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At least 595 records · Page 33
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Solid Electrolyte Bimodal Grain Structures for Improved Cycling Performance

Here, the application of solid-state electrolytes in Li batteries is hampered by the occurrence of Li-dendrite-caused short circuits. To avoid cell failure, the electrolytes can only be stressed with rather low current densities, severely restricting their performance. As grain size and pore distributions significantly affect dendrite growth in ceramic electrolytes such as Li 7 La 3 Zr 2 O 12 and its variants; here, a “detour and buffer” strategy to bring the superiority of both coarse and fine grains into play, is proposed. To validate the mechanism, a coarse/fine bimodal grain microstructure is obtained by seeding unpulverized large particles in the green body. The rearrangement of coarse grains and fine pores is fine-tuned by changing the ratio of pulverized and unpulverized powders. The optimized bimodal microstructure, obtained when the two powders are equally mixed, allows, without extra interface decoration, cycling for over 2000 h as the current density is increased from 1.0 mA·cm -2 , and gradually, up to 2.0 mA·cm -2 . The “detour and buffer” effects are confirmed from postmortem analysis. The complex grain boundaries formed by fine grains discourage the direct infiltration of Li. Simultaneously, the coarse grains further increase the tortuosity of the Li path. This study sheds light on the microstructure optimization for the polycrystalline solid-state electrolytes.

25 ENERGY STORAGE↗
DOE OSTI2024

Holographic tensor networks with bulk gauge symmetries

Abstract Tensor networks are useful toy models for understanding the structure of entanglement in holographic states and reconstruction of bulk operators within the entanglement wedge. They are, however, constrained to only prepare so-called “fixed-area states” with flat entanglement spectra, limiting their utility in understanding general features of holographic entanglement. Here, we overcome this limitation by constructing a variant of random tensor networks that enjoys bulk gauge symmetries. Our model includes a gauge theory on a general graph, whose gauge-invariant states are fed into a random tensor network. We show that the model satisfies the quantum-corrected Ryu-Takayanagi formula with a nontrivial area operator living in the center of a gauge-invariant algebra. We also demonstrate nontrivial,n-dependent contributions to the Rényi entropy and Rényi mutual information from this area operator, a feature shared by general holographic states.

Physics↗
DOE OSTI2023

A Bis(imidazole)-based cysteine labeling tool for metalloprotein assembly

Precise metal-protein coordination by design remains a considerable challenge. Polydentate, high-metal-affinity protein modifications, both chemical and recombinant, can enable metal localization. However, these constructs are often bulky, conformationally and stereochemically ill-defined, or coordinately saturated. Here, we expand the biomolecular metal-coordination toolbox with the irreversible attachment to cysteine of bis(1-methylimidazol-2-yl)ethene (“BMIE”), which generates a compact imidazole-based metal-coordinating ligand. Conjugate additions of small-molecule thiols (thiocresol and N-Boc-Cys) with BMIE confirm general thiol reactivity. The BMIE adducts are shown to complex the divalent metal ions Cu ++ and Zn ++ in bidentate (N 2 ) and tridentate (N 2 S*) coordination geometries. Cysteine-targeted BMIE modification (>90% yield at pH 8.0) of a model protein, the S203C variant of carboxypeptidase G2 (CPG2), measured with ESI-MS, confirms its utility as a site-selective bioconjugation method. ICP-MS analysis confirms mono-metallation of the BMIE-modified CPG2 protein with Zn ++ , Cu ++ , and Co ++ . EPR characterization of the BMIE-modified CPG2 protein reveals the structural details of the site selective 1:1 BMIE-Cu ++ coordination and symmetric tetragonal geometry under physiological conditions and in the presence of various competing and exchangeable ligands (H 2 O/HO – , tris, and phenanthroline). An X-ray protein crystal structure of BMIE-modified CPG2-S203C demonstrates that the BMIE modification is minimally disruptive to the overall protein structure, including the carboxypeptidase active sites, although Zn ++ metalation could not be conclusively discerned at the resolution obtained. The carboxypeptidase catalytic activity of BMIE-modified CPG2-S203C was also assayed and found to be minimally affected. Finally, these features, combined with ease of attachment, define the new BMIE-based ligation as a versatile metalloprotein design tool, and enable future catalytic and structural applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

