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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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All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Smart connected worker edge platform for smart manufacturing: Part 2—Implementation and on‐site deployment case study

Abstract In this paper, we describe specific deployments of the Smart Connected Worker (SCW) Edge Platform for Smart Manufacturing through implementation of four instructive real‐world use cases that illustrate the role of people in a Smart Manufacturing paradigm through which affordable, scalable, accessible, and portable (ASAP) information technology (IT) acquires and contextualizes data into information for transmission to operation technologies (OT). For case one, the platform captures the relationships between energy consumption and human workflows for improved energy productivity while workers interact with machines during semiconductor manufacturing. The platform utilizes human cognition to identify anomalous machine behavior for root cause analysis of system faults via neural network (NN) that recognize alarm postures of workers with cameras. For case two, a smart assembly line is demonstrated for state monitoring and fault detection. Machine learning (ML) models are used to recognize system states and identify fault scenarios with human intervention. For case three, the platform monitors human–machine interactions to classify manufacturing machine states for proper operations and energy productivity. Internal energy states of individual or collections of manufacturing equipment are determined via NN based algorithms that disaggregate signals associated with smart metering typically deployed at manufacturing facilities. These methods predict the real time energy profile of each machine from the total energy profile of a manufacturing site. For case four, a software defined sensor system built with scientific workflow engines is demonstrated for contextualizing data from laser surface refraction for characterization, and diagnostics in the processing of additively manufactured titanium alloy.

Donovan, Richard P.↗
DOE OSTI2018

Simultaneous Stabilization of LiNi 0.76 Mn 0.14 Co 0.10 O 2 Cathode and Lithium Metal Anode by Lithium Bis(oxalato)borate as Additive

Abstract The long‐term cycling performance, rate capability, and voltage stability of lithium (Li) metal batteries with LiNi 0.76 Mn 0.14 Co 0.10 O 2 (NMC76) cathodes is greatly enhanced by lithium bis(oxalato)borate (LiBOB) additive in the LiPF 6 ‐based electrolyte. With 2 % LiBOB in the electrolyte, a Li∥NMC76 cell is able to achieve a high capacity retention of 96.8 % after 200 cycles at C/3 rate (1 C=200 mA g −1 ), which is the best result reported for a Ni‐rich NMC cathode coupled with Li metal anode. The significantly enhanced electrochemical performance can be ascribed to the stabilization of both the NMC76 cathode/electrolyte and Li‐metal‐anode/electrolyte interfaces. The LiBOB‐containing electrolyte not only facilitates the formation of a more compact solid–electrolyte interphase on the Li metal surface, it also forms a enhanced cathode electrolyte interface layer, which efficiently prevents the corrosion of the cathode interface and mitigates the formation of the disordered rock‐salt phase after cycling. The fundamental findings of this work highlight the importance of recognizing the dual effects of electrolyte additives in simultaneously stabilizing both cathode and anode interfaces, so as to enhance the long‐term cycle life of high‐energy‐density battery systems.

Zhao, Wengao↗
DOE OSTI2020

Combining Chemistry, Material Science, Inspiration from nature, and Serendipity to Develop Stimuli-responsive Polymeric Materials

Neither of us can remember people talking about stimuli-responsive polymers when we were students. Even though this was still in the last century, it was almost 70 years after Staudinger's seminal paper "uber Polymerisation"![1] By the time we entered graduate school in the early 1990 s, the first papers on polymer light emitting diodes appeared, while research on electrically conducting, nonlinear optical, and other "functional" polymers was already in full swing. Looking back, there were some stimuli-responsive materials that were around at the time, but it took the better part of the last 30 years until the field had developed into what we think is one of the most vibrant areas of polymer science. Before the potential usefulness of this class of materials was recognized, researchers were focused on developing polymeric materials that would not respond to external influences, and in fact maintain (in particular) their mechanical properties in a wide range of environments. This has led to the development of many environmentally robust polymers, which have come to impact basically every aspect of our daily life. Ironically, this long-sought stability now comes back to haunt us in the form of plastic pollution, but this is another story. The concept of materials that adapt their properties in response to changing environmental conditions might appear like a complete reversal with respect to the original goals of creating stable materials. However, eventually a) it was recognized that materials that respond to a specific stimulus in a predictable and useful manner would significantly broaden the potential usefulness of polymers, and b) the field of polymer science had developed to the point where the rational design, preparation, and characterization of such materials became possible. The expression 'stimuli-responsive polymer' had been first used in the 1980's, however its use really only gained popularity a few decades later. In the early days, terms such as environmentally-sensitive or environmentally-responsive polymers, stimuli-reversible or stimuli-sensitive polymers, or polymers with phase transitions have also been used.

