Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “fusion proteins”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Targeted protein degradation systems to enhance Wnt signaling

Molecules that facilitate targeted protein degradation (TPD) offer great promise as novel therapeutics. The human hepatic lectin asialoglycoprotein receptor (ASGR) is selectively expressed on hepatocytes. We have previously engineered an anti-ASGR1 antibody-mutant RSPO2 (RSPO2RA) fusion protein (called SWEETS) to drive tissue-specific degradation of ZNRF3/RNF43 E3 ubiquitin ligases, which achieved hepatocyte-specific enhanced Wnt signaling, proliferation, and restored liver function in mouse models, and an antibody–RSPO2RA fusion molecule is currently in human clinical trials. In the current study, we identified two new ASGR1- and ASGR1/2-specific antibodies, 8M24 and 8G8. High-resolution crystal structures of ASGR1:8M24 and ASGR2:8G8 complexes revealed that these antibodies bind to distinct epitopes on opposing sides of ASGR, away from the substrate-binding site. Both antibodies enhanced Wnt activity when assembled as SWEETS molecules with RSPO2RA through specific effects sequestering E3 ligases. In addition, 8M24-RSPO2RA and 8G8-RSPO2RA efficiently downregulate ASGR1 through TPD mechanisms. These results demonstrate the possibility of combining different therapeutic effects and degradation mechanisms in a single molecule.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Controlling Protein Enrichment in Lipid Sponge Phase Droplets using SNAP–Tag Bioconjugation

All cells use organized lipid compartments to facilitate specific biological functions. Membrane-bound organelles create defined spatial environments that favor unique chemical reactions while isolating incompatible biological processes. Despite the fundamental role of cellular organelles, there is a scarcity of methods for preparing functional artificial lipid-based compartments. In this work, we demonstrate a robust bioconjugation system for sequestering proteins into zwitterionic lipid sponge phase droplets. Incorporation of benzylguanine (BG)-modified phospholipids that form stable covalent linkages with an O 6 -methylguanine DNA methyltransferase (SNAP-tag) fusion protein enables programmable control of protein capture. We show that this methodology can be used to anchor hydrophilic proteins at the lipid-aqueous interface, concentrating them within an accessible but protected chemical environment. SNAP-tag technology enables the integration of proteins that regulate complex biological functions in lipid sponge phase droplets, and should facilitate the development of advanced lipid-based artificial organelles.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2000

A calcium-dependent protein kinase can inhibit a calmodulin-stimulated Ca2+ pump (ACA2) located in the endoplasmic reticulum of Arabidopsis

The magnitude and duration of a cytosolic Ca(2+) release can potentially be altered by changing the rate of Ca(2+) efflux. In plant cells, Ca(2+) efflux from the cytoplasm is mediated by H(+)/Ca(2+)-antiporters and two types of Ca(2+)-ATPases. ACA2 was recently identified as a calmodulin-regulated Ca(2+)-pump located in the endoplasmic reticulum. Here, we show that phosphorylation of its N-terminal regulatory domain by a Ca(2+)-dependent protein kinase (CDPK isoform CPK1), inhibits both basal activity ( approximately 10%) and calmodulin stimulation ( approximately 75%), as shown by Ca(2+)-transport assays with recombinant enzyme expressed in yeast. A CDPK phosphorylation site was mapped to Ser(45) near a calmodulin binding site, using a fusion protein containing the N-terminal domain as an in vitro substrate for a recombinant CPK1. In a full-length enzyme, an Ala substitution for Ser(45) (S45/A) completely blocked the observed CDPK inhibition of both basal and calmodulin-stimulated activities. An Asp substitution (S45/D) mimicked phosphoinhibition, indicating that a negative charge at this position is sufficient to account for phosphoinhibition. Interestingly, prior binding of calmodulin blocked phosphorylation. This suggests that, once ACA2 binds calmodulin, its activation state becomes resistant to phosphoinhibition. These results support the hypothesis that ACA2 activity is regulated as the balance between the initial kinetics of calmodulin stimulation and CDPK inhibition, providing an example in plants for a potential point of crosstalk between two different Ca(2+)-signaling pathways.

