Structures of plasmepsin X from Plasmodium falciparum reveal a novel inactivation mechanism of the z
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Kesari, Pooja↗
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Results for “novel mechanism”
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Discovery, Characterization, and Structure of a Cell Active PAD2 Inhibitor Acting through a Novel Allosteric Mechanism
Not provided.
Biochemistry & Molecular Biology↗
Novel aerospace mechanisms: A passive tether damping device for tethered satellite, and a pin/latch structural interface system
Presented here is a collection of development tasks that have been accomplished over the past year at the Marshall Space Flight Center's Structures and Dynamics Laboratory. Dissemination of task findings are reported for the following reasons: the task involves new or evolving technology (as in the case of a tethered satellite), and the tasks depict a technique that could have application to extravehicular activity (EVA) or robotic assembly of space structures (the pin/latch system).
Redmon, John W., Jr.↗
A novel cache mechanism
This cache mechanism is transparent but does not contain associative circuits. It does not rely on locality of reference of instructions or data. No redundant instructions or data are encached. Items in the cache are accessed without address arithmetic. A cache miss is detected by the simplest test; compare two bits. These features would result in faster access, higher hit rate, reduced chip area, and less power dissipation in comparison with associative systems of similar size.
Gunawardena, J. A.↗
Novel Diffusion Mechanisms during the Oxidation of Silicon Germanium/Silicon Heterostructures.
Abstract not provided.
Thornton, Chappel Sharrock↗
Elucidating Novel Diffusion Mechanisms during Si/SiGe Oxidation.
Abstract not provided.
Thornton, Chappel Sharrock↗
Debye mechanism of giant microwave absorption in superconductors
Here, we discuss a novel mechanism of microwave absorption in superconductors, which is similar to the Debye absorption mechanism in molecular gases. The contribution of this mechanism to the ac conductivity is proportional to the inelastic quasiparticle relaxation time $τ_{\text{in}}$ rather than the elastic one $τ_{\text{el}}$ and therefore it can be much larger than the conventional one. The Debye contribution to the linear conductivity arises only in the presence of a dc supercurrent in the system and its magnitude depends strongly on the orientation of the microwave field relative to the supercurrent. The Debye contribution to the nonlinear conductivity exists even in the absence of dc supercurrent, and it is proportional to $τ_{\text{in}}$. Therefore the nonlinear threshold is anomalously low. Microwave absorption measurements may provide direct information about $τ_{\text{in}}$ in superconductors.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Hold Down and Release Mechanism Hardware Simulator for Ground Deployment Testing
Hold Down and Release Mechanisms (HDRMs) are a common piece of spacecraft hardware which restrain components during launch, transit, and later allow them to be extended, jettisoned, separated, etc. at the spacecraft’s destination. Due to prohibitively high cost, long lead times, and limited reset capability, testing of mechanisms that require HDRMs is often difficult. This project explored the possibility of designing HDRM-analogue devices that would replicate the function of flight HDRMs during ground-based testing for a fraction of the cost of a flight HDRM. These devices were designed with the requirements of the Spin Eject Mechanism to be used on the Mars Sample Return (MSR) Capture, Containment, and Return System (CCRS) in mind. A trade study was conducted to determine the optimal internal mechanism design of the device, comparing several mechanisms from existing HDRMs to several simpler, more novel mechanisms. CAD software was used to create a preliminary design of the device utilizing a mix of commercial off-the-shelf parts and custom-manufactured parts. Several straightforward analyses were conducted to determine the most effective models for the off-the-shelf parts. A prototype largely composed of 3D-printed components was also created to proof the design concept. Although this HDRM simulator was designed for a particular mechanism for the CCRS mission, its general design is useful for ground testing of a variety of mechanisms requiring similar HDRM simulators.
Kian Vilhauer↗
The Role of Gravity Mechanotransduction in Regulating Stem Cell Tissue Regenerative Potential at the Single Cell Expressome Level
Gravity is an omnipresent force on Earth, and all living organisms have evolved under the influence of constant gravity. Mechanical forces generated by gravity are potent modulators of stem cell based tissue regenerative mechanisms, inducing cell fate decisions and tissue specific commitment. A novel mechanical unloading investigation assessed the formation, morphology, and gene expression of embryoid bodies (EB), a transitory cell model of early differentiation. After 15 days of spaceflight, the mechanotransduction-null EB cells showed upregulated proliferative mechanisms while differentiation cues were silenced.
