Artificial Intelligence-Guided De Novo Molecular Design Targeting COVID-19
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SEARCH · Engineering Papers
Results for “molecular modelling”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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High-Throughput Screening of Promising Redox-Active Molecules with MolGAT
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Greenhouse Gas Emission Mitigation Potential of Chemicals Produced from Biomass
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Storage-Induced Collapse of Lignin Macromolecular Structure and Its Impacts on the Biorefinery
Lignin plays a vital role in the economics of biorefineries, serving as a source of process energy and a feedstock for sustainable fuels and chemical production. While understanding lignin’s chemical composition is crucial, emerging evidence suggests that a more comprehensive understanding of its macromolecular structure is critical to explaining its complex behavior in the biorefinery. This study investigated the partial collapse of the lignin network in corn stover feedstock after harvest and storage as a result of the microbial digestion of hemicellulose. Fluorescence microscopy was used to detect the collapse of lignin in terms of lignin’s inter-molecular interaction and the re-orientation of lignin’s chromophores, by the changes in lignin’s fluorescence lifetime, anisotropy, and the number of effective emitters. With minimal sample perturbation, our in-situ microscopic results revealed lignin's coil-globule transition phenomena, which was only previously predicted by molecular dynamics modeling extracted lignin in solvent. This collapse of lignin macromolecular structure was confirmed by results from NMR, IR, Raman, and powder X-ray diffraction. We also investigated the impact of this storage-induced collapse on the downstream biorefinery processes. Our study revealed that the two major approaches for lignin valorization in the lignin-first biorefinery model, namely monomer extraction and milled wood lignin extraction, were negatively impacted by the lignin collapse. As changes during storage are a source of feedstock variability, our study highlights the importance of understanding the effect of feedstock handling on biorefinery operations and economics.
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Ultra-fast Proton Conduction and Photocatalytic Water Splitting in a Pillared Metal–Organic Framework
Proton-exchange membrane fuel cells enable the portable utilization of hydrogen (H 2 ) as an energy resource. Current electrolytic materials have limitation, and there is an urgent need to develop new materials showing especially high proton conductivity. Here, we report the ultra-fast proton conduction in a novel metal–organic framework, MFM-808, which adopts an unprecedented topology and a unique structure consisting of two-dimensional layers of {Zr 6 }-clusters. By replacing the bridging formate with sulfate ligands within {Zr 6 }-layers, the modified MFM-808-SO 4 exhibits an exceptional proton conductivity of 0.21 S·cm –1 at 85 °C and 99% relative humidity. Modeling by molecular dynamics confirms that proton transfer is promoted by an efficient two-dimensional conducting network assembled by sulfate–{Zr 6 }-layers. MFM-808-SO 4 also possesses excellent photocatalytic activity for water splitting to produce H 2 , paving a new pathway to achieve a renewable hydrogen-energy cycle.
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Dynamic Nanocrystal Superlattices with Thermally Triggerable Lubricating Ligands
The size-dependent and collective physical properties of nanocrystals (NCs) and their self-assembled superlattices (SLs) enable the study of mesoscale phenomena and the design of metamaterials for a broad range of applications. However, the limited mobility of NC building blocks in dried NCSLs often hampers the potential for employing postdeposition methods to produce high-quality NCSLs. In this study, we present tailored promesogenic ligands that exhibit a lubricating property akin to thermotropic liquid crystals. The lubricating ability of ligands is thermally triggerable, allowing the dry solid NC aggregates deposited on the substrates with poor ordering to be transformed into NCSLs with high crystallinity and preferred orientations. The interplay between the dynamic behavior of NCSLs and the molecular structure of the ligands is elucidated through a comprehensive analysis of their lubricating efficacy using both experimental and simulation approaches. Coarse-grained molecular dynamic modeling suggests that a shielding layer from mesogens prevents the interdigitation of ligand tails, facilitating the sliding between outer shells and consequently enhancing the mobility of NC building blocks. Further, the dynamic organization of NCSLs can also be triggered with high spatial resolution by laser illumination. The principles, kinetics, and utility of lubricating ligands could be generalized to unlock stimuli-responsive metamaterials from NCSLs and contribute to the fabrication of NCSLs.
