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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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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

MHC-II dynamics are maintained in HLA-DR allotypes to ensure catalyzed peptide exchange

Presentation of antigenic peptides by major histocompatibility complex class II (MHC-II) proteins determines T helper cell reactivity. The MHC-II genetic locus displays a large degree of allelic polymorphism influencing the peptide repertoire presented by the resulting MHC-II protein allotypes. During antigen processing, the human leukocyte antigen (HLA) molecule HLA-DM (DM) encounters these distinct allotypes and catalyzes exchange of the placeholder peptide CLIP by exploiting dynamic features of MHC-II. Here, we investigate 12 highly abundant CLIP-bound HLA-DRB1 allotypes and correlate dynamics to catalysis by DM. Despite large differences in thermodynamic stability, peptide exchange rates fall into a target range that maintains DM responsiveness. A DM-susceptible conformation is conserved in MHC-II molecules, and allosteric coupling between polymorphic sites affects dynamic states that influence DM catalysis. As exemplified for rheumatoid arthritis, we postulate that intrinsic dynamic features of peptide–MHC-II complexes contribute to the association of individual MHC-II allotypes with autoimmune disease.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Deep Sequencing of MHC-Adapted Viral Lines Reveals Complex Recombinational Exchanges With Endogenous Retroviruses Leading to High-Frequency Variants

Experimental evolution (serial passage) of Friend virus complex (FVC) in mice demonstrates phenotypic adaptation to specific host major histocompatibility complex (MHC) genotypes. These evolved viral lines show increased fitness and virulence in their host-genotype-of-passage, but display fitness and virulence tradeoffs when infecting unfamiliar host MHC genotypes. Here, we deep sequence these viral lines in an attempt to discover the genetic basis of FVC adaptation. The principal prediction for genotype-specific adaptation is that unique mutations would rise to high frequency in viral lines adapted to each host MHC genotype. This prediction was not supported by our sequencing data as most observed high-frequency variants were present in each of our independently evolved viral lines. However, using a multi-variate approach to measure divergence between viral populations, we show that populations of replicate evolved viral lines from the same MHC congenic mouse strain were more similar to one another than to lines derived from different MHC congenic mouse strains, suggesting that MHC genotype does predictably act on viral evolution in our model. Sequence analysis also revealed rampant recombination with endogenous murine leukemia virus sequences (EnMuLVs) that are encoded within the BALB/c mouse genome. The highest frequency variants in all six lines contained a 12 bp insertion from a recombinant EnMuLV source, suggesting such recombinants were either being favored by selection or were contained in a recombinational hotspot. Interestingly, they did not reach fixation, as if they are low fitness. The amount of background mutations linked to FVC/EnMuLV variable sites indicated that FVC/EnMuLV recombinants had not reached mutation selection equilibrium and thus, that EnMuLV sequences are likely continuously introgressing into the replicating viral population. These discoveries raise the question: is the expression of EnMuLV sequences in mouse splenocytes that permit recombination with exogenous FVC a pathogen or host adaptation?

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Cas9-derived peptides presented by MHC Class II that elicit proliferation of CD4 + T-cells

CRISPR–Cas9 mediated genome editing offers unprecedented opportunities for treating human diseases. There are several reports that demonstrate pre-existing immune responses to Cas9 which may have implications for clinical development of CRISPR-Cas9 mediated gene therapy. Here we use 209 overlapping peptides that span the entire sequence of Staphylococcus aureus Cas9 (SaCas9) and human peripheral blood mononuclear cells (PBMCs) from a cohort of donors with a distribution of Major Histocompatibility Complex (MHC) alleles comparable to that in the North American (NA) population to identify the immunodominant regions of the SaCas9 protein. We also use an MHC Associated Peptide Proteomics (MAPPs) assay to identify SaCas9 peptides presented by MHC Class II (MHC-II) proteins on dendritic cells. Using these two data sets we identify 22 SaCas9 peptides that are both presented by MHC-II proteins and stimulate CD4 + T-cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Toward Guided Mutagenesis: Gaussian Process Regression Predicts MHC Class II Antigen Mutant Binding