Rowan, Stuart J.↗
DOE OSTI2020

Solar cell efficiency tables (version 57)

Abstract Consolidated tables showing an extensive listing of the highest independently confirmed efficiencies for solar cells and modules are presented. Guidelines for inclusion of results into these tables are outlined, and new entries since June 2020 are reviewed. In this issue, charts showing efficiency improvements since 1993 are included as well as cell and module area definitions and an updated list of recognized test centres.

Green, Martin↗
DOE OSTI2017

The Institute of Resilient Communities [Book Chapter]

Here, resilience is the key to a prosperous global and modern society; Efforts to mitigate physical damage, economic loss, and to protect social and political infrastructures in response to catastrophic events, such as a nuclear accident or a natural disaster, are essential for communities to survive and thrive in the aftermath of such incidents. The 2011 Fukushima Dai-ichi nuclear power plant accident serves as an example of the risks associated with advanced technologies and the need to minimize physical as well as psychological effects on local and global communities. Other examples can be found reflecting the misperception of risks including concerns associated with vaccination or genetically modified organisms. While we have to recognize the risks associated with the development, implementation, and utilization of advanced technologies, we also have to recognize that the impact of not adopting them can have much more detrimental effects to individuals, communities, and even societies. We have established the Institute for Resilient Communities in Berkeley, CA in collaboration with Japanese partners to address the needs for better scientific and technological capabilities to assess, predict, and minimize the impact of disruptive events in the future and to enhance the understanding of associated risks to the public. While the initial focus resides in radiological resilience and is closely related to the events in Fukushima more than 5 years ago, the goal is to establish a broader framework for researchers, educators, and communities to enhance resilience locally and globally together.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2019

Invasive intraductal papillary mucinous neoplasms of the pancreas: relationships between mural nodules detected on thin-section contrast-enhanced MDCT and invasive components

Purpose: To elucidate the relationships between mural nodules (MNs) and invasive components in patients with invasive intraductal papillary mucinous neoplasm (IPMN) on the basis of thin-section contrast-enhanced multidetector CT (CE-MDCT) and pathologic findings. Methods: This retrospective study included 28 patients with surgically confirmed invasive IPMN. Two radiologists independently evaluated the thin-section (1-mm section thickness, no overlap) triple-phase CE-MDCT images for MNs, invasive components, and the continuity between them using a five-point scale (confidence scores of 1–3 as negative, 4 and 5 as positive). Kappa statistic was used to evaluate interobserver agreement. The CE-MDCT findings were correlated with pathologic findings. Results: Interobserver agreement was good or excellent. MNs consisting of tumor cells were recognized in 12 (42.9%) of 28 patients with no discrepancy between the two radiologists. Invasive components were detected in 85.7% and 82.1% in the pancreatic parenchymal phase for radiologist 1 and 2, respectively, and recognized as hypoattenuating areas. Pathologic continuities between MNs and invasive components were confirmed in five (41.7%) of 12 patients with MNs and these were detected on CE-MDCT. When combined seven patients without continuities between MNs and invasive components and 16 patients without MNs, the invasive components pathologically derived from non-nodular low-height papillary epithelium in 23 (82.1%) of 28 patients. Conclusions: The invasive components derived more often from low-height papillary epithelium without MN appearance on CE-MDCT than from MN. Careful attention should be paid to the existence of an invasive component even in the absence of an enhancing MN.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Parametric Optimization of Erosive Wear Response of TiAlN-Coated Aluminium Alloy Using Taguchi Method

In this research work, high-velocity oxy-fuel thermal spraying is used to develop TiAlN coatings on AA1050 and AA5083 aluminium alloy substrates. Slurry wear behavior of coatings is evaluated using jet-type test rig. Surface studies were carried out to investigate the potential erosion mechanism. The influence of key parameters identified using the Taguchi analysis is also corroborated with a wear model. The potential mechanism identified by wear model is in excellent convergence with that observed experimentally. Mixed ploughing and cutting, formation of platelets, abrasion grooves and cracks are witnessed as primary mechanisms causing loss of coating. Results indicate that impact velocity is recognized as a highly contributing parameter with contribution ratio of 79.24 and 83.75% followed by impingement angle with contribution ratio of 15.81 and 11.58% for AA1050 and AA5083, respectively. The important sequences of the control parameters are recognized to be impact velocity > impingement angle > erodent feed rate > erodent size for AA1050 and impact velocity > impingement angle > erodent size > erodent feed rate for AA5083. The best possible combination of control parameters for AA1050 and AA5083 to achieve minimal wear rate with respect to impact velocity, erodent size, impingement angle and erodent feed rate is 30 m/s, 225 µm, 30°, 160 g/min and 25 m/s, 150 µm, 30°, 160 g/min, respectively.