On the Rapid Calculation of Binding Affinities for Antigen and Antibody Design and Affinity Maturation Simulations

The accurate and efficient calculation of protein-protein binding affinities is an essential component in antibody and antigen design and optimization, and in computer modeling of antibody affinity maturation. Such calculations remain challenging despite advances in computer hardware and algorithms, primarily because proteins are flexible molecules, and thus, require explicit or implicit incorporation of multiple conformational states into the computational procedure. The astronomical size of the amino acid sequence space further compounds the challenge by requiring predictions to be computed within a short time so that many sequence variants can be tested. In this study, we compare three classes of methods for antibody/antigen (Ab/Ag) binding affinity calculations: (i) a method that relies on the physical separation of the Ab/Ag complex in equilibrium molecular dynamics (MD) simulations, (ii) a collection of 18 scoring functions that act on an ensemble of structures created using homology modeling software, and (iii) methods based on the molecular mechanics-generalized Born surface area (MM-GBSA) energy decomposition, in which the individual contributions of the energy terms are scaled to optimize agreement with the experiment. When applied to a set of 49 antibody mutations in two Ab/HIV gp120 complexes, all of the methods are found to have modest accuracy, with the highest Pearson correlations reaching about 0.6. In particular, the most computationally intensive method, i.e., MD simulation, did not outperform several scoring functions. The optimized energy decomposition methods provided marginally higher accuracy, but at the expense of requiring experimental data for parametrization. Within each method class, we examined the effect of the number of independent computational replicates, i.e., modeled structures or reinitialized MD simulations, on the prediction accuracy. We suggest using about ten modeled structures for scoring methods, and about five simulation replicates for MD simulations as a rule of thumb for obtaining reasonable convergence. We anticipate that our study will be a useful resource for practitioners working to incorporate binding affinity calculations within their protein design and optimization process.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1997

A survey of the chemical properties of the M17 and Cepheus A cloud cores

We present the results of a systematic survey of the chemical properties of two giant molecular cloud (GMC) cores in M17 and Cepheus A. In all, we have mapped the emission from 32 molecular transitions of 13 molecules and seven isotopic variants over a 4' x 5' region in each core. Each map includes known sites of massive star formation, as well as the more extended quiescent material. In M17 most molecules have emission peaks away from the H II region/molecular cloud interface, while two species, HC3N and CH3C2H, deviate from this structure with sharp maxima closer to this interface. In Cepheus A the core is influenced by a compact high-velocity molecular outflow and a more extended low-velocity flow. The molecular emission distributions in this source are generally quite similar, with most molecules peaking near the center of the core to the east of the compact H II region HW 2. A few molecules, SO, CH3OH, H13CN, and C18O, have more extended emission. Only two molecules, CO and HCO+, appear to trace the high- and low-velocity outflows; all other species are tracing the quiescent core. We have used the results of previous studies of the density and temperature of the dense gas in the same cloud cores to derive accurate abundances relative to CO for several positions in each core. The principal result is that the chemical composition of all the cores we have surveyed (which include OMC-1 as well as M17 and Cepheus A) show remarkable similarity, both within a given core and among the cores. This suggests that the chemical processes are similar in quiescent GMC core material. In M17 the lack of variation of molecular abundances is remarkable because the radiation field and the gas temperature are known to vary appreciably throughout the surveyed region, suggesting that the bulk of the emission arises from gas that is well shielded from radiation.

Non-NASA Center↗
DOE OSTI2020

Mechanism of Catalysis by L -Asparaginase

Two bacterial type II L -asparaginases, from Escherichia coli and Dickeya chrysanthemi, have played a critical role for more than 40 years as therapeutic agents against juvenile leukemias and lymphomas. Despite a long history of successful pharmacological applications and the apparent simplicity of the catalytic reaction, controversies still exist regarding major steps of the mechanism. In this report, we provide a detailed description of the reaction catalyzed by E. coli type II L -asparaginase (EcAII). Our model was developed on the basis of new structural and biochemical experiments combined with previously published data. The proposed mechanism is supported by quantum chemistry calculations based on density functional theory. In this work, we provide strong evidence that EcAII catalyzes the reaction according to the double-displacement (ping-pong) mechanism, with formation of a covalent intermediate. Several steps of catalysis by EcAII are unique when compared to reactions catalyzed by other known hydrolytic enzymes. Here, the reaction is initiated by a weak nucleophile, threonine, without direct assistance of a general base, although a distant general base is identified. Furthermore, tetrahedral intermediates formed during the catalytic process are stabilized by a never previously described motif. Although the scheme of the catalytic mechanism was developed only on the basis of data obtained from EcAII and its variants, this novel mechanism of enzymatic hydrolysis could potentially apply to most (and possibly all) L -asparaginases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Using Domain Insertion to Create Sulfite Reductases That Present Chemical-Dependent Activities