NASA Discipline Plant Biology↗
NASA NTRS1996

Activation of a Ca(2+)-dependent protein kinase involves intramolecular binding of a calmodulin-like regulatory domain

Ca(2+)-dependent protein kinases (CDPKs) are regulated by a C-terminal calmodulin-like domain (CaM-LD). The CaM-LD is connected to the kinase by a short junction sequence which contains a pseudosubstrate autoinhibitor. To understand how the CaM-LD regulates a CDPK, a recombinant CDPK (isoform CPK-1 from Arabidopsis, accession no. L14771) was made as a fusion protein in Escherichia coli. We show here that a truncated CDPK lacking a CaM-LD (e.g. mutant delta NC-26H) can be activated by exogenous calmodulin or an isolated CaM-LD (Kact approximately 2 microM). We propose that Ca2+ activation of a CDPK normally occurs through intramolecular binding of the CaM-LD to the junction. When the junction and CaM-LD are made as two separate polypeptides, the CaM-LD can bind the junction in a Ca(2+)-dependent fashion with a dissociation constant (KD) of 6 x 10(-6) M, as determined by kinetic binding analyses. When the junction and CaM-LD are tethered in a single polypeptide (e.g. in protein JC-1), their ability to engage in bimolecular binding is suppressed (e.g. the tethered CaM-LD cannot bind a separate junction). A mutation which disrupts the putative CaM-LD binding sequence (e.g. substitution LRV-1444 to DLPG) appears to block intramolecular binding, as indicated by the restored ability of a tethered CaM-LD to engage in bimolecular binding. This mutation, in the context of a full-length enzyme (mutant KJM46H), appears to block Ca2+ activation. Thus, a disruption of intramolecular binding correlates with a disruption of the Ca2+ activation mechanism. CDPKs provide the first example of a member of the calmodulin superfamily where a target binding sequence is located within the same polypeptide.

Non-NASA Center↗
DOE OSTI2026

Hyperfusogenic Mutations Destabilize the Postfusion Six-Helix Bundle of the Measles Virus Fusion Glycoprotein

Fusion of the host membrane and viral envelope by class I viral fusion proteins is driven by the assembly of a postfusion six-helix bundle formed through antiparallel interactions between N-terminal (HR1) and C-terminal (HR2) heptad-repeat regions. Although mutations in these regions of the measles virus (MeV) fusion (F) glycoprotein are known to promote neuropathogenic and hyperfusogenic phenotypes, their effects on postfusion core stability have not been systematically examined. Here, we combine peptide biophysics and X-ray crystallography to interrogate how mutations within the HR2 domain, present in native neuropathogenic MeV isolates (e.g., L454W and N462K) and laboratory-generated hyperfusogenic variants (e.g., L454M and T461A), influence postfusion 6HB assembly. Circular dichroism (CD) spectroscopy reveals that, with few exceptions, these mutations decrease postfusion core stability, despite their association with enhanced fusion activity. We also report the first crystal structure of the wild-type MeV postfusion core as well as structures of six hyperfusogenic variants, enabling high-resolution comparison of the molecular basis of destabilization. Structural analysis shows that these effects arise from localized perturbations to steric packing, hydrogen bonding networks, and helix-stabilizing interactions within HR2, while the overall 6HB architecture remains conserved. Together, these results indicate that hyperfusogenic mutations are not associated with stabilization of the postfusion state and are instead consistent with models in which hyperfusogenicity arises from a reduction in the energetic barrier to fusion, potentially through effects on prefusion stability or triggering efficiency. These findings establish key sequence-structure–stability relationships governing coiled-coil assembly and provide a framework for the design of HR1- and HR2-based fusion inhibitors.

Genetics↗
DOE OSTI2025

Use of Split‐Intein Proteins to Design a Small Molecule Biosensor in Plants

Understanding how plants perceive their environment is fundamental to advancing agricultural productivity and sustainability. Many biological small molecules, including those involved in microbial recognition, act rapidly at the plant cell surface, but the absence of tools to visualise these dynamics has limited our ability to dissect plant–microbe communication. To address this gap, we sought to create a genetically encoded biosensor that couples ligand-induced protein dimerization with the production of a fluorescent reporter. Inteins are peptide regions that excise themselves from precursor proteins and ligate the flanking chains (exteins). When each half of a split intein is fused to one of two dimerizing proteins, ligand binding brings them into proximity, inducing intein splicing and ligation of flanking extein sequences (Kang et al. 2022). Similar to previous studies, we split the yeast vacuolar ATPase subunit 1 (VMA1) intein, creating a protein biosensor that produces eGFP upon protein dimerization after ligand binding (Figure 1A) (Mootz et al. 2003). Specifically, eGFP halves (i.e., non-functional N- and C-terminal GFP fragments) were fused to the intein halves, resulting in two fusion proteins: N-terminal GFP::N-terminal intein and C-terminal intein::C-terminal GFP (Figure 1A).