36 MATERIALS SCIENCE↗
DOE OSTI2017

A suite of benchmark and challenge problems for enhanced geothermal systems

A diverse suite of numerical simulators is currently being applied to predict or understand the performance of enhanced geothermal systems (EGS). To build confidence and identify critical development needs for these analytical tools, the United States Department of Energy, Geothermal Technologies Office sponsored a Code Comparison Study (GTO-CCS), with participants from universities, industry, and national laboratories. A principal objective for the study was to create a community forum for improvement and verification of numerical simulators for EGS modeling. Teams participating in the study were those representing U.S. national laboratories, universities, and industries, and each team brought unique numerical simulation capabilities to bear on the problems. Two classes of problems were developed during the study, benchmark problems and challenge problems. The benchmark problems were structured to test the ability of the collection of numerical simulators to solve various combinations of coupled thermal, hydrologic, geomechanical, and geochemical processes. This class of problems was strictly defined in terms of properties, driving forces, initial conditions, and boundary conditions. The challenge problems were based on the enhanced geothermal systems research conducted at Fenton Hill, near Los Alamos, New Mexico, between 1974 and 1995. The problems involved two phases of research, stimulation, development, and circulation in two separate reservoirs. The challenge problems had specific questions to be answered via numerical simulation in three topical areas: (1) reservoir creation/stimulation, (2) reactive and passive transport, and (3) thermal recovery. Whereas the benchmark class of problems were designed to test capabilities for modeling coupled processes under strictly specified conditions, the stated objective for the challenge class of problems was to demonstrate what new understanding of the Fenton Hill experiments could be realized via the application of modern numerical simulation tools by recognized expert practitioners. Lastly, we present the suite of benchmark and challenge problems developed for the GTO-CCS, providing problem descriptions and sample solutions.

15 GEOTHERMAL ENERGY↗
DOE OSTI2024

Transport from electron-scale turbulence in toroidal magnetic confinement devices

Plasma transport driven by turbulence ultimately determines the energy confinement performance of controlled fusion devices regardless of their confinement schemes and configurations. A large variety of plasma instabilities have been proposed for driving turbulence responsible for anomalous plasma transport beyond classical/neoclassical transport due to collisions. Although ion-scale turbulence usually dominates due to its large eddy size and saturation level, electron-scale turbulence has been recognized to be important in regions where ion-scale turbulence is suppressed (e.g., in internal transport barrier and in spherical tokamak H-mode plasmas) or is close to marginality. Electron-scale turbulence has been shown to nonlinearly interact with ion-scale turbulence, which modifies the dynamics of both and affects the resulting plasma transport, particularly when ion-scale instability is weakly driven. In this review paper, we focus on electron-scale turbulence that is believed to operate in magnetically confinement fusion devices and aim to provide a review of theoretical, numerical, and experimental developments in understanding electron-scale turbulence and its role in driving anomalous plasma turbulence. In particular, we focus on the electrostatic electron temperature gradient (ETG) mode which is the most widely recognized plasma instability underlying electron-scale turbulence observed in magnetically confined plasmas. Finally, we note that there are other less studied instabilities that might be responsible for observed electron-scale turbulence, most notably ubiquitous mode, and short-wavelength ion temperature gradient (SWITG) mode, which will be briefly touched on in this review.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Quantifying and visualizing the microscopic degrees of freedom of grain boundaries in the Wigner–Seitz cell of the displacement-shift-complete lattice