Antigen-specific immunotherapies (ASI) require successful loading and presentation of antigen peptides into the major histocompatibility complex (MHC) binding cleft. One route of ASI design is to mutate native antigens for either stronger or weaker binding interaction to MHC. Exploring all possible mutations is costly both experimentally and computationally. To reduce experimental and computational expense, here we investigate the minimal amount of prior data required to accurately predict the relative binding affinity of point mutations for peptide-MHC class II (pMHCII) binding. Using data from different residue subsets, we interpolate pMHCII mutant binding affinities by Gaussian process (GP) regression of residue volume and hydrophobicity. We apply GP regression to an experimental data set from the Immune Epitope Database, and theoretical data sets from NetMHCIIpan and Free Energy Perturbation calculations. We find that GP regression can predict binding affinities of nine neutral residues from a six-residue subset with an average R 2 coefficient of determination value of 0.62 ± 0.04 (±95% CI), average error of 0.09 ± 0.01 kcal/mol (±95% CI), and with an receiver operating characteristic (ROC) AUC value of 0.92 for binary classification of enhanced or diminished binding affinity. Similarly, metrics increase to an R2 value of 0.69 ± 0.04, average error of 0.07 ± 0.01 kcal/mol, and an ROC AUC value of 0.94 for predicting seven neutral residues from an eight-residue subset. Our work finds that prediction is most accurate for neutral residues at anchor residue sites without register shift. This work holds relevance to predicting pMHCII binding and accelerating ASI design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Dynamics-Based Peptide–MHC Binding Optimization by a Convolutional Variational Autoencoder: A Use-Case Model for CASTELO

An unsolved challenge in the development of antigen-specific immunotherapies is determining the optimal antigens to target. Comprehension of antigen–major histocompatibility complex (MHC) binding is paramount toward achieving this goal. Here, we apply CASTELO, a combined machine learning-molecular dynamics (ML-MD) approach, to identify per-residue antigen binding contributions and then design novel antigens of increased MHC-II binding affinity for a type 1 diabetes-implicated system. We build upon a small-molecule lead optimization algorithm by training a convolutional variational autoencoder (CVAE) on MD trajectories of 48 different systems across four antigens and four HLA serotypes. We develop several new machine learning metrics including a structure-based anchor residue classification model as well as cluster comparison scores. ML-MD predictions agree well with experimental binding results and free energy perturbation-predicted binding affinities. Moreover, ML-MD metrics are independent of traditional MD stability metrics such as contact area and root-mean-square fluctuations (RMSF), which do not reflect binding affinity data. Finally, our work supports the role of structure-based deep learning techniques in antigen-specific immunotherapy design.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide–MHC Binding Predictions

The reliable prediction of the affinity of candidate peptides for the MHC is important for predicting their potential antigenicity and thus influences medical applications, such as decisions on their inclusion in T cell–based vaccines. In this study, we present a rapid, predictive computational approach that combines a popular, sequence-based artificial neural network method, NetMHCpan 4.0, with three-dimensional structural modeling. We find that the ensembles of bound peptide conformations generated by the programs MODELLER and Rosetta FlexPepDock are less variable in geometry for strong binders than for low-affinity peptides. In tests on 1271 peptide sequences for which the experimental dissociation constants of binding to the well-characterized murine MHC allele H-2D b are known, by applying thresholds for geometric fluctuations the structure-based approach in a standalone manner drastically improves the statistical specificity, reducing the number of false positives. Furthermore, filtering candidates generated with NetMHCpan 4.0 with the structure-based predictor led to an increase in the positive predictive value (PPV) of the peptides correctly predicted to bind very strongly (i.e., Kd < 100 nM) from 40 to 52% (p = 0.027). The combined method also significantly improved the PPV when tested on five human alleles, including some with limited data for training. Overall, an average increase of 10% in the PPV was found over the standalone sequence-based method. The combined method should be useful in the rapid design of effective T cell–based vaccines.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

