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At least 667 records · Page 37

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DOE OSTI2022

A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals

As an essential enzyme of SARS-CoV-2, the COVID-19 pathogen, main protease (M Pro ) is a viable target to develop antivirals for the treatment of COVID-19. By varying chemical compositions at both P2 and P3 positions and the N-terminal protection group, we synthesized 18 tripeptidyl M Pro inhibitors that contained also an aldehyde warhead and β-(S-2-oxopyrrolidin-3-yl)-alaninal at the P1 position. Systematic characterizations of these inhibitors were conducted, including their in vitro enzymatic inhibition potency, X-ray crystal structures of their complexes with M Pro , their inhibition of M Pro transiently expressed in 293T cells, and cellular toxicity and SARS-CoV-2 antiviral potency of selected inhibitors. These inhibitors have a large variation of determined in vitro enzymatic inhibition IC 50 values that range from 4.8 to 650 nM. Here, the determined in vitro enzymatic inhibition IC 50 values reveal that relatively small side chains at both P2 and P3 positions are favorable for achieving high in vitro M Pro inhibition potency, the P3 position is tolerable toward unnatural amino acids with two alkyl substituents on the α-carbon, and the inhibition potency is sensitive toward the N-terminal protection group. X-ray crystal structures of M Pro bound with 16 inhibitors were determined. In all structures, the M Pro active site cysteine interacts covalently with the aldehyde warhead of the bound inhibitor to form a hemithioacetal that takes an S configuration. For all inhibitors, election density around the N-terminal protection group is weak indicating possible flexible binding of this group to M Pro . In M Pro , large structural variations were observed on residues N142 and Q189. Unlike their high in vitro enzymatic inhibition potency, most inhibitors showed low potency to inhibit M Pro that was transiently expressed in 293T cells. Inhibitors that showed high potency to inhibit M Pro transiently expressed in 293T cells all contain O-tert-butyl-threonine at the P3 position. These inhibitors also exhibited relatively low cytotoxicity and high antiviral potency. Overall, our current and previous studies indicate that O-tert-butyl-threonine at the P3 site is a key component to achieve high cellular and antiviral potency for tripeptidyl aldehyde inhibitors of M Pro .

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Differential contagiousness of respiratory disease across the United States

The initial contagiousness of a communicable disease within a given population is quantified by the basic reproduction number, $R_0$. This number depends on both pathogen and population properties. On the basis of compartmental models that reproduce Coronavirus Disease 2019 (COVID-19) surveillance data, we used Bayesian inference and the next-generation matrix approach to estimate region-specific $R_0$ values for 280 of 384 metropolitan statistical areas (MSAs) in the United States (US), which account for 95% of the US population living in urban areas and 82% of the total population. We focused on MSA populations after finding that these populations were more uniformly impacted by COVID-19 than state populations. Our maximum a posteriori (MAP) estimates for $R_0$ range from 1.9 to 7.7 and quantify the relative susceptibilities of regional populations to spread of respiratory diseases.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2022

Gene drive by Fusarium SKC1 is dependent on its competing allele

The Fusarium verticillioides SKC1 gene driver is transmitted to offspring in a biased manner through spore killing. The mechanism that allows SKC1 to kill non-SKC1 offspring while sparing others is poorly understood. Here we report that gene drive by SKC1 is dependent on SKC1's competing allele. We propose that SKC1's competing allele influences the ability of a genome defense process to detect SKC1, and we provide evidence that this genome defense process is meiotic silencing by unpaired DNA (MSUD). Furthermore, our findings suggest that the successful deployment of gene drivers to control pathogenic fungi will require researchers to consider how competing alleles influence the ability of gene drivers to be detected by genome defense processes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Effects of red imported fire ant ( Solenopsis invicta ) control on carrion use by vertebrate scavengers