Here we introduce a grain boundary (GB) translation vector, t ws , to describe and quantify the domain of the microscopic degrees of freedom of GBs. It has long been recognized that for fixed macroscopic degrees of freedom of a GB there exists a large multiplicity of states characterized by different relative grain translations. More recently another degree of freedom, [n], the number of GB atoms, has emerged and is now recognized as an equally important component of GB structural multiplicity. In this work, we show that all GB microstates can be uniquely characterized by their value of t ws , which is located within the Wigner–Seitz (WS) cell of the Displacement-Shift-Complete lattice (DSCL) of the GB. The GB translation vector captures information about both the translation state and the number of GB atoms. We show that the density of GB microstates inside the WS cell of the DSCL is not uniform and can form clusters that correspond to different GB phases. Further, the vectors connecting the centers of the clusters correspond to the Burgers vectors of GB phase junctions, which can be predicted without building the junctions. Using t ws , we quantify GB excess shear and argue that it is defined up to a DSCL vector, which has implications for thermodynamic equilibrium conditions. Additionally, this work generalizes the definition of the number of GB atoms [n] to asymmetric boundaries.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Crystal structure and thermodynamic dissection of chitin oligosaccharide binding to the LysM module of chitinase-A from Pteris ryukyuensis

Highlights: • Crystal structure of a LysM module from Pteris ryukyuensis chitinase-A (PrLysM2) was determined at a resolution of 1.8 Å. • LysM module recognizes chitin oligosaccharides in a shallow groove on the molecule. • Thermodynamic dissection of the binding energetics of (GlcNAc){sub 6} to PrLysM2 was carried out. • The binding site comprises of five sugar-binding subsites. We determined the crystal structure of a LysM module from Pteris ryukyuensis chitinase-A (PrLysM2) at a resolution of 1.8 Å. Structural and binding analysis of PrLysM2 indicated that this module recognizes chitin oligosaccharides in a shallow groove comprised of five sugar-binding subsites on one side of the molecule. The free energy changes (ΔG{sub r}°) for binding of (GlcNAc){sub 6}, (GlcNAc){sub 5}, and (GlcNAc){sub 4} to PrLysM2 were determined to be −5.4, −5,4 and −4.6 kcal mol{sup −1}, respectively, by ITC. Thermodynamic dissection of the binding energetics of (GlcNAc){sub 6} revealed that the driving force is the enthalpy change (ΔH{sub r}° = −11.7 ± 0.2 kcal/mol) and the solvation entropy change (−TΔS{sub solv}° = −5.9 ± 0.6 kcal/mol). This is the first description of thermodynamic signatures of a chitin oligosaccharide binding to a LysM module.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Site-specific aptamer inhibitors of Thermus RNA polymerase

Highlights: • ssDNA aptamers recognize specific epitopes of Thermus aquaticus core RNA polymerase. • Aptamers sense RNA polymerase interactions with transcription factors and antibiotics. • Aptamers inhibit transcriptional activity of the RNA polymerase core enzyme. Bacterial RNA polymerase (RNAP) is an RNA-synthesizing molecular machine and a target for antibiotics. In transcription, RNAP can interact with DNA sequence-specifically, during promoter recognition by the σ-containing holoenzyme, or nonspecifically, during productive RNA elongation by the core RNAP. We describe high-affinity single-stranded DNA aptamers that are specifically recognized by the core RNAP from Thermus aquaticus. The aptamers interact with distinct epitopes inside the RNAP main channel, including the rifamycin pocket, and sense the binding of other RNAP ligands such as rifamycin and the σ{sup A} subunit. The aptamers inhibit RNAP activity and can thus be used for functional studies of transcription and development of novel RNAP inhibitors.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Incomplete clearance of apoptotic cells by core 1-derived O-glycan-deficient resident peritoneal macrophages

Highlights: • Cosmc-deficient resident peritoneal macrophages exhibited impaired efferocytosis. • Hypoglycosylated Tim4-FLAG could normally recognize phosphatidylserine. • Cosmc-deficient macrophages showed a reduction in Tim4 protein expression. The core 1 β1,3-galactosyltransferase-specific molecular chaperon (Cosmc) is essential for the synthesis of the core 1 structure of mucin-type O-glycans. To clarify the physiological role of core 1-derived O-glycans in macrophages, we exploited the LysM-Cre transgene to generate a conditional Cosmc mutant allele (conditional Cosmc knockout; cKO) in myeloid cells. cKO mice developed normally with no gross phenotypic abnormalities or abnormal peripheral blood counts. Resident peritoneal macrophages (rpMacs) of cKO mice exhibited impaired engulfment of apoptotic cells but showed normal macrophage differentiation and counts. T-cell immunoglobulin and mucin domain-containing molecule 4 (Tim4) is a phosphatidylserine (PS) receptor expressed on rpMacs and possesses a heavily O-glycosylated domain. Tim4 tethers apoptotic cells through PS binding. Expression of the Tim4 transcript was unchanged in cKO rpMacs, whereas flow cytometric, Western and dot blot analyses revealed that Tim4 protein expression in cKO rpMacs was significantly lower than that in wild-type (WT) rpMacs. Moreover, the expression levels of other efferocytosis-related molecules, Mertk, Itgav and Itgb3, were normal in rpMacs. In addition, hypoglycosylated Tim4-FLAG fusion protein sufficiently recognized PS. These results demonstrated that core 1-derived O-glycan is required for Tim4-dependent normal efferocytosis and may contribute to the stable expression of the Tim4 glycoprotein.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Epitope-based ligation of ICAM-1: Therapeutic target for protection against the development of rheumatoid arthritis