Juran, Cassandra M.↗
Giant Spontaneous Magnetostriction in MnTe Driven by a Novel Magnetostructural Coupling Mechanism
A comprehensive x-ray scattering study of spontaneous magnetostriction in hexagonal MnTe, an antiferromagnetic semiconductor with a Néel temperature of T N = 307 K, is presented. The largest spontaneous magnetovolume effect known for an antiferromagnet is observed, reaching a volume contraction of |ΔV/V| > 7 × 10 -3 . This can be justified semiquantitatively by considering bulk material properties, the spatial dependence of the superexchange interaction, and the geometrical arrangement of magnetic moments in MnTe. The highly unusual linear scaling of the magnetovolume effect with the short-range magnetic correlations, beginning in the paramagnetic state well above T N , points to a novel physical mechanism, which is explained in terms of a trilinear coupling of the elastic strain with superposed distinct domains of the antiferromagnetic order parameter. Furthermore, this novel mechanism for coupling lattice strain to robust short-range magnetic order casts new light on magnetostrictive phenomena and also provides a template by which the exceptional magnetostrictive properties of MnTe might be realized in a wide range of other functional materials.
36 MATERIALS SCIENCE↗
Gamma Radiolysis of Phenyl-Substituted TODGAs: Part II
The radiolytic degradation chemistry of three phenylated analogs of $N,N,N’,N’$-tetraoctyl diglycolamide (TODGA) was investigated: 2-(2-(di-$n$-octylamino)-2-oxoethoxy)-$N,N$-di-$n$-octyl-2-phenylacetamide (PhTODGA), which has a phenyl substituent bound to a central methylene, 2-(2-(di-$n$-octylamino)-2-oxo-1-phenylethoxy)-$N,N$-di-$n$-octylpropanamide (PhMeTODGA), which also contains a methyl substituent bound to the methylene on the other side of the ether moiety, and, 2-(2-$N$-$n$-hexyl-$N$-phenylamino)-2-oxoethoxy)-$N$-$n$-hexyl-$N$-phenylacetamide (DHDPDGA), which has phenyl substituents located on the amide groups instead of the central methylenes. In Part II of this series of papers radiolytic degradation products were identified after separation with liquid chromatography by High Resolution, Accurate-Mass mass spectrometry and collision-induced dissociation. At least twenty-two radiolytic degradation products were identified for PhTODGA, twenty-nine for PhMeTODGA, and over three dozen for DHDPDGA. The suite of radiolytic degradation products of these three investigated ligands was significantly larger than has been reported for previously studied diglycolamides, owing to their asymmetric nature, and to the identification of several new degradation mechanisms, including addition of methyl, hydroxyl, and nitrogen oxide radicals, that have not been previously reported for diglycolamides. Degradation products that contained addition of a NO 2 or NO 3 group were particularly prevalent for DHDPDGA, likely due to the phenyl side-groups. In conclusion, several of these newly observed mechanisms do not appear to depend on the presence of the phenyl groups, suggesting these novel mechanisms may apply to other diglycolamides.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
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↗
Pressurized DNA state inside herpes capsids—A novel antiviral target
Drug resistance in viruses represents one of the major challenges of healthcare. As part of an effort to provide a treatment that avoids the possibility of drug resistance, we discovered a novel mechanism of action (MOA) and specific compounds to treat all nine human herpesviruses and animal herpesviruses. The novel MOA targets the pressurized genome state in a viral capsid, “turns off” capsid pressure, and blocks viral genome ejection into a cell nucleus, preventing viral replication. This work serves as a proof-of-concept to demonstrate the feasibility of a new antiviral target—suppressing pressure-driven viral genome ejection —that is likely impervious to developing drug resistance. This pivotal finding presents a platform for discovery of a new class of broad-spectrum treatments for herpesviruses and other viral infections with genome-pressure-dependent replication. A biophysical approach to antiviral treatment such as this is also a vital strategy to prevent the spread of emerging viruses where vaccine development is challenged by high mutation rates or other evasion mechanisms.