Domain insertion can be used to create oxidoreductases whose activities are dependent upon analyte binding. To date, most domain insertion studies have targeted relatively small oxidoreductases of known structure, so it remains unclear how to apply this protein engineering approach to large hetero-oligomeric proteins that require dynamic conformational changes for catalysis. To address this question, we studied the effects of peptide and domain insertions on the activity of NADPH-dependent sulfite reductase (SiR) from Escherichia coli, a dodecameric oxidoreductase containing four hemoprotein and eight flavoprotein subunits. SiR mutational tolerance was first evaluated using systematic octapeptide insertion and a cellular selection, which identified regions across the hemoprotein structure that retain parent-like activity following insertion. When a ligand-binding domain was inserted at backbone locations tolerant to peptide insertion, including sites proximal and distal from the intersubunit interfaces, ∼90% retained catalytic activity, and >50% presented activity that is regulated by an endocrine disruptor. With one domain insertion variant, the conditional production of sulfide could be monitored electrochemically from cells using a bioelectrochemical reactor. These results show how systematic peptide insertion can be used to inform domain insertion in a large heterooligomeric protein complex, and they illustrate how SiR can be engineered to convert chemical information in the environment into a redox-active metabolite that diffuses across the cell membrane.

bacteria↗
DOE OSTI2024

NANO.PTML model for read-across prediction of nanosystems in neurosciences. computational model and experimental case of study

Abstract Neurodegenerative diseases involve progressive neuronal death. Traditional treatments often struggle due to solubility, bioavailability, and crossing the Blood-Brain Barrier (BBB). Nanoparticles (NPs) in biomedical field are garnering growing attention as neurodegenerative disease drugs (NDDs) carrier to the central nervous system. Here, we introduced computational and experimental analysis. In the computational study, a specific IFPTML technique was used, which combined Information Fusion (IF) + Perturbation Theory (PT) + Machine Learning (ML) to select the most promising Nanoparticle Neuronal Disease Drug Delivery (N2D3) systems. For the application of IFPTML model in the nanoscience, NANO.PTML is used. IF-process was carried out between 4403 NDDs assays and 260 cytotoxicity NP assays conducting a dataset of 500,000 cases. The optimal IFPTML was the Decision Tree (DT) algorithm which shown satisfactory performance with specificity values of 96.4% and 96.2%, and sensitivity values of 79.3% and 75.7% in the training (375k/75%) and validation (125k/25%) set. Moreover, the DT model obtained Area Under Receiver Operating Characteristic (AUROC) scores of 0.97 and 0.96 in the training and validation series, highlighting its effectiveness in classification tasks. In the experimental part, two samples of NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) were synthesized by thermal decomposition of an iron(III) oleate (FeOl) precursor and structurally characterized by different methods. Additionally, in order to make the as-synthesized hydrophobic NPs (Fe 3 O 4 _A and Fe 3 O 4 _B) soluble in water the amphiphilic CTAB (Cetyl Trimethyl Ammonium Bromide) molecule was employed. Therefore, to conduct a study with a wider range of NP system variants, an experimental illustrative simulation experiment was performed using the IFPTML-DT model. For this, a set of 500,000 prediction dataset was created. The outcome of this experiment highlighted certain NANO.PTML systems as promising candidates for further investigation. The NANO.PTML approach holds potential to accelerate experimental investigations and offer initial insights into various NP and NDDs compounds, serving as an efficient alternative to time-consuming trial-and-error procedures.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Resistance, Resilience, and Recovery of Dryland Soil Bacterial Communities Across Multiple Disturbances