The MHC Associated Peptide Proteomics assay is a useful tool for the non-clinical assessment of immunogenicity

The propensity of therapeutic proteins to elicit an immune response, poses a significant challenge in clinical development and safety of the patients. Assessment of immunogenicity is crucial to predict potential adverse events and design safer biologics. In this study, we employed MHC Associated Peptide Proteomics (MAPPS) to comprehensively evaluate the immunogenic potential of re-engineered variants of immunogenic FVIIa analog (Vatreptacog Alfa). Our finding revealed the correlation between the protein sequence affinity for MHCII and the number of peptides identified in a MAPPS assay and this further correlates with the reduced T-cell responses. Moreover, MAPPS enable the identification of “relevant” T cell epitopes and may contribute to the development of biologics with lower immunogenic potential.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

A Mobile Hot Cell for Conditioning Disused Sealed Radioactive Sources for Storage or Transportation

An innovative Mobile Hot Cell (MHC) has been developed for conditioning Disused Sealed Radioactive Sources (DSRS) category 1 and 2 for storage or transportation. The MHC is designed to provide both Radiological and Biological containment with a maximum capacity of 1000 Ci Co60 or 5000Ci Cs137 source and can be transported via standard cargo containers. This project has been supported through the National Nuclear Safety Administration (NNSA) Offsite Source Recovery Program (OSRP). The project is intended for the international community rather than domestic although domestic use is a possibility. Many countries have significant stockpiles of these devices that are often stored in less-than-optimal circumstances. This necessitates that these devices be addressed expeditiously, and the sources secured. The MHC utilizes robotics, automation, and other non-traditional methods for disassembling, characterizing, and packaging these sources that have reached end of life or are otherwise not needed. These innovative approaches are necessary to facilitate an expedited timeline to efficiently and safely secure these sources in a non-proliferation effort. Conditioning efforts include disassembling the device such as a teletherapy head used for cancer treatment, or blood/research irradiators such that the radioactive sources may be removed safely. The sources are then characterized. Leak checks are performed, dimensions are verified, and serial numbers are confirmed. Upon completion, the sources are typically placed into a Standard Forms Capsule which is seal welded closed. It is leak tested and placed into a Long-Term Storage Shield (LTSS) which can either be secured for storage directly or loaded into an appropriate cask for transportation. Further innovations include multiple deployment scenarios that include a full deployment of MHC components, deployment of the MHC automation internal components to an existing hot cell, deployment of minimally required MHC components and incorporation of sand for shielding, and integration of the MHC for Silo Storage, or Bore Hole Storage efforts. The MHC has evolved from a very specific use case to a “Swiss Army Knife” type of a tool in that it can be readily adapted to a large variety of situations. Innovative approaches such as the use of robotics, Computer Numeric Control (CNC) machining centers, automated welding equipment, HDMI Cameras, and LED lighting are some of the developed technologies incorporated into the MHC design. Shielding is accomplished with a steel walled Base Box which is surrounded by four nesting doll shield shells which when combined limits the external dose rate to 5mr/hr when a 1000 Ci Co60 source is exposed inside.

99 - GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Idaho National Laboratory’s Mobile Hot Cell Transportation: Engineering Solutions for Global Disused Sealed Radioactive Sources.