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The Power of Many: An Ensemble Approach to Spectral Similarity
Quantifying the similarity between two mass spectra─a known reference mass spectrum and an unidentified sample mass spectrum─is at the heart of compound identification workflows in gas chromatography–mass spectrometry (GC-MS). The reference spectrum most like the sample is assigned as its identification (provided some quantitative similarity threshold is met, e.g., 80%) and thus accurately measuring similarity is essential. Significant research has gone toward developing metrics for this purpose, each of which has attempted to improve upon existing methods by incorporating GC-MS-specific information (e.g., peak ratios or retention times) or adopting various statistical and algorithmic frameworks. While this active development has led to a plethora of similarity metrics with demonstrated value across different contexts, the unfortunate consequence has been confusion surrounding which metric should be used as a global standard. No such metric is currently accepted as the standard method because different metrics have demonstrated optimal performance in different contexts. In this work, we propose an ensemble approach to spectral similarity scoring that combines the collective information from across existing similarity metrics to form an improved, globally representative similarity metric as a step toward establishing a global standard method. In conclusion, the resulting ensemble metrics are evaluated on over 88,000 spectra of varying complexity and demonstrate improved abilities to accurately rank the correct reference spectrum as the top-matching candidate for a sample relative to the rankings generated by individual similarity scores.
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Host receptor-targeted therapeutic approach to counter pathogenic New World mammarenavirus infections
Five New World mammarenaviruses (NWMs) cause life-threatening hemorrhagic fever (HF). Cellular entry by these viruses is mediated by human transferrin receptor 1 (hTfR1). Here, we demonstrate that an antibody (ch128.1/IgG1) which binds the apical domain of hTfR1, potently inhibits infection of attenuated and pathogenic NWMs in vitro. Computational docking of the antibody Fab crystal structure onto the known structure of hTfR1 shows an overlapping receptor-binding region shared by the Fab and the viral envelope glycoprotein GP1 subunit that binds hTfR1, and we demonstrate competitive inhibition of NWM GP1 binding by ch128.1/IgG1 as the principal mechanism of action. Importantly, ch128.1/IgG1 protects hTfR1-expressing transgenic mice against lethal NWM challenge. Additionally, the antibody is well-tolerated and only partially reduces ferritin uptake. Our findings provide the basis for the development of a novel, host receptor-targeted antibody therapeutic broadly applicable to the treatment of HF of NWM etiology.
59 BASIC BIOLOGICAL SCIENCES↗
Computational identification of HCV neutralizing antibodies with a common HCDR3 disulfide bond motif in the antibody repertoires of infected individuals
Despite recent success in hepatitis C virus (HCV) treatment using antivirals, an HCV vaccine is still needed to prevent reinfections in treated patients, to avert the emergence of drug-resistant strains, and to provide protection for people with no access to the antiviral therapeutics. The early production of broadly neutralizing antibodies (bNAbs) associates with HCV clearance. Several potent bNAbs bind a conserved HCV glycoprotein E2 epitope using an unusual heavy chain complementarity determining region 3 (HCDR3) containing an intra-loop disulfide bond. Isolation of additional structurally-homologous bNAbs would facilitate the recognition of key determinants of such bNAbs and guide rational vaccine design. Here we report the identification of new antibodies containing an HCDR3 disulfide bond motif using computational screening with the Rosetta software. Using the newly-discovered and already-known members of this antibody family, we review the required HCDR3 amino acid composition and propose determinants for the bent versus straight HCDR3 loop conformation observed in these antibodies.