Carrion is an important resource, and competition for carrion by microbial, invertebrate, and vertebrate scavenging communities is great. In particular, carrion is important to facultative and obligate vertebrate scavengers globally, and these species provide an irreplaceable ecological service by efficiently removing carcasses, which potentially harbor pathogens, from the environment. Although vertebrates efficiently acquire carcasses, they compete intensively with invertebrate and microbial communities, especially during warmer months when invertebrate and microbial activity peaks. The presence of invasive invertebrates may further exacerbate competition among scavenging groups; however, little is known about how invasive invertebrates can influence invertebrate scavenger dynamics and ultimately competition with vertebrate scavengers. The red imported fire ant (Solenopsis invicta; RIFA) is an invasive species of particular interest in North America, as it is a dominant predator and decomposer throughout much their range. We hypothesized that in areas where abundant, RIFA can outcompete vertebrates for carrion resources, altering nutrient cycling and food web dynamics. We tested this hypothesis by experimentally excluding RIFA from rabbit carcasses and found strong seasonal effects in our data; however, surprisingly, we found no effect of RIFA control on vertebrate scavenging efficiency, rates of carcass detection, carcass persistence, or the richness of local scavengers. Rather, we observed a highly efficient vertebrate scavenging community that assimilated 87.4% of carcasses during our study. Furthermore, this high rate of vertebrate scavenging efficiency was maintained in both control (93.0%) and RIFA treatment (81.8%) sites, suggesting presence of abundant RIFA populations did not limit vertebrate acquisition of carrion. Future research should focus on the interactions of RIFA with the remaining invertebrate scavenging community to further investigate whether RIFA impact the assimilation of carrion resources within invertebrate communities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Structural characterization of strawberry pomace

Strawberries are a nutrient dense food rich in vitamins, minerals, non-nutrient antioxidant phenolics, and fibers. Strawberry fiber bioactive structures are not well characterized and limited information is available about the interaction between strawberry fiber and phenolics. Therefore, we analyzed commercial strawberry pomace in order to provide a detailed carbohydrate structural characterization, and to associate structures with functions. The pomace fraction, which remained after strawberry commercial juice extraction, contained mostly insoluble (49.1 % vs. 5.6 % soluble dietary fiber) dietary fiber, with pectin, xyloglucan, xylan, β-glucan and glucomannan polysaccharides; glucose, fructose, xylose, arabinose, galactose, fucose and galacturonic acid free carbohydrates; protein (15.6 %), fat (8.34 %), and pelargonidin 3-glucoside (562 μg/g). Oligosaccharides from fucogalacto-xyloglucan, methyl-esterified rhamnogalacturonan I with branched arabinogalacto-side chains, rhamnogalacturonan II, homogalacturonan and β-glucan were detected by MALDI-TOF MS, NMR and glycosyl-linkage analysis. Previous reports suggest that these oligosaccharide and polysaccharide structures have prebiotic, bacterial pathogen anti-adhesion, and cholesterol-lowering activity, while anthocyanins are well-known antioxidants. A strawberry pomace microwave acid-extracted (10 min, 80 °C) fraction had high molar mass (2376 kDa) and viscosity (3.75 dL/g), with an extended rod shape. A random coil shape, that was reported previously to bind to phenolic compounds, was observed for other strawberry microwave-extracted fractions. These strawberry fiber structural details suggest that they can thicken foods, while the polysaccharide and polyphenol interaction indicates great potential as a multiple-function bioactive food ingredient important for gut and metabolic health.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Kinetic analysis of Cas12a and Cas13a RNA-Guided nucleases for development of improved CRISPR-Based diagnostics