Dryland ecosystems are sensitive to perturbations and generally slow to recover post disturbance. The microorganisms residing in dryland soils are especially important as they contribute to soil structure and nutrient cycling. Disturbance can have particularly strong effects on dryland soil structure and function, yet the natural resistance and recovery of the microbial components of dryland soils has not been well documented. In this study, the recovery of surface soil bacterial communities from multiple physical and environmental disturbances is assessed. Samples were collected from three field sites in the vicinity of Moab, UT, United States, 6 to 7 years after physical and climate disturbance manipulations had been terminated, allowing for the assessment of community recovery. Additionally, samples were collected in a transect that included three habitat patches: the canopy zone soils under the dominant shrubs, the interspace soils that are colonized by biological soil crusts, and edge soils at the plot borders. Field site and habitat patch were significant factors structuring the bacterial communities, illustrating that sites and habitats harbored unique soil microbiomes. Across the different sites and disturbance treatments, there was evidence of significant bacterial community recovery, as bacterial biomass and diversity were not significantly different than control plots. There was, however, a small number of 16S rRNA gene amplicon sequence variants that distinguished particular treatments, suggesting that legacy effects of the disturbances still remained. Taken together, these data suggest that dryland bacterial communities may possess a previously unappreciated potential to recover within years of the original disturbance.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cross-reactive sarbecovirus antibodies induced by mosaic RBD nanoparticles

Broad immune responses are needed to mitigate viral evolution and escape. To induce antibodies against conserved receptor-binding domain (RBD) regions of SARS-like betacoronavirus (sarbecovirus) spike proteins that recognize SARS-CoV-2 variants of concern and zoonotic sarbecoviruses, we developed mosaic-8b RBD nanoparticles presenting eight sarbecovirus RBDs arranged randomly on a 60-mer nanoparticle. Mosaic-8b immunizations protected animals from challenges from viruses whose RBDs were matched or mismatched to those on nanoparticles. Here, we describe neutralizing mAbs isolated from mosaic-8b-immunized rabbits, some on par with Pemgarda, the only currently FDA-approved therapeutic mAb. Deep mutational scanning, in vitro selection of spike resistance mutations, and single-particle cryo-electron microscopy structures of spike–antibody complexes demonstrated targeting of conserved RBD epitopes. Rabbit mAbs included critical D-gene segment RBD-recognizing features in common with human anti-RBD mAbs, despite rabbit genomes lacking an equivalent human D-gene segment, thus demonstrating that the immune systems of humans and other mammals can utilize different antibody gene segments to arrive at similar modes of antigen recognition. These results suggest that animal models can be used to elicit anti-RBD mAbs with similar properties to those raised in humans, which can then be humanized for therapeutic use, and that mosaic RBD nanoparticle immunization coupled with multiplexed screening represents an efficient way to generate and select broadly cross-reactive therapeutic pan-sarbecovirus and pan-SARS-CoV-2 variant mAbs.

Science & Technology - Other Topics↗
DOE OSTI2021

A combination of cross-neutralizing antibodies synergizes to prevent SARS-CoV-2 and SARS-CoV pseudovirus infection

Coronaviruses have caused several human epidemics and pandemics including the ongoing coronavirus disease 2019 (COVID-19). Prophylactic vaccines and therapeutic antibodies have already shown striking effectiveness against COVID-19. Nevertheless, concerns remain about antigenic drift in SARS-CoV-2 as well as threats from other sarbecoviruses. Cross-neutralizing antibodies to SARS-related viruses provide opportunities to address such concerns. Here, we report on crystal structures of a cross-neutralizing antibody, CV38-142, in complex with the receptor-binding domains from SARS-CoV-2 and SARS-CoV. Recognition of the N343 glycosylation site and water-mediated interactions facilitate cross-reactivity of CV38-142 to SARS-related viruses, allowing the antibody to accommodate antigenic variation in these viruses. CV38-142 synergizes with other cross-neutralizing antibodies, notably COVA1-16, to enhance neutralization of SARS-CoV and SARS-CoV-2, including circulating variants of concern B.1.1.7 and B.1.351. Overall, this study provides valuable information for vaccine and therapeutic design to address current and future antigenic drift in SARS-CoV-2 and to protect against zoonotic SARS-related coronaviruses.