Title: Idaho National Laboratory’s Mobile Hot Cell Transportation: Engineering Solutions for Global Disused Sealed Radioactive Sources. Abstract: The Mobile Hot Cell (MHC), currently under development by Idaho National Laboratory (INL) for the Off-Site Source Recovery Project (OSRP), is designed to help international partners meet the unique challenges of end-of-life radioactive material management. The MHC will provide a critical resource for countries that require assistance securing and disposing of Disused Sealed Radioactive Sources (DSRS) and orphaned sources in challenging environments, allowing these sources to be secured against misuse and nefarious activities. The MHC is a rapidly deployable system for conditioning and preparing end-of-life radioactive sources for transportation or storage. It is designed to handle sources of up to 1,000 Ci Co-60 equivalent while maintaining full radiological and biological containment. It will be deployable within 48 hours of an alert, making it ideal for emergency situations. The MHC features an operational suite for control, support racks for electronics, pneumatics, and welding systems, and a modular robust steel structure providing radiological shielding and internal robotic support. This design allows configurations for multiple device types to be conditioned and the ability to safely manage routine issues such as leaking or damaged sources. The MHC has been designed with the transportation challenges of rapid deployment to difficult environments in mind. The system weighs approximately 150,000 pounds, with individual systems breaking down into pieces not exceeding 20,000 pounds. Components are to be transportable on standard 20ft ISO containers, with shielding shells on 20ft flat racks. It is estimated that a total of eight containers and flat racks will be required. The use of 20ft containers, as opposed to 40ft containers, minimizes the impact on less developed road infrastructures, enabling the MHC to be positioned in constrained environments such as hospital parking lots. The system’s modularity also allows for deployment using smaller equipment, such as a 10-ton boom truck or forklift, which is crucial given the potential logistical challenges in different countries. This transportation strategy, evaluated in collaboration with Utah State University, ensures the MHC can be deployed via ground, rail, sea, or air, addressing the primary concern of international transport logistics.

99 - GENERAL AND MISCELLANEOUS↗
DOE OSTI2023

Decision-making Framework to Support the End-of-Life Management of High-Activity Radioactive Sources

Sealed radioactive sources are used for an extremely wide range of purposes, including as radiation sources in various nuclear facilities, universities, hospitals, biomedical and industrial applications, as well as for geological prospecting and exploration. The proper management of these sealed radioactive sources once they have reached their end-of-life is still a global challenge. Very few field-tested Mobile Hot Cells (MHC) exist in the world to support the end-of-life management of disused high-activity radioactive sources. One of the critical challenges that a source recovery team encounters on each site is to find adequate space, and access to that space to complete the staging and recapture process with a MHC; this process is tedious, uncertain, and time-consuming. Therefore, it is essential to understand the planning and management of the MHC setup and takedown. Currently, there isn't an single capable planning tool that will provide an effective medium to plan, inform, educate, and communicate knowledge about the environment where the MHC will be deployed. We present a novel approach for the planning and management of the deployment of the MHC to several different sites that relies on technology. Furthermore, this planning tool will support collaboration, promote information sharing, and foster better decision making processes, resulting in a more efficient, and reliable setup and source recovery with the MHC.

61 RADIATION PROTECTION AND DOSIMETRY↗
DOE OSTI2021

Primary photodissociation mechanisms of pyruvic acid on S 1 : observation of methylhydroxycarbene and its chemical reaction in the gas phase

Pyruvic acid, a representative alpha-keto carboxylic acid, is one of the few organic molecules destroyed in the troposphere by solar radiation rather than by reactions with free radicals. To date, only its stable final products were identified, often with contribution from secondary chemistry, making it difficult to elucidate photodissociation mechanisms following excitation to the lowest singlet excited-state (S 1 ) and the role of the internal hydrogen bond in the most-stable Tc conformer. Using multiplexed photoionization mass spectrometry we report the first direct experimental evidence, via the observation of singlet methylhydroxycarbene (MHC) following 351 nm excitation, supporting the decarboxylation mechanism previously proposed. Decarboxylation to MHC + CO 2 represents 97–100% of product branching at 351 nm. We observe vinyl alcohol and acetaldehyde, which we attribute to isomerization of MHC. We also observe a 3 ± 2% yield of the Norrish Type I photoproducts CH 3 CO + DOCO, but only from d 1 -pyruvic acid. At 4 Torr pressure, we measure a photodissociation quantum yield of $1.0^{+0}_{–0.4}$, consistent with IUPAC recommendations. However, our measured product branching fractions disagree with IUPAC. In light of previous calculations, these results support a mechanism in which hydrogen transfer on the S 1 excited state occurs at least partially by tunneling, in competition with intersystem crossing to the T 1 state. Here, we present the first evidence of a bimolecular reaction of MHC in the gas phase, where MHC reacts with pyruvic acid to produce a C 4 H 8 O 2 product. This observation implies that some MHC produced from pyruvic acid in Earth's troposphere will be stabilized and participate in chemical reactions with O 2 and H 2 O, and should be considered in atmospheric modeling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Hybrid Electrochemical Hydrogen/Metal Hydride Compressor (Final Technical Report)