Bacterial CRISPR systems provide acquired immunity against invading nucleic acids by activating RNA-programmable RNases and DNases. Cas13a and Cas12a enzymes bound to CRISPR RNA (crRNA) recognize specific nucleic acid targets, initiating cleavage of the targets as well as non-target (trans) nucleic acids. Here, we examine the kinetics of single-turnover target and multi-turnover trans-nuclease activities of both enzymes. High-turnover, non-specific Cas13a trans-RNase activity is coupled to rapid binding of target RNA. By contrast, low-turnover Cas12a trans-nuclease activity is coupled to relatively slow cleavage of target DNA, selective for DNA over RNA, indifferent to base identity, and preferential for single-stranded substrates. Combining multiple crRNA increases detection sensitivity of targets, an approach we use to quantify pathogen DNA in samples from patients suspected of Buruli ulcer disease. Results reveal that these enzymes are kinetically adapted to play distinct roles in bacterial adaptive immunity and show how kinetic analysis can be applied to CRISPR-based diagnostics.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Network analysis uncovers the communication structure of SARS-CoV-2 spike protein identifying sites for immunogen design

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has triggered myriad efforts to understand the structure and dynamics of this complex pathogen. The spike glycoprotein of SARS-CoV-2 is a significant target for immunogens as it is the means by which the virus enters human cells, while simultaneously sporting mutations responsible for immune escape. These functional and escape processes are regulated by complex molecular-level interactions. Our study presents quantitative insights on domain and residue contributions to allosteric communication, immune evasion, and local- and global-level control of functions through the derivation of a weighted graph representation from all-atom MD simulations. Focusing on the ancestral form and the D614G-variant, we provide evidence of the utility of our approach by guiding the selection of a mutation that alters the spike’s stability. Taken together, the network approach serves as a valuable tool to evaluate communication “hot-spots” in proteins to guide design of stable immunogens.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2023

Decrease in multiple complement proteins associated with development of islet autoimmunity and type 1 diabetes

Type 1 diabetes (T1D) is a chronic condition caused by autoimmune destruction of the insulin-producing pancreatic ß-cells. While it is known that gene-environment interactions play a key role in triggering the autoimmune process leading to T1D, the pathogenic mechanism leading to the appearance of islet autoantibodies - biomarkers of autoimmunity – is poorly understood. Here we show that disruption of the complement system precedes the detection of islet autoantibodies and persists through diagnosis. Our results suggest that children who exhibit islet autoimmunity and progress to clinical T1D are complement deficient relative to those who do not progress within a similar timeframe. Thus, the complement pathway, an understudied mechanistic and therapeutic target in T1D, merits increased attention for use as protein biomarkers of prediction and potentially prevention of T1D.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies

Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NP RBD ) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NP RBD were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NP RBD complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Subject-specific multi-scale modeling of the fate of inhaled aerosols

Determining the fate of inhaled aerosols in the respiratory system is essential in assessing the potential toxicity of inhaled airborne materials, responses to airborne pathogens, or in improving inhaled drug delivery. The availability of high-resolution clinical lung imaging and advances in the reconstruction of lung airways from CT images have led to the development of subject-specific in-silico 3D models of aerosol dosimetry, often referred to as computational fluid-particle-dynamics (CFPD) models. As CFPD models require extensive computing resources, they are typically confined to the upper and large airways. These models can be combined with lower-dimensional models to form multiscale models that predict the transport and deposition of inhaled aerosols in the entire respiratory tract. Understanding where aerosols deposit is only the first of potentially several key events necessary to predict an outcome, being a detrimental health effect or a therapeutic response. To that end, multiscale approaches that combine CFPD with physiologically-based pharmacokinetics (PBPK) models have been developed to evaluate the absorption, distribution, metabolism, and excretion (ADME) of toxic or medicinal chemicals in one or more compartments of the human body. CFPD models can also be combined with host cell dynamics (HCD) models to assess regional immune system responses. Here, this paper reviews the state of the art of these different multiscale approaches and discusses the potential role of personalized or subject-specific modeling in respiratory health.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Structural analysis of carbohydrate binding by the macrophage mannose receptor CD206