3D structure↗
NASA NTRS2008

Using Piezoelectric Devices to Transmit Power through Walls

A method denoted wireless acoustic-electric feed-through (WAEF) has been conceived for transmitting power and/or data signals through walls or other solid objects made of a variety of elastic materials that could be electrically conductive or nonconductive. WAEF would make it unnecessary to use wires, optical fibers, tubes, or other discrete wall-penetrating signal-transmitting components, thereby eliminating the potential for structural weakening or leakage at such penetrations. Avoidance of such penetrations could be essential in some applications in which maintenance of pressure, vacuum, or chemical or biological isolation is required. In a basic WAEF setup, a transmitting piezoelectric transducer on one side of a wall would be driven at resonance to excite ultrasonic vibrations in the wall. A receiving piezoelectric transducer on the opposite side of the wall would convert the vibrations back to an ultrasonic AC electric signal, which would then be detected and otherwise processed in a manner that would depend on the modulation (if any) applied to the signal and whether the signal was used to transmit power, data, or both. An electromechanical-network model has been derived as a computationally efficient means of analyzing and designing a WAEF system. This model is a variant of a prior model, known in the piezoelectric-transducer art as Mason's equivalent-circuit model, in which the electrical and mechanical dynamics, including electromechanical couplings, are expressed as electrical circuit elements that can include inductors, capacitors, and lumped-parameter complex impedances. The real parts of the complex impedances are used to account for dielectric, mechanical, and coupling losses in all components (including all piezoelectric-transducer, wall, and intermediate material layers). In an application to a three-layer piezoelectric structure, this model was shown to yield the same results as do solutions of the wave equations of piezoelectricity and acoustic propagation in their full complexity.

Sherrit, Stewart↗
DOE OSTI2023

The reactive flow evolution of the polymer-bonded explosive PBX 9502: Experiments and model validation in extreme pressure regimes

The shock-to-detonation transition properties of the triaminotrinitrobenzene based PBX 9502 high explosive (HE) are experimentally and computationally explored in extremely high input pressure conditions. These include both slightly sub-Chapman–Jouguet and overdriven input pressure conditions, namely, ∼25 and ∼31 GPa, respectively. Our experiments capture the transient buildup of a shock-induced reaction via measurement of HE and polymethyl methacrylate window interface particle velocity profiles for a variety of sample thicknesses for this insensitive HE. These observations necessitate extremely thin explosive samples, and the high rates of reaction provide a considerable challenge to optical diagnostics. Samples at these thicknesses also provide an opportunity for evaluation of potential micro-structure effects on the resulting shock-to-detonation-transition measurements. To address this, the thin samples are also characterized via x-ray micro-computed tomography. Finally, a pair of previously established continuum-level detonation performance modeling approaches for PBX 9502 were used to analyze the experiments. The employed model variants crucially differ in their definition of each model’s empirical reaction rate functional form, utilization of shock state quantities, and local flow variable dependencies. As a result, the present experiments provide a novel platform to evaluate the quantitative and qualitative consequences stemming from these modeling choices in a challenging initiation scenario, largely beyond the chosen calibration range of either model. This new experimental information will provide a platform for both improved physics and model parameterizations for this well-studied explosive.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A New Approach to Distributed Hypothesis Testing and Non-Bayesian Learning: Improved Learning Rate and Byzantine-Resilience

Here, we study a setting where a group of agents, each receiving partially informative private signals, seek to collaboratively learn the true underlying state of the world (from a finite set of hypotheses) that generates their joint observation profiles. To solve this problem, we propose a distributed learning rule that differs fundamentally from existing approaches, in that it does not employ any form of “belief-averaging”. Instead, agents update their beliefs based on a min-rule. Under standard assumptions on the observation model and the network structure, we establish that each agent learns the truth asymptotically almost surely. As our main contribution, we prove that with probability 1, each false hypothesis is ruled out by every agent exponentially fast, at a network-independent rate that is strictly larger than existing rates. We then develop a computationally-efficient variant of our learning rule that is provably resilient to agents who do not behave as expected (as represented by a Byzantine adversary model) and deliberately try to spread misinformation.