Boone, Brandon A. [Oak Ridge National Laboratory (↗
NASA NTRS1998

A novel calmodulin-regulated Ca2+-ATPase (ACA2) from Arabidopsis with an N-terminal autoinhibitory domain

To study transporters involved in regulating intracellular Ca2+, we isolated a full-length cDNA encoding a Ca2+-ATPase from a model plant, Arabidopsis, and named it ACA2 (Arabidopsis Ca2+-ATPase, isoform 2). ACA2p is most similar to a "plasma membrane-type" Ca2+-ATPase, but is smaller (110 kDa), contains a unique N-terminal domain, and is missing a long C-terminal calmodulin-binding regulatory domain. In addition, ACA2p is localized to an endomembrane system and not the plasma membrane, as shown by aqueous-two phase fractionation of microsomal membranes. ACA2p was expressed in yeast as both a full-length protein (ACA2-1p) and an N-terminal truncation mutant (ACA2-2p; Delta residues 2-80). Only the truncation mutant restored the growth on Ca2+-depleted medium of a yeast mutant defective in both endogenous Ca2+ pumps, PMR1 and PMC1. Although basal Ca2+-ATPase activity of the full-length protein was low, it was stimulated 5-fold by calmodulin (50% activation around 30 nM). In contrast, the truncated pump was fully active and insensitive to calmodulin. A calmodulin-binding sequence was identified within the first 36 residues of the N-terminal domain, as shown by calmodulin gel overlays on fusion proteins. Thus, ACA2 encodes a novel calmodulin-regulated Ca2+-ATPase distinguished by a unique N-terminal regulatory domain and a non-plasma membrane localization.

Non-NASA Center↗
DOE OSTI2024

The CRISPR effector Cam1 mediates membrane depolarization for phage defence

Prokaryotic type III CRISPR–Cas systems provide immunity against viruses and plasmids using CRISPR-associated Rossman fold (CARF) protein effectors. Recognition of transcripts of these invaders with sequences that are complementary to CRISPR RNA guides leads to the production of cyclic oligoadenylate second messengers, which bind CARF domains and trigger the activity of an effector domain. Whereas most effectors degrade host and invader nucleic acids, some are predicted to contain transmembrane helices without an enzymatic function. Whether and how these CARF–transmembrane helix fusion proteins facilitate the type III CRISPR–Cas immune response remains unknown. Here we investigate the role of cyclic oligoadenylate-activated membrane protein 1 (Cam1) during type III CRISPR immunity. Structural and biochemical analyses reveal that the CARF domains of a Cam1 dimer bind cyclic tetra-adenylate second messengers. In vivo, Cam1 localizes to the membrane, is predicted to form a tetrameric transmembrane pore, and provides defence against viral infection through the induction of membrane depolarization and growth arrest. These results reveal that CRISPR immunity does not always operate through the degradation of nucleic acids, but is instead mediated via a wider range of cellular responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Targeting KDM4 for treating PAX3-FOXO1–driven alveolar rhabdomyosarcoma

Chimeric transcription factors drive lineage-specific oncogenesis but are notoriously difficult to target. Alveolar rhabdomyosarcoma (RMS) is an aggressive childhood soft tissue sarcoma transformed by the pathognomonic Paired Box 3–Forkhead Box O1 (PAX3-FOXO1) fusion protein, which governs a core regulatory circuitry transcription factor network. Here, we show that the histone lysine demethylase 4B (KDM4B) is a therapeutic vulnerability for PAX3-FOXO1 + RMS. Genetic and pharmacologic inhibition of KDM4B substantially delayed tumor growth. Suppression of KDM4 proteins inhibited the expression of core oncogenic transcription factors and caused epigenetic alterations of PAX3-FOXO1–governed superenhancers. Combining KDM4 inhibition with cytotoxic chemotherapy led to tumor regression in preclinical PAX3-FOXO1 + RMS subcutaneous xenograft models. In summary, we identified a targetable mechanism required for maintenance of the PAX3-FOXO1–related transcription factor network, which may translate to a therapeutic approach for fusion-positive RMS.