The human mannose receptor expressed on macrophages and hepatic endothelial cells scavenges released lysosomal enzymes, glycopeptide fragments of collagen, and pathogenic microorganisms and thus reduces damage following tissue injury. The receptor binds mannose, fucose, or N-acetylglucosamine (GlcNAc) residues on these targets. C-type carbohydrate recognition domain 4 (CRD4) of the receptor contains the site for Ca 2+ -dependent interaction with sugars. To investigate the details of CRD4 binding, glycan array screening was used to identify oligosaccharide ligands. The strongest signals were for glycans that contain either Manα1-2Man constituents or fucosein various linkages. The mechanisms of binding to monosaccharides and oligosaccharide substructures present in many of these ligands were examined in multiple crystal structures of CRD4. Binding of mannose residues to CRD4 results primarily from interaction of the equatorial 3- and 4-OH groups with a conserved principal Ca 2+ common to almost all sugar-binding C-type CRDs. In the Manα1-2Man complex, supplementary interactions with the reducing mannose residue explain the enhanced affinity for this disaccharide. Bound GlcNAc also interacts with the principal Ca 2+ through equatorial 3- and 4-OH groups, whereas fucose residues can bind in several orientations, through either the 2- and 3-OH groups or the 3- and 4-OH groups. Secondary contacts with additional sugars in fucose-containing oligosaccharides, such as the Lewis-a trisaccharide, provide enhanced affinity for these glycans. These results explain many of the biologically important interactions of the mannose receptor with both mammalian glycoproteins and microbes such as yeast and suggest additional classes of ligands that have not been previously identified

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Characterization of two distinct neutrophil serine protease–binding modes within a Staphylococcus aureus innate immune evasion protein family

Extracellular adherence protein domain (EAPs) proteins are a class of innate immune evasion proteins secreted by the human pathogen Staphylococcus aureus. EAPs are potent and selective inhibitors of cathepsin-G (CG) and neutrophil elastase (NE), which are the two most abundant neutrophil serine proteases (NSPs). Previous work from our group has shown that the prototypical EAP, EapH1, relies on plasticity within a single inhibitory site to block the activities of CG and NE. However, whether other EAPs follow similar structure–function relationships is unclear. To address this question, we studied the inhibitory properties of the first (Eap1) and second (Eap2) domains of the modular extracellular adherence protein of S. aureus and determined their structures when bound to CG and NE, respectively. We observed that both Eap1 and Eap2 displayed time-dependent inhibition of CG (on the order of 10 -9 M) and of NE (on the order of 10 -10 M). We also found that whereas the structures of Eap1 and Eap2 bound to CG showed an overall inhibitory mode like that seen previously for EapH1, the structures of Eap1 and Eap2 bound to NE revealed a new inhibitory mode involving a distal region of the EAP domain. Using site-directed mutagenesis of Eap1 and Eap2, along with enzyme assays, we confirmed the roles of interfacial residues in NSP inhibition. Taken together, our work demonstrates that EAPs can form structurally divergent complexes with two closely related serine proteases and further suggests that certain EAPs may be capable of inhibiting two NSPs simultaneously.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

ER stress and viral defense: Advances and future perspectives on plant unfolded protein response in pathogenesis

Viral infections pose significant threats to crop productivity and agricultural sustainability. The frequency and severity of these infections are increasing, and pathogens are evolving rapidly under the influence of climate change. This underscores the importance of exploring the fundamental mechanisms by which plants defend themselves against dynamic viral threats. One such mechanism is the unfolded protein response (UPR), which is activated when the protein folding demand exceeds the capacity of the endoplasmic reticulum, particularly under adverse environmental conditions. While the key regulators of the UPR in response to viral infections have been identified, our understanding of how they modulate the UPR to suppress plant viral infections at the molecular and genetic levels is still in its infancy. Recent findings have shown that, in response to plant viral infections, the UPR swiftly reprograms transcriptional changes to support cellular, metabolic, and physiological processes associated with cell viability. However, the underlying mechanisms and functional outcomes of these changes remain largely unexplored. Here, we highlight recent advances in plant UPR research and summarize key findings related to viral infection–induced UPR, focusing on the balance between prosurvival and prodeath strategies. We also discuss the potential of systems-level approaches to uncover the full extent of the functional link between the UPR and plant responses to viral infections.