Various alternatives to traditional mechanical compressor systems have been considered, including MHC and EHC. Both MHCs and EHCs are solid-state systems that have no moving parts other than valves. Both are quiet and have low maintenance requirements. However, strength and material issues as well as water and heat management issues have challenged EHCs, especially, when operated at very high pressures. Similarly, low efficiency, especially, when staging is required to attain high, pressure ratios, has challenged MHCs and has made them too complex and expensive. Material degradation, due to hydrogen impurity effects, has also created issues for MHCs. One novel alternative evaluated here is to combine EHC and MHC technologies in a way to maximize their advantages and to minimize each of their challenges to improve the overall systems performance on a path to meet or exceed current DOE targets. A hybrid EH/MH compressor takes advantage of lower maintenance and operating costs as well as increased reliability associated with both the MHC and EHC technologies over traditional mechanical compressors. Neither the MHC nor the EHC have any moving parts other than valves. The hybrid system also takes advantage of the higher efficiency and lower cost of the EHC by operating at lower delivery pressures combined with the robust and simple operation of a single-stage, MH compressor at higher pressures. Both MHC and EHC technologies are scalable and can be used for a variety of hydrogen compression and delivery applications.

08 HYDROGEN↗
DOE OSTI2024

Experimental Structures of Antibody/MHC-I Complexes Reveal Details of Epitopes Overlooked by Computational Prediction

Abstract mAbs to MHC class I (MHC-I) molecules have proved to be crucial reagents for tissue typing and fundamental studies of immune recognition. To augment our understanding of epitopic sites seen by a set of anti–MHC-I mAb, we determined X-ray crystal structures of four complexes of anti–MHC-I Fabs bound to peptide/MHC-I/β2-microglobulin (pMHC-I). An anti–H2-Dd mAb, two anti–MHC-I α3 domain mAbs, and an anti–β2-microglobulin mAb bind pMHC-I at sites consistent with earlier mutational and functional experiments, and the structures explain allelomorph specificity. Comparison of the experimentally determined structures with computationally derived models using AlphaFold Multimer showed that although predictions of the individual pMHC-I heterodimers were quite acceptable, the computational models failed to properly identify the docking sites of the mAb on pMHC-I. The experimental and predicted structures provide insight into strengths and weaknesses of purely computational approaches and suggest areas that merit additional attention.

Immunology↗
DOE OSTI2025

Approach to Evaluating Reorganization Energies of Interfacial Electrochemical Reactions

Reaction rate coefficients for electron-transfer processes at the electrode–electrolyte interface are commonly estimated by using the Butler–Volmer equation, but their values are inaccurate beyond a few tenths of volts of overpotential. The Marcus–Hush–Chidsey (MHC) formalism yields correct asymptotic behavior of the rate coefficients vs applied overpotential but has complex dependencies on the redox system’s intrinsic parameters, which can be difficult to model or measure. In this work, we bridge the two kinetics formalisms to estimate the reorganization energy, one of the important parameters for the MHC formalism, and investigate its dependence on other intrinsic parameters such as activation barriers, electronic coupling strength, and the density of states of the electrode surface. We examine the sensitivity of the reorganization energy to these parameters, establish some general relationships for accurately predicting rate coefficients using the MHC formalism over a wide range of applied overpotentials, and compare this approach to calculating MHC rate constants with other empirical approaches for the mechanisms of CO 2 reduction on different metal electrode surfaces.

Butler−Volmer↗