Cell Biology↗
DOE OSTI2021

Mutagenesis of Human Cytomegalovirus Glycoprotein L Disproportionately Disrupts gH/gL/gO over gH/gL/pUL128-131

Herein, cell-free and cell-to-cell spread of herpesviruses involves a core fusion apparatus comprised of the fusion protein glycoprotein B (gB) and the regulatory factor gH/gL. The human cytomegalovirus (HCMV) gH/gL/gO and gH/gL/pUL128-131 facilitate spread in different cell types. The gO and pUL128-131 components bind distinct receptors, but how the gH/gL portions of the complexes functionally compare is not understood. We previously characterized a panel of gL mutants by transient expression and showed that many were impaired for gH/gL-gB-dependent cell-cell fusion but were still able to form gH/gL/pUL128-131 and induce receptor interference. Here, the gL mutants were engineered into the HCMV BAC clones TB40/e-BAC4 (TB), TR, and Merlin (ME), which differ in their utilization of the two complexes for entry and spread. Several of the gL mutations disproportionately impacted gH/gL/gO-dependent entry and spread over gH/gL/pUL128-131 processes. The effects of some mutants could be explained by impaired gH/gL/gO assembly, but other mutants impacted gH/gL/gO function. Soluble gH/gL/gO containing the L201 mutant failed to block HCMV infection despite unimpaired binding to PDGFRα, indicating the existence of other important gH/gL/gO receptors. Another mutant (L139) enhanced the gH/gL/gO-dependent cell-free spread of TR, suggesting a “hyperactive” gH/gL/gO. Recently published crystallography and cryo-electron microscopy studies suggest structural conservation of the gH/gL underlying gH/gL/gO and gH/gL/pUL128-131. However, our data suggest important differences in the gH/gL of the two complexes and support a model in which gH/gL/gO can provide an activation signal for gB.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRSDate not supplied

Maize Rough Endosperm6 (rgh6) Encodes A Predicted Dead-Box RNA Helicase and Affects Mirna Processing in Endosperm Development

Maize rough endosperm (rgh) mutants have defective kernels with a rough, etched, or pitted endosperm surface. Molecular genetic analysis of this mutant class has identified multiple RNA processing proteins critical to endosperm development. Here, we report on the developmental and molecular function of the rgh6 locus. The rgh6 mutant was isolated from the UniformMu transposon tagging population. Mutant kernels have reduced endosperm size and defective embryos that develop in a more apical position than typical for defective embryos. TB translocation crosses revealed that rgh6 mutant endosperm inhibits normal embryo development. Positional cloning of the rgh6 locus found that it encodes a predicted DEAD-box RNA helicase. Consistent with a predicted function for RNA processing, transient expression of a RGH6-GFP fusion protein is localized to nucleolus and nuclear speckles in Nicotiana benthamiana leaves. Rgh6 transcripts are highly expressed in endosperm epidermal cell types such as the aleurone, basal endosperm cell layer, embryo surrounding region, and endosperm adjacent to scutellum. Markers of these cell types show increased levels in rgh6 mutant kernels. Mutant endosperm tissues have increased precursor microRNA (pre-miRNA) and decreased mature miRNA relative to normal sibling endosperm, indicating that rgh6 is required for miRNA processing. The transcript levels for most miRNA target genes accumulate to a higher level in rgh6 mutant tissue. These results suggest that miRNA processing and regulation of miRNA target genes are required for normal endosperm development.

Plant Sciences↗
DOE OSTI2026

Leveraging Hydration Forces for Size-Specific Nanoparticle Enrichment with a Redox-Responsive Silica-Binding Elastin-Like Polypeptide