Highlights: • MD-3 mAb recognizes particular epitope on domain 2 of human ICAM-1. • MD-3 mAb leads to antigen-specific T cell suppression against bovine collagen. • MD-3 mAb effectively prevents progression of collagen-induced arthritis. Identification of a particular epitope on the domain 2 of human ICAM-1 led us to focus on its role in the treatment of rheumatoid arthritis (RA). Key observations from our previous xenotransplantation research included the generation of tolerogenic DCs, antigen-specific T-cell tolerance, and reduced production of inflammatory cytokines. The critically important point is the fact that it works initially on DC maturation. Ligation of this epitope with a recognizing antibody, MD-3, was also able to create a tolerogenic environment in RA in a manner sililar to that created by xenotransplantation. In this study, we noted that the disease progression, in terms of arthritis score and histopathology of joints, was significantly less severe in the MD-3-treated group than in the vehicle-treated group. Defective production of IL-6 and reduced proliferation of collagen-specific T cells were most remarkable laboratory findings. This type of ligation has a greater advantage over other types of therapeutics, in a sense that simple injection of this antibody inhibits antigen-specific T cell response. Due to the possibility of viral infection in this process, we regularly monitored cytomegalovirus reactivation status without detection of any viral gene replication. We are hoping that remarkable specializations that this interaction has, would be a promising target for therapeutic antibody in RA.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Activation of TLR3 and its adaptor TICAM-1 increases miR-21 levels in extracellular vesicles released from human cells

Highlights: • Activation of TLR3 increases miR-21 levels in extracellular vesicles. • TLR3 requires TICAM-1 adaptor to increase miR-21 levels in extracellular vesicles. • YBX-1 is involved in TLR3-mediated increase of miR-21 levels. Pattern-recognition receptors (PRRs) recognizes viral RNAs and trigger the innate immune responses. Toll-like receptor 3 (TLR3), a PRR, recognizes viral double-stranded RNA (dsRNA) in endolysosomes, whereas cytoplasmic dsRNA is sensed by another PRR, MDA5. TLR3 and MDA5 utilize TICAM-1 and MAVS, respectively, to trigger the signal for inducing innate immune responses. Extracellular vesicles (EVs) include the exosomes and microvesicles; an accumulating body of evidence has shown that EVs delivers functional RNA, such as microRNAs (miRNAs), to other cells and thus mediate intercellular communications. Therefore, EVs carrying miRNAs affect innate immune responses in macrophages and dendritic cells. However, the mechanism underlying the regulation of miRNA levels in EVs remains unclear. To elucidate the mechanism, we sought to reveal the pathway that control miRNA expression levels in EVs. Here, we found that TLR3 stimulation increased miR-21 levels in EVs released from various types of human cells. Ectopic expression of the TLR3 adaptor, TICAM-1, increased miR-21 levels in EVs but not intracellular miR-21 levels, suggesting that TICAM-1 augmented sorting of miR-21 to EVs. In contrast, the MDA5 adaptor, MAVS, did not increase miR-21 levels in EVs. The siRNA for TICAM-1 reduced EV miR-21 levels after stimulation of TLR3. Collectively, our data indicate a novel role of the TLR3-TICAM-1 pathway in controlling miR-21 levels in EVs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Cleavage of molybdopterin synthase MoaD-MoaE linear fusion by JAMM/MPN+ domain containing metalloprotease DR0402 from Deinococcus radiodurans