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Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry
Targeted protein degradation (TPD) is a promising approach in drug discovery for degrading proteins implicated in diseases. A key step in this process is the formation of a ternary complex where a heterobifunctional molecule induces proximity of an E3 ligase to a protein of interest (POI), thus facilitating ubiquitin transfer to the POI. In this work, we characterize 3 steps in the TPD process. (1) We simulate the ternary complex formation of SMARCA2 bromodomain and VHL E3 ligase by combining hydrogen-deuterium exchange mass spectrometry with weighted ensemble molecular dynamics (MD). (2) We characterize the conformational heterogeneity of the ternary complex using Hamiltonian replica exchange simulations and small-angle X-ray scattering. (3) We assess the ubiquitination of the POI in the context of the full Cullin-RING Ligase, confirming experimental ubiquitinomics results. Differences in degradation efficiency can be explained by the proximity of lysine residues on the POI relative to ubiquitin.
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Dual domain recognition determines SARS-CoV-2 PLpro selectivity for human ISG15 and K48-linked di-ubiquitin
The Papain-like protease (PLpro) is a domain of a multi-functional, non-structural protein 3 of coronaviruses. PLpro cleaves viral polyproteins and posttranslational conjugates with poly-ubiquitin and protective ISG15, composed of two ubiquitin-like (UBL) domains. Across coronaviruses, PLpro showed divergent selectivity for recognition and cleavage of posttranslational conjugates despite sequence conservation. We show that SARS-CoV-2 PLpro binds human ISG15 and K48-linked di-ubiquitin (K48-Ub 2 ) with nanomolar affinity and detect alternate weaker-binding modes. Crystal structures of untethered PLpro complexes with ISG15 and K48-Ub 2 combined with solution NMR and cross-linking mass spectrometry revealed how the two domains of ISG15 or K48-Ub 2 are differently utilized in interactions with PLpro. Analysis of protein interface energetics predicted differential binding stabilities of the two UBL/Ub domains that were validated experimentally. We emphasize how substrate recognition can be tuned to cleave specifically ISG15 or K48-Ub 2 modifications while retaining capacity to cleave mono-Ub conjugates. These results highlight alternative druggable surfaces that would inhibit PLpro function.
60 APPLIED LIFE SCIENCES↗
Substrate binding-induced conformational transitions in the omega-3 fatty acid transporter MFSD2A
Major Facilitator Superfamily Domain containing 2 A (MFSD2A) is a transporter that is highly enriched at the blood-brain and blood-retinal barriers, where it mediates Na + -dependent uptake of ω-3 fatty acids in the form of lysolipids into the brain and eyes, respectively. Despite recent structural insights, it remains unclear how this process is initiated, and driven by Na + . Here, we perform Molecular Dynamics simulations which demonstrate that substrates enter outward facing MFSD2A from the outer leaflet of the membrane via lateral openings between transmembrane helices 5/8 and 2/11. The substrate headgroup enters first and engages in Na + -bridged interactions with a conserved glutamic acid, while the tail is surrounded by hydrophobic residues. This binding mode is consistent with a “trap-and-flip” mechanism and triggers transition to an occluded conformation. Furthermore, using machine learning analysis, we identify key elements that enable these transitions. These results advance our molecular understanding of the MFSD2A transport cycle.
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De novo design of knotted tandem repeat proteins
De novo protein design methods can create proteins with folds not yet seen in nature. These methods largely focus on optimizing the compatibility between the designed sequence and the intended conformation, without explicit consideration of protein folding pathways. Deeply knotted proteins, whose topologies may introduce substantial barriers to folding, thus represent an interesting test case for protein design. Here we report our attempts to design proteins with trefoil (3 1 ) and pentafoil (5 1 ) knotted topologies. We extended previously described algorithms for tandem repeat protein design in order to construct deeply knotted backbones and matching designed repeat sequences (N = 3 repeats for the trefoil and N = 5 for the pentafoil). We confirmed the intended conformation for the trefoil design by X ray crystallography, and we report here on this protein’s structure, stability, and folding behaviour. The pentafoil design misfolded into an asymmetric structure (despite a 5-fold symmetric sequence); two of the four repeat-repeat units matched the designed backbone while the other two diverged to form local contacts, leading to a trefoil rather than pentafoil knotted topology. Our results also provide insights into the folding of knotted proteins.