Elastin-like polypeptides (ELPs) are low-complexity proteins that coacervate above a characteristic lower critical solution temperature (LCST). While the thermoresponsiveness of ELPs has been widely exploited in the biomedical and biomaterials fields, their ability to mediate nanoparticle assembly below their transition temperature remains largely unexplored. Here, we show that unmodified ELPs induce the reversible flocculation of silica nanoparticles (SiNPs) by forming backbone hydrogen bonds with surface silanols. Interparticle bridging is modulated by ELP length and concentration and by the presence of N- and C-terminal anchoring groups such as a cysteine residue and a Car9 silica-binding peptide. Using a redox-responsive fusion protein consisting of disulfide-bonded ELP domains terminated by Car9 segments, we stabilize 20 nm SiNPs under oxidizing conditions while triggering particle flocculation upon addition of reductant. We find that SiNP sedimentation under reducing conditions exhibits a sharp dependency on particle size that arises from the curvature-dependent structure of surface silanols. While the isolated silanols of SiNPs smaller than 30 nm are efficiently engaged by the ELP domains of Car9-anchored proteins, repulsion forces associated with the presence of a layer of molecular water together with increased electrostatic repulsion preclude efficient engagement of H-bonded silanols displayed on the surface of SiNPs larger than 60 nm. We harness these findings to selectively enrich SiNPs based on size and expand the concept to titania (TiO2) by demonstrating that rutile nanoparticles can be stabilized or sedimented with solid-binding ELPs by adjusting the solution pH to promote or discourage the formation of a hydration layer. These strategies should prove broadly useful for the separation of other oxides and their polymorphs and provide a tunable strategy for nanoparticle assembly and bioinspired colloidal design.

ELP↗
NASA NTRS1999

Model system for plant cell biology: GFP imaging in living onion epidermal cells

The ability to visualize organelle localization and dynamics is very useful in studying cellular physiological events. Until recently, this has been accomplished using a variety of staining methods. However, staining can give inaccurate information due to nonspecific staining, diffusion of the stain or through toxic effects. The ability to target green fluorescent protein (GFP) to various organelles allows for specific labeling of organelles in vivo. The disadvantages of GFP thus far have been the time and money involved in developing stable transformants or maintaining cell cultures for transient expression. In this paper, we present a rapid transient expression system using onion epidermal peels. We have localized GFP to various cellular compartments (including the cell wall) to illustrate the utility of this method and to visualize dynamics of these compartments. The onion epidermis has large, living, transparent cells in a monolayer, making them ideal for visualizing GFP. This method is easy and inexpensive, and it allows for testing of new GFP fusion proteins in a living tissue to determine deleterious effects and the ability to express before stable transformants are attempted.

NASA Discipline Plant Biology↗
DOE OSTI2022

The Magnetosome Protein, Mms6 from Magnetospirillum magneticum Strain AMB-1, Is a Lipid-Activated Ferric Reductase

Magnetosomes of magnetotactic bacteria consist of magnetic nanocrystals with defined morphologies enclosed in vesicles originated from cytoplasmic membrane invaginations. Although many proteins are involved in creating magnetosomes, a single magnetosome protein, Mms6 from Magnetospirillum magneticum strain AMB-1, can direct the crystallization of magnetite nanoparticles in vitro. The in vivo role of Mms6 in magnetosome formation is debated, and the observation that Mms6 binds Fe3+ more tightly than Fe2+ raises the question of how, in a magnetosome environment dominated by Fe3+, Mms6 promotes the crystallization of magnetite, which contains both Fe3+ and Fe2+. Here we show that Mms6 is a ferric reductase that reduces Fe3+ to Fe2+ using NADH and FAD as electron donor and cofactor, respectively. Reductase activity is elevated when Mms6 is integrated into either liposomes or bicelles. Analysis of Mms6 mutants suggests that the C-terminal domain binds iron and the N-terminal domain contains the catalytic site. Although Mms6 forms multimers that involve C-terminal and N-terminal domain interactions, a fusion protein with ubiquitin remains a monomer and displays reductase activity, which suggests that the catalytic site is fully in the monomer. However, the quaternary structure of Mms6 appears to alter the iron binding characteristics of the C-terminal domain. These results are consistent with a hypothesis that Mms6, a membrane protein, promotes the formation of magnetite in vivo by a mechanism that involves reducing iron.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Arabinogalactan Structures of Repetitive Serine-Hydroxyproline Glycomodule Expressed by Arabidopsis Cell Suspension Cultures

