He system simulations produce a larger number of successful trajectories (i.e. leading to Sc-EMFs) with more realistic cage-size distribution than simulations of the Sc/C system. The main Sc encapsulation mechanism involves nucleation of several hexagons and pentagons with Sc atoms already at the early stages of carbon vapor condensation. In such proto-cages, both Sc-C σ-bonds and coordination bonds between Sc atoms and the π-system of the carbon network are present. Sc atoms are thus rather labile and can move along the carbon network, but the overall bonding is sufficiently strong to prevent dissociation even at temperatures around 2000 kelvin. Further growth of the fullerene cage results in the encapsulation of one or two Sc atoms within the fullerene. In agreement with experimental studies, an extension of the simulations to Fe and Ti as the metal component showed that Fe-EMFs are not formed at all, whereas Ti is prone to form Ti-EMFs with small cage sizes, including Ti@C28-Td and Ti@C30-C2v(3).

Large-Scale Quantum-Mechanical Molecular Dynamics Simulations Using Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method.

The fully analytic gradient is developed for density-functional tight-binding (DFTB) combined with the fragment molecular orbital (FMO) method (FMO-DFTB). The response terms arising from the coupling of the electronic state to the embedding potential are derived, and the gradient accuracy is demonstrated on water clusters and a polypeptide. The radial distribution functions (RDFs) obtained with FMO-DFTB are found to be similar to those from conventional DFTB, while the computational cost is greatly reduced; for 256 water molecules one molecular dynamics (MD) step takes 73.26 and 0.68 s with full DFTB and FMO-DFTB, respectively, showing a speed-up factor of 108. FMO-DFTB/MD is applied to 100 ps MD simulations of liquid hydrogen halides and is found to reproduce experimental RDFs reasonably well.

Key Structures and Interactions for Binding of Mycobacterium tuberculosis Protein Kinase B Inhibitors from Molecular Dynamics Simulation.

Substituted aminopyrimidine inhibitors have recently been introduced as antituberculosis agents. These inhibitors show impressive activity against protein kinase B, a Ser/Thr protein kinase that is essential for cell growth of M. tuberculosis. However, up to now, X-ray structures of the protein kinase B enzyme complexes with the substituted aminopyrimidine inhibitors are currently unavailable. Consequently, structural details of their binding modes are questionable, prohibiting the structural-based design of more potent protein kinase B inhibitors in the future. Here, molecular dynamics simulations, in conjunction with molecular mechanics/Poisson-Boltzmann surface area binding free-energy analysis, were employed to gain insight into the complex structures of the protein kinase B inhibitors and their binding energetics. The complex structures obtained by the molecular dynamics simulations show binding free energies in good agreement with experiment. The detailed analysis of molecular dynamics results shows that Glu93, Val95, and Leu17 are key residues responsible to the binding of the protein kinase B inhibitors. The aminopyrazole group and the pyrimidine core are the crucial moieties of substituted aminopyrimidine inhibitors for interaction with the key residues. Our results provide a structural concept that can be used as a guide for the future design of protein kinase B inhibitors with highly increased antagonistic activity.

Elucidating the structural basis of diphenyl ether derivatives as highly potent enoyl-ACP reductase inhibitors through molecular dynamics simulations and 3D-QSAR study.

Diphenyl ether derivatives are good candidates for anti-tuberculosis agents that display a promising potency for inhibition of InhA, an essential enoyl-acyl carrier protein (ACP) reductase involved in fatty acid biosynthesis pathways in Mycobacterium tuberculosis. In this work, key structural features for the inhibition were identified by 3D-QSAR CoMSIA models, constructed based on available experimental binding properties of diphenyl ether inhibitors, and a set of four representative compounds was subjected to MD simulations of inhibitor-InhA complexes for the calculation of binding free energies. The results show that bulky groups are required for the R1 substituent on the phenyl A ring of the inhibitors to favor a hydrophobic pocket formed by residues Phe149, Met155, Pro156, Ala157, Tyr158, Pro193, Met199, Val203, Leu207, Ile215, and Leu218. Small substituents with a hydrophilic property are required at the R3 and R4 positions of the inhibitor phenyl B rings to form hydrogen bonds with the backbones of Gly96 and Met98, respectively. For the R2 substituent, small substituents with simultaneous hydrophilic or hydrophobic properties are required to favor the interaction with the pyrophosphate moiety of NAD(+) and the methyl side chain of Ala198, respectively. The reported data provide structural guidance for the design of new and potent diphenyl ether-based inhibitors with high inhibitory activities against M. tuberculosis InhA.

Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method.

We developed the energy and its gradient for the self-consistent-charge density-functional tight-binding (DFTB) method, combined with the fragment molecular orbital (FMO) approach, FMO-DFTB, including an optional a posteriori treatment for dispersion interaction, and evaluated its accuracy as well as computational efficiency for a set of representative systems: polypeptides, a DNA segment, and a small protein. The error in the total energy of FMO-DFTB versus full SCC-DFTB was below 1 kcal/mol for the polyalanine system consisting of about 2000 atoms partitioned into fragments containing 2 residues, and the optimized structures had root-mean-square deviations below 0.1 Å. The scaling of FMO-DFTB with the system size N is only marginally larger than linear [O(N(1.2)) in the worst case]. A parallelization efficiency of 94% was achieved using 128 CPU cores, and we demonstrate the applicability of FMO-DFTB for systems containing more than one million atoms by performing a geometry optimization of a fullerite cluster.

Step-edge self-assembly during graphene nucleation on a nickel surface: QM/MD simulations.

Quantum chemical molecular dynamics simulations of graphene nucleation on the Ni(111) surface show that graphene creates its own step-edge as it forms. This "step-edge self-assembly" is driven by the formation of thermodynamically favorable Ni-C σ-bonds at the graphene edge. This dynamic aspect of the Ni(111) catalyst is in contrast to the commonly accepted view that graphene nucleates on a pre-existing, static catalyst step-edge. Simulations also show that, simply by manipulating the subsurface carbon density, preferential formation of single-layer graphene instead of multi-layer graphene can be achieved on nickel catalysts.

Quantum chemical investigation of epoxide and ether groups in graphene oxide and their vibrational spectra.

We present a detailed analysis of the factors influencing the formation of epoxide and ether groups in graphene nanoflakes using conventional density functional theory (DFT), the density-functional tight-binding (DFTB) method, π-Hückel theory, and graph theoretical invariants. The relative thermodynamic stability associated with the chemisorption of oxygen atoms at various positions on hexagonal graphene flakes (HGFs) of D(6h)-symmetry is determined by two factors - viz. the disruption of the π-conjugation of the HGF and the geometrical deformation of the HGF structure. The thermodynamically most stable structure is achieved when the former factor is minimized, and the latter factor is simultaneously maximized. Infrared (IR) spectra computed using DFT and DFTB reveal a close correlation between the relative thermodynamic stabilities of the oxidized HGF structures and their IR spectral activities. The most stable oxidized structures exhibit significant IR activity between 600 and 1800 cm(-1), whereas less stable oxidized structures exhibit little to no activity in this region. In contrast, Raman spectra are found to be less informative in this respect.

Formation mechanism of polycyclic aromatic hydrocarbons in benzene combustion: Quantum chemical molecular dynamics simulations.

High temperature quantum chemical molecular dynamics simulations on the polycyclic aromatic hydrocarbon (PAH) formation during combustion of benzene were performed using the density-functional tight-binding (DFTB) method. Systems with varying H/C of 0.8, 0.6, 0.4, and 0.2 and temperatures of T(n)=2500 K and T(n)=3000 K were employed for the study of the PAH formation and growth mechanism, and trajectories were analyzed by recording average C:H compositions, common elementary reactions and molecular species, ring count, and other characteristic quantities as functions of time. We found that at H/C=0.8 mostly short polyacetylenic hydrocarbons were formed, and no significant PAH growth was found. At lower H/C ratio, longer polyacetylenic chains started to form and new five- and six-membered rings were created due to chain entanglement. Significant PAH growth forming only pericondensed PAHs was observed at lower H/C ratios of 0.4 and 0.2. In addition, smaller hydrocarbon species, such as C(2)H(2), C(2)H, and C(2), are constantly produced by fragmentation of hydrocarbons (unimolecular reactions) and remain common species, although they are simultaneously consumed by the H-abstraction-C(2)H(2)-addition growth mechanism. Hydrogen is found to have a clear inhibitive effect on PAH and carbon cluster growth in general, in agreement with recent experimental observations.

Quantum chemical molecular dynamics simulation of single-walled carbon nanotube cap nucleation on an iron particle.