Highlights: • D. radiodurans encodes a fused MPT synthase, MoaD-MoaE fusion protein DR2607. • JAMM/MPN{sup +} metalloprotease DR0402 (JAMM{sub DR}) can cleave the MoaD-MoaE fusion. • JAMM{sub DR} recognizes the MoaD region in the cleavage process of MoaD-MoaE fusion. Molybdenum cofactor (Moco), molybdopterin (MPT) complexed with molybdenum, is an essential cofactor required for the catalytic center of diverse enzymes in all domains of life. Since Moco cannot be taken up as a nutrient unlike many other cofactors, Moco requires de novo biosynthesis. During the synthesis of MPT, the sulfur atom on the C-terminus of MoaD is transferred to cyclic pyranopterin monophosphate (cPMP) which is bound in the substrate pocket of MoaE. MoaD is a ubiquitin-like (Ubl) protein and has a C-terminal di-Gly motif which is a common feature of Ubl proteins. Despite the importance of free C terminal di-Gly motif of MoaD as a sulfur carrier, some bacteria encode a fused MPT synthase in which MoaD- and MoaE-like domains are located on a single peptide. Although it has recently been reported that the fused MPT synthase MoaX from Mycobacterium tuberculosis is posttranslationally cleaved into functional MoaD and MoaE in M. smegmatis, the protease responsible for the cleavage of MoaD-MoaE fusion protein has remained unknown to date. Here we report that the JAMM/MPN{sup +} domain containing metalloprotease DR0402 (JAMM{sub DR}) from Deinococcus radiodurans can cleave the MoaD-MoaE fusion protein DR2607, the sole MPT synthase in D. radiodurans, generating the MoaD having a C-terminal di-Gly motif. Furthermore, JAMM{sub DR} can also cleave off the MoaD from MoaD-eGFP fusion protein suggesting that JAMM{sub DR} recognizes the MoaD region rather than MoaE region in the cleaving process of MoaD-MoaE fusion protein.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Structural basis for multiple gene regulation by human DUX4

Highlights: • DUX4 is a master regulator that controls the expression of multiple genes. • DUX4-DH/DNA complex structure was solved at high resolution. • DH1 and DH2 domains of DUX4 play important role in consensus sequence recognition. • DUX4 can tolerate length and/or identity variation in target DNA linker region. DUX4 plays critical role in the molecular pathogenesis of the neuromuscular disorder facioscapulohumeral muscular dystrophy and acute lymphoblastic leukemia in humans. As a master transcription regulator, DUX4 can also bind the promoters and activate the transcription of hundreds ZGA-associated genes. Here we report on the structural and biochemical studies of DUX4 double homeodomains (DUX4-DH), representing the only structures contain both homeodomain 1 (HD1) and homeodomain 2 (HD2). HD1 and HD2 adopt classical homeobox fold; via the helix inserted into the major groove and the N-terminal extended loop inserted into the minor groove, HD1 and HD2 recognize the box1 (5′-TAA-3′) and box2 (5′-TGA-3′) nucleotides of the consensus sequence, respectively. Among the box1 and box2 linking nucleotides (CCTAA), the two adenine residues are reported to be highly conserved; however, they are not directly recognized by DUX4-DH in the structures. Besides different nucleotides, our ITC analysis indicated that DUX4-DH can also tolerate various changes in the linker length. Our studies not only revealed the basis for target DNA recognition by DUX4, but also advanced our understanding on multiple gene activation by DUX4.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Dual arginine recognition of LRRK2 phosphorylated Rab GTPases

Parkinson’s-disease-associated LRRK2 is a multidomain Ser/Thr kinase that phosphorylates a subset of Rab GTPases to control their effector functions. Rab GTPases are the prime regulators of membrane trafficking in eukaryotic cells. Rabs exert their biological effects by recruitment of effector proteins to subcellular compartments via their Rab-binding domain (RBD). Effectors are modular and typically contain additional domains that regulate various aspects of vesicle formation, trafficking, fusion, and organelle dynamics. The RBD of effectors is typically an α-helical coiled coil that recognizes the GTP conformation of the switch 1 and switch 2 motifs of Rabs. LRRK2 phosphorylates Rab8a at T72 (pT72) of its switch 2 α-helix. This post-translational modification enables recruitment of RILPL2, an effector that regulates ciliogenesis in model cell lines. A newly identified RBD motif of RILPL2, termed the X-cap, has been shown to recognize the phosphate via direct interactions between an arginine residue (R132) and pT72 of Rab8a. Here, we show that a second distal arginine (R130) is also essential for phospho-Rab binding by RILPL2. Through structural, biophysical, and cellular studies, we find that R130 stabilizes the primary R132:pT72 salt bridge through favorable enthalpic contributions to the binding affinity. These findings may have implications for the mechanism by which LRRK2 activation leads to assembly of phospho-Rab complexes and subsequent control of their membrane trafficking functions in cells.

59 BASIC BIOLOGICAL SCIENCES↗