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Mechanism of DNA origami folding elucidated by mesoscopic simulations
Abstract Many experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.
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A structural homology approach to identify potential cross-reactive antibody responses following SARS-CoV-2 infection
Abstract The emergence of the novel SARS-CoV-2 virus is the most important public-health issue of our time. Understanding the diverse clinical presentations of the ensuing disease, COVID-19, remains a critical unmet need. Here we present a comprehensive listing of the diverse clinical indications associated with COVID-19. We explore the theory that anti-SARS-CoV-2 antibodies could cross-react with endogenous human proteins driving some of the pathologies associated with COVID-19. We describe a novel computational approach to estimate structural homology between SARS-CoV-2 proteins and human proteins. Antibodies are more likely to interrogate 3D-structural epitopes than continuous linear epitopes. This computational workflow identified 346 human proteins containing a domain with high structural homology to a SARS-CoV-2 Wuhan strain protein. Of these, 102 proteins exhibit functions that could contribute to COVID-19 clinical pathologies. We present a testable hypothesis to delineate unexplained clinical observations vis-à-vis COVID-19 and a tool to evaluate the safety-risk profile of potential COVID-19 therapies.
60 APPLIED LIFE SCIENCES↗
Monatomic ions influence substrate permeation across bacterial microcompartment shells
Abstract Bacterial microcompartments (BMCs) are protein organelles consisting of an inner enzymatic core encased within a selectively permeable shell. BMC shells are modular, tractable architectures that can be repurposed with new interior enzymes for biomanufacturing purposes. The permeability of BMC shells is function-specific and regulated by biophysical properties of the shell subunits, especially its pores. We hypothesized that ions may interact with pore residues in a manner that influences the substrate permeation process. In vitro activity comparisons between native and broken BMCs demonstrated that increasing NaCl negatively affects permeation rates. Molecular dynamics simulations of the dominant shell protein (BMC-H) revealed that chloride ions preferentially occupy the positive pore, hindering substrate permeation, while sodium cations remain excluded. Overall, these results demonstrate that shell properties influence ion permeability and leverages the integration of experimental and computational techniques to improve our understanding of BMC shells towards their repurposing for biotechnological applications.
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The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase
TMEM16F is a Ca 2+ -activated phospholipid scramblase in the TMEM16 family of membrane proteins. Unlike other TMEM16s exhibiting a membrane-exposed hydrophilic groove that serves as a translocation pathway for lipids, the experimentally determined structures of TMEM16F shows the groove in a closed conformation even under conditions of maximal scramblase activity. It is currently unknown if/how TMEM16F groove can open for lipid scrambling. Here we describe the analysis of ~400 µs all-atom molecular dynamics (MD) simulations of the TMEM16F revealing an allosteric mechanism leading to an open-groove, lipid scrambling competent state of the protein. The groove opens into a continuous hydrophilic conduit that is highly similar in structure to that seen in other activated scramblases. The allosteric pathway connects this opening to an observed destabilization of the Ca 2+ ion bound at the distal site near the dimer interface, to the dynamics of specific protein regions that produces the open-groove state to scramble phospholipids.
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Fe protein docking transduces conformational changes to MoFe nitrogenase active site in a nucleotide-dependent manner
The reduction of dinitrogen to ammonia catalyzed by nitrogenase involves a complex series of events, including ATP hydrolysis, electron transfer, and activation of metal clusters for N 2 reduction. Early evidence shows that an essential part of the mechanism involves transducing information between the nitrogenase component proteins through conformational dynamics. Here, millisecond time-resolved hydrogen-deuterium exchange mass spectrometry was used to unravel peptide-level protein motion on the time scale of catalysis of Mo-dependent nitrogenase from Azotobacter vinelandii. Normal mode analysis calculations complemented this data, providing insights into the specific signal transduction pathways that relay information across protein interfaces at distances spanning 100 Å. Together, these results show that conformational changes induced by protein docking are rapidly transduced to the active site, suggesting a specific mechanism for activating the metal cofactor in the enzyme active site.
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