Arabinogalactan-proteins (AGPs) are members of the hydroxyproline-rich glycoprotein (HRGP) superfamily. They are heavily glycosylated with arabinogalactans, which are usually composed of a β-1,3-linked galactan backbone with 6-O-linked galactosyl, oligo-1,6-galactosyl, or 1,6-galactan side chains that are further decorated with arabinosyl, glucuronosyl, rhamnosyl, and/or fucosyl residues. Here, our work with Hyp-O-polysaccharides isolated from (Ser-Hyp)32-EGFP (enhanced green fluorescent protein) fusion glycoproteins overexpressed in transgenic Arabidopsis suspension culture is consistent with the common structural features of AGPs isolated from tobacco. In addition, this work confirms the presence of β-1,6-linkage on the galactan backbone identified previously in AGP fusion glycoproteins expressed in tobacco suspension culture. Furthermore, the AGPs expressed in Arabidopsis suspension culture lack terminal-rhamnosyl residues and have a much lower level of glucuronosylation compared with those expressed in tobacco suspension culture. These differences not only suggest the presence of distinct glycosyl transferases for AGP glycosylation in the two systems, but also indicate the existence of minimum AG structures for type II AG functional features.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Impact of structural biology and the protein data bank on us fda new drug approvals of low molecular weight antineoplastic agents 2019–2023

Abstract Open access to three-dimensional atomic-level biostructure information from the Protein Data Bank (PDB) facilitated discovery/development of 100% of the 34 new low molecular weight, protein-targeted, antineoplastic agents approved by the US FDA 2019–2023. Analyses of PDB holdings, the scientific literature, and related documents for each drug-target combination revealed that the impact of structural biologists and public-domain 3D biostructure data was broad and substantial, ranging from understanding target biology (100% of all drug targets), to identifying a given target as likely druggable (100% of all targets), to structure-guided drug discovery (>80% of all new small-molecule drugs, made up of 50% confirmed and >30% probable cases). In addition to aggregate impact assessments, illustrative case studies are presented for six first-in-class small-molecule anti-cancer drugs, including a selective inhibitor of nuclear export targeting Exportin 1 (selinexor, Xpovio), an ATP-competitive CSF-1R receptor tyrosine kinase inhibitor (pexidartinib,Turalia), a non-ATP-competitive inhibitor of the BCR-Abl fusion protein targeting the myristoyl binding pocket within the kinase catalytic domain of Abl (asciminib, Scemblix), a covalently-acting G12C KRAS inhibitor (sotorasib, Lumakras or Lumykras), an EZH2 methyltransferase inhibitor (tazemostat, Tazverik), and an agent targeting the basic-Helix-Loop-Helix transcription factor HIF-2α (belzutifan, Welireg).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Evaluating the potential of disaggregated memory systems for HPC applications

Summary Disaggregated memory is a promising approach that addresses the limitations of traditional memory architectures by enabling memory to be decoupled from compute nodes and shared across a data center. Cloud platforms have deployed such systems to improve overall system memory utilization, but performance can vary across workloads. High‐performance computing (HPC) is crucial in scientific and engineering applications, where HPC machines also face the issue of underutilized memory. As a result, improving system memory utilization while understanding workload performance is essential for HPC operators. Therefore, learning the potential of a disaggregated memory system before deployment is a critical step. This paper proposes a methodology for exploring the design space of a disaggregated memory system. It incorporates key metrics that affect performance on disaggregated memory systems: memory capacity, local and remote memory access ratio, injection bandwidth, and bisection bandwidth, providing an intuitive approach to guide machine configurations based on technology trends and workload characteristics. We apply our methodology to analyze thirteen diverse workloads, including AI training, data analysis, genomics, protein, fusion, atomic nuclei, and traditional HPC bookends. Our methodology demonstrates the ability to comprehend the potential and pitfalls of a disaggregated memory system and provides motivation for machine configurations. Our results show that eleven of our thirteen applications can leverage injection bandwidth disaggregated memory without affecting performance, while one pays a rack bisection bandwidth penalty and two pay the system‐wide bisection bandwidth penalty. In addition, we also show that intra‐rack memory disaggregation would meet the application's memory requirement and provide enough remote memory bandwidth.

Ding, Nan↗
DOE OSTI2025

Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF‐Trap

The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half‐life. A prime example is VEGF‐Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)‐1 and VEGFR‐2. The Fc region's role in N‐glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near‐physiological temperature structures of the N‐glycan‐bound Fc fragment of IgG1 subtype from a biosimilar VEGF‐Trap are presented, determined using the SPring‐8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan‐binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N‐glycans on protein stability. These findings offer new insights into the molecular basis of Fc‐mediated functions and provide valuable information for the design of next‐generation therapeutics.

60 APPLIED LIFE SCIENCES↗