The atomic scale details of single-walled carbon nanotube (SWNT) nucleation on metal catalyst particles are elusive to experimental observations. Computer simulation of metal-catalyzed SWNT nucleation is a challenging topic but potentially of great importance to understand the factors affecting SWNT diameters, chirality, and growth efficiency. In this work, we use nonequilibrium density functional tight-binding molecular dynamics simulations and report nucleation of sp(2)-carbon cap structures on an iron particle consisting of 38 atoms. One C(2) molecule was placed every 1.0 ps around an Fe(38) cluster for 30 ps, after which a further 410 ps of annealing simulation without carbon supply was performed. We find that sp(2)-carbon network nucleation and annealing processes occur in three sequential and repetitive stages: (A) polyyne chains on the metal surface react with each other to evolve into a Y-shaped polyyne junction, which preferentially form a five-membered ring as a nucleus; (B) polyyne chains on the first five-membered ring form an additional fused five- or six-membered ring; and (C) pentagon-to-hexagon self-healing rearrangement takes place with the help of short-lived polyyne chains, stabilized by the mobile metal atoms. The observed nucleation process resembles the formation of a fullerene cage. However, the metal particle plays a key role in differentiating the nucleation process from fullerene cage formation, most importantly by keeping the growing cap structure from closing into a fullerene cage and by keeping the carbon edge "alive" for the addition of new carbon material.

Quantum chemical molecular dynamics simulations of dynamic fullerene self-assembly in benzene combustion.

Using density-functional tight-binding (DFTB)-based quantum chemical molecular dynamics at 2500 and 3000 K, we have performed simulations of benzene combustion by gradually reducing the hydrogen to carbon (H/C) ratio. The accuracy of DFTB for these simulations was found to be on the order of 7-9 kcal/mol when compared to higher-level B3LYP and G3-like quantum chemical methods in extensive benchmark calculations. Ninety direct-dynamics trajectories were run for up to 225 ps simulation time, during which hydrocarbon cluster size, curvature, and C(x)H(y) composition, carbon hybridization type, and ring count statistics were recorded. Giant fullerene cage formation was observed only after hydrogen was completely eliminated from the reaction mixture, with yields of around 50% at 2500 K and 42% at 3000 K. Cage sizes are mostly in the range from 152 to 202 carbon atoms, with the distribution shifting toward larger cages at lower temperature. In contrast to previous simulations of dynamics fullerene assembly from ensembles of C(2) molecules, we find that the resulting cages show smaller number of attached carbon chains (antenna) surviving until cage closure. Again, no direct formation pathway for C(60) from smaller fragments was observed. Our results challenge the idealized picture of "ordered" growth of PAHs along a route involving only maximally condensed and fully hydrogenated graphene platelets, and favor instead fleeting open-chains with ring structures attached, featuring a large number of hydrogen defects, pentagons, and other nonhexagon ring species.

Rapid growth of a single-walled carbon nanotube on an iron cluster: density-functional tight-binding molecular dynamics simulations.

Continued growth of a single-walled carbon nanotube (SWNT) on an Fe cluster at 1500 K is demonstrated using quantum chemical molecular dynamics simulations based on the self-consistent-charge density-functional tight-binding (SCC-DFTB) method. In order to deal with charge transfer between carbon and metal particles and the multitude of electronic states, a finite electronic temperature approach is applied. We present trajectories of 45 ps length, where a continuous supply of carbon atoms is directed toward the C-Fe boundary between a 7.2 A long armchair (5,5) SWNT fragment and an attached Fe(38) cluster. The incident carbon atoms react readily at the C-Fe interface to form C- and C(2)-extensions on the tube rim that attach to the Fe cluster. These bridging sp-hybridized carbon fragments are vibrationally excited and highly mobile and, therefore, become engaged in frequent bond formation and breaking processes between their constituent C and the Fe atoms. The sp-hybridized carbon bridge dynamics and their reactions with the Fe-attached nanotube end bring about formations of new five-, six-, and seven-membered carbon rings extending the tube sidewall, resulting in overall continued growth of the nanotube on the Fe cluster up to nearly twice its length. Due to the random nature of new polygon formation, sidewall growth is observed as an irregular process without clear SWNT chirality preference. Compared to fullerene formation, heptagon formation is considerably promoted.