ER stress↗

DOE OSTI2022

Morphological and Phenotypic Characteristics of the Bovine Nasopharyngeal Mucosa and Associated Lymphoid Tissue

The mammalian nasopharynx is an anatomically complex region of the upper respiratory tract that directly communicates with the nasal cavity, laryngopharynx, oesophagus and trachea. The nasopharyngeal mucosa contains moderate quantities of mucosa-associated lymphoid tissue (MALT) that is appropriately located for immunological sampling but also creates vulnerability to pathogens. In recent years, the nasopharynx has been inculpated in the pathogenesis of important diseases of cattle (foot-and-mouth disease) and humans (COVID-19), yet the tissue has never been described in detail in any species. In order to characterize the morphology and cellular composition of the bovine nasopharynx, samples of mucosa were collected from the nasopharynx of five 8–13-month-old steers and examined using light microscopy, immunohistochemistry and multichannel immunofluorescence. Morphologically, the nasopharyngeal epithelium was highly heterogeneous, with a continuum ranging from stratified squamous epithelium to highly attenuated, follicle-associated epithelium (FAE). Distribution of MALT was similarly regionally variable ranging from absent to clusters of multiple lymphoid follicles. Phenotypic characterization demonstrated dense distributions of dendritic cells and T lymphocytes surrounding lymphoid follicles, which comprised mostly B lymphocytes. The FAE overlaying the lymphoid follicles also contained higher numbers of dendritic cells and lymphocytes compared with the adjacent non-lymphoid epithelium, although cytotoxic T cells were notably scarce in the FAE. The bovine nasopharyngeal lymphoid tissue had comparable elements to other MALTs with specific differences that may help to elucidate the pathogenesis of infectious agents that have specific tropism for this tissue.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Using SWMM for emergency response planning: A case study evaluating biological agent transport under various rainfall scenarios and urban surfaces

To assist in emergency preparedness for a biological agent terrorist attack or accidental pathogen release, potential contaminant levels and migration pathways of spores spread by urban stormwater were evaluated using a Storm Water Management Model (SWMM) of U.S. Coast Guard Base Elizabeth City, North Carolina. The high temporal-spatial resolution SWMM model was built using spore concentrations in stormwater runoff from asphalt, grass, and concrete collected from a point-scale field study. The subsequent modeled contamination scenarios included a notional plume release and point releases mimicking the field study under three rainfall conditions. The rainfall scenarios included a 6-hour natural rainfall event on Dec. 8, 2021 and two design storms (2-year and 100-year events). The observed spore concentrations from asphalt and concrete from the actual field experiment were applied to calibrate the washoff parameters in the SWMM model, using an exponential washoff function. The calibrated washoff coefficient (c 1 ) and exponent (c 2 ) were 0.01 and 1.00 for asphalt, 0.05 and 1.45 for grass, and 2.45 and 1.00 for concrete, respectively. The calibrated SWMM model simulated spore concentrations in runoff at times and magnitudes similar to the field study data. In the point release modeled scenario, the concrete surface generated 55.6% higher average spore concentrations than asphalt. Similarly, in the field experiment, a 175% (p < 0.05) higher average spore concentration in surface runoff was observed from concrete than from asphalt. Here, this study demonstrates how SWMM may be used to evaluate spore washoff from urban surfaces under different precipitation amounts, intensities, and durations, and how visualized spatial migration pathways in stormwater runoff may be used for emergency planning and remediation.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Predicting river turbidity in Pine Island Bayou using machine learning techniques coupled with variational mode decomposition