42 ENGINEERING↗
DOE OSTI2021

A Prevalent Focused Human Antibody Response to the Influenza Virus Hemagglutinin Head Interface

Novel animal influenza viruses emerge, initiate pandemics, and become endemic seasonal variants that have evolved to escape from prevalent herd immunity. These processes often outpace vaccine-elicited protection. Focusing immune responses on conserved epitopes may impart durable immunity. We describe a focused, protective antibody response, abundant in memory and serum repertoires, to a conserved region at the influenza virus hemagglutinin (HA) head interface. Structures of 11 examples, 8 reported here, from seven human donors demonstrate the convergence of responses on a single epitope. The 11 are genetically diverse, with one class having a common, IGκV1-39, light chain. All of the antibodies bind HAs from multiple serotypes. The lack of apparent genetic restriction and potential for elicitation by more than one serotype may explain their abundance. We define the head interface as a major target of broadly protective antibodies with the potential to influence the outcomes of influenza virus infection.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Quantum Chemical Computation of Omicron Mutations Near Cleavage Sites of the Spike Protein

The attachment of the spike protein in SARS-CoV-2 to host cells and the initiation of viral invasion are two critical processes in the viral infection and transmission in which the presence of unique furin (S1/S2) and TMPRSS2 (S2') cleavage sites play a pivotal role. We provide a detailed analysis of the impact of the BA.1 Omicron mutations vicinal to these cleavage sites using a novel computational method based on the amino acid–amino acid bond pair unit (AABPU), a specific protein structural unit as a proxy for quantifying the atomic interaction. Our study is focused mainly on the spike region between subdomain 2 (SD2) and the central helix (CH), which contains both S1/S2 and S2' cleavage sites. Based on ab initio quantum calculations, we have identified several key features related to the electronic structure and bonding of the Omicron mutations that significantly increase the size of the relevant AABPUs and the positive charge. These findings enable us to conjecture on the biological role of Omicron mutations and their specific effects on cleavage sites and identify the principles that can be of some value in analyzing new variants.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Time-periodic steady-state solution of fluid-structure interaction and cardiac flow problems through multigrid-reduction-in-time

In this study, a time-periodic MGRIT algorithm is proposed as a means to reduce the time-to-solution of numerical algorithms by exploiting the time periodicity inherent to many applications in science and engineering. The time-periodic MGRIT algorithm is applied to a variety of linear and nonlinear single- and multiphysics problems that are periodic-in-time. It is demonstrated that the proposed parallel-in-time algorithm can obtain the same time-periodic steady-state solution as sequential time-stepping. It is shown that the required number of MGRIT iterations can be estimated a priori and that the new MGRIT variant can significantly and consistently reduce the time-to-solution compared to sequential time-stepping, irrespective of the number of dimensions, linear or nonlinear PDE models, single-physics or coupled problems and the employed computing resources. The numerical experiments demonstrate that the time-periodic MGRIT algorithm enables a greater level of parallelism yielding faster turnaround, and thus, facilitating more complex and more realistic problems to be solved.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5

Engineered monoclonal antibodies have proven to be highly effective therapeutics in recent viral outbreaks. However, despite technical advancements, an ability to rapidly adapt or increase antibody affinity and by extension, therapeutic efficacy, has yet to be fully realized. We endeavored to stand-up such a pipeline using molecular modeling combined with experimental library screening to increase the affinity of F5, a monoclonal antibody with potent neutralizing activity against Venezuelan Equine Encephalitis Virus (VEEV), to recombinant VEEV (IAB) E1E2 antigen. We modeled the F5/E1E2 binding interface and generated predictions for mutations to improve binding using a Rosetta-based approach and dTERMen, an informatics approach. The modeling was complicated by the fact that a high-resolution structure of F5 is not available and the H3 loop of F5 exceeds the length for which current modeling approaches can determine a unique structure. A subset of the predicted mutations from both methods were incorporated into a phage display library of scFvs. This library and a library generated by error-prone PCR were screened for binding affinity to the recombinant antigen. Results from the screens identified favorable mutations which were incorporated into 12 human-IgG1 variants. The best variant, containing eight mutations, improved KD from 0.63 nM (parental) to 0.01 nM. While this did not improve neutralization or therapeutic potency of F5 against IAB, it did increase cross-reactivity to other closely related VEEV epizootic and enzootic strains, demonstrating the potential of this method to rapidly adapt existing therapeutics to emerging viral strains.

affinity-maturation↗