Elevated turbidity levels pose significant public health risks by facilitating the transport of harmful pollutants, including metals, organic compounds, and pathogenic microorganisms into the surface water. These conditions create serious challenges for public recreational water use and drinking water treatment, leading to economic losses and health risks. This study utilizes water monitoring data in Pine Island Bayou, Texas, and develops a Sequence-to-Sequence (S2S) model to predict turbidity using Attention-based Gated Recurrent Units with Encoder-Decoder (AT-GRU-ED) and Long Short-Term Memory (LSTM), coupled with Variational Mode Decomposition (VMD). Compared to the model without VMD, the model demonstrates satisfactory 72-hour turbidity prediction performance, achieving MAEs of 2.60 and 3.29 NTU (reductions of 53% and 58%), RMSEs of 21.08 and 31.49 NTU (reductions of 82% and 80%), and R² values of 0.96 and 0.84 on the validation and test sets, respectively. Feature importance analysis reveals that water temperature is the dominant factor influencing seasonal turbidity patterns, while real-time hourly rainfall significantly contributes to short-term variability. Turbidity typically peaks within 48 hours after rainfall events due to lagged effects from surface runoff and upstream flow. Findings suggest suspending recreational water use and water supply pumping for three days after heavy rainfall can benefit public health and improve water treatment processes. Discharges above 100 m3/s are found to accelerate sediment dilution and transport, reducing turbidity levels more quickly after the peak. In conclusion, the proposed model demonstrates reliable 72-hour turbidity prediction, supporting decision-making for water treatment plant operations and providing early warning for public recreational water use.

Deep learning↗

DOE OSTI2022

Recombinant FimH Adhesin Demonstrates How the Allosteric Catch Bond Mechanism Can Support Fast and Strong Bacterial Attachment in the Absence of Shear

The FimH protein of Escherichia coli is a model two-domain adhesin that is able to mediate an allosteric catch bond mechanism of bacterial cell attachment, where the mannose-binding lectin domain switches from an ‘inactive’ conformation with fast binding to mannose to an ‘active’ conformation with slow detachment from mannose. Because mechanical tensile force favors separation of the domains and, thus, FimH activation, it has been thought that the catch bonds can only be manifested in a fluidic shear-dependent mode of adhesion. Here, we used recombinant FimH variants with a weakened inter-domain interaction and show that a fast and sustained allosteric activation of FimH can also occur under static, non-shear conditions. Moreover, it appears that lectin domain conformational activation happens intrinsically at a constant rate, independently from its ability to interact with the pilin domain or mannose. However, the latter two factors control the rate of FimH deactivation. Thus, the allosteric catch bond mechanism can be a much broader phenomenon involved in both fast and strong cell-pathogen attachments under a broad range of hydrodynamic conditions. In conclusion, this concept that allostery can enable more effective receptor-ligand interactions is fundamentally different from the conventional wisdom that allostery provides a mechanism to turn binding off under specific conditions.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Self-inhibited State of Venezuelan Equine Encephalitis Virus (VEEV) nsP2 Cysteine Protease: A Crystallographic and Molecular Dynamics Analysis

The Venezuelan equine encephalitis virus (VEEV) belongs to the Togaviridae family and is pathogenic to both humans and equines. The VEEV non-structural protein 2 (nsP2) is a cysteine protease (nsP2pro) that processes the polyprotein and thus it is a drug target for inhibitor discovery. The atomic structure of the VEEV nsP2 catalytic domain was previously characterized by both X-ray crystallography and computational studies. A modified nsP2pro harboring a N475A mutation in the N terminus was observed to exhibit an unexpected conformation: the N-terminal residues bind to the active site, mimicking binding of a substrate. The large conformational change of the N terminus was assumed to be induced by the N475A mutation, as N475 has an important role in stabilization of the N terminus and the active site. This conformation was first observed in the N475A mutant, but we also found it while determining a crystal structure of the catalytically active nsP2pro containing the wild-type N475 active site residue and K741A/K767A surface entropy reduction mutations. This suggests that the N475A mutation is not a prerequisite for self-inhibition. Here, we describe a high resolution (1.46 Å) crystal structure of a truncated nsP2pro (residues 463–785, K741A/K767A) and analyze the structure further by molecular dynamics to study the active and self-inhibited conformations of nsP2pro and its N475A mutant. A comparison of the different conformations of the N-terminal residues sheds a light on the interactions that play an important role in the stabilization of the enzyme.

59 BASIC BIOLOGICAL SCIENCES↗