59 BASIC BIOLOGICAL SCIENCES↗
Internally Catalyzed Hydrogen Atom Transfer (I-CHAT)—A New Class of Reactions in Combustion Chemistry
The current paradigm of low-T combustion and autoignition of hydrocarbons is based on the sequential two-step oxygenation of fuel radicals. The key chain-branching occurs when the second oxygenation adduct (OOQOOH) is isomerized releasing an OH radical and a key ketohydroperoxide (KHP) intermediate. The subsequent homolytic dissociation of relatively weak O–O bonds in KHP generates two more radicals in the oxidation chain leading to ignition. Based on the recently introduced intramolecular “catalytic hydrogen atom transfer” mechanism (J. Phys. Chem. 2024, 128, 2169), abbreviated here as I-CHAT, we have identified a novel unimolecular decomposition channel for KHPs to form their classical isomers—enol hydroperoxides (EHP). The uncertainty in the contribution of enols is typically due to the high computed barriers for conventional (“direct”) keto–enol tautomerization. Remarkably, the I-CHAT dramatically reduces such barriers. The novel mechanism can be regarded as an intramolecular version of the intermolecular relay transfer of H-atoms mediated by an external molecule following the general classification of such processes (Catal. Rev.-Sci. Eng. 2014, 56, 403). Here, we present a detailed mechanistic and kinetic analysis of the I-CHAT-facilitated pathways applied to n-hexane, n-heptane, and n-pentane models as prototype molecules for gasoline, diesel, and hybrid rocket fuels. We particularly examined the formation kinetics and subsequent dissociation of the γ-enol-hydroperoxide isomer of the most abundant pentane-derived isomer γ-C5-KHP observed experimentally. To gain molecular-level insight into the I-CHAT catalysis, we have also explored the role of the internal catalyst moieties using truncated models. All applied models demonstrated a significant reduction in the isomerization barriers, primarily due to the decreased ring strain in transition states. In addition, the longer-range and sequential H-migration processes were also identified and illustrated via a combined double keto–enol conversion of heptane-2,6-diketo-4-hydroperoxide as a potential chain-branching model. To assess the possible impact of the I-CHAT channels on global fuel combustion characteristics, we performed a detailed kinetic analysis of the isomerization and decomposition of γ-C5-KHP comparing I-CHAT with key alternative reactions—direct dissociation and Korcek channels. Calculated rate parameters were implemented into a modified version of the n-pentane kinetic model developed earlier using RMG automated model generation tools (ACS Omega, 2023, 8, 4908). Simulations of ignition delay times revealed the significant effect of the new pathways, suggesting an important role of the I-CHAT pathways in the low-T combustion of large alkanes.
Biochemistry & Molecular Biology↗
A lipoprotein allosterically activates the CwlD amidase during Clostridioides difficile spore formation
Spore-forming pathogens like Clostridioides difficile depend on germination to initiate infection. During gemination, spores must degrade their cortex layer, which is a thick, protective layer of modified peptidoglycan. Cortex degradation depends on the presence of the spore-specific peptidoglycan modification, muramic-∂-lactam (MAL), which is specifically recognized by cortex lytic enzymes. In C . difficile , MAL production depends on the CwlD amidase and its binding partner, the GerS lipoprotein. To gain insight into how GerS regulates CwlD activity, we solved the crystal structure of the CwlD:GerS complex. In this structure, a GerS homodimer is bound to two CwlD monomers such that the CwlD active sites are exposed. Although CwlD structurally resembles amidase_3 family members, we found that CwlD does not bind Zn 2+ stably on its own, unlike previously characterized amidase_3 enzymes. Instead, GerS binding to CwlD promotes CwlD binding to Zn 2+ , which is required for its catalytic mechanism. Thus, in determining the first structure of an amidase bound to its regulator, we reveal stabilization of Zn 2+ co-factor binding as a novel mechanism for regulating bacterial amidase activity. Our results further suggest that allosteric regulation by binding partners may be a more widespread mode for regulating bacterial amidase activity than previously thought.
59 BASIC BIOLOGICAL SCIENCES↗
Discovery of GuaB inhibitors with efficacy against Acinetobacter baumannii infection
ABSTRACT Guanine nucleotides are required for growth and viability of cells due to their structural role in DNA and RNA, and their regulatory roles in translation, signal transduction, and cell division. The natural antibiotic mycophenolic acid (MPA) targets the rate-limiting step inde novoguanine nucleotide biosynthesis executed by inosine-5´-monophosphate dehydrogenase (IMPDH). MPA is used clinically as an immunosuppressant, but whetherin vivoinhibition of bacterial IMPDH (GuaB) is a valid antibacterial strategy is controversial. Here, we describe the discovery of extremely potent small molecule GuaB inhibitors (GuaBi) specific to pathogenic bacteria with a low frequency of on-target spontaneous resistance and bactericidal efficacyin vivoagainstAcinetobacter baumanniimouse models of infection. The spectrum of GuaBi activity includes multidrug-resistant pathogens that are a critical priority of new antibiotic development. Co-crystal structures ofA. baumannii, Staphylococcus aureus, andEscherichia coliGuaB proteins bound to inhibitors show comparable binding modes of GuaBi across species and identifies key binding site residues that are predictive of whole-cell activity across both Gram-positive and Gram-negative clades of Bacteria. The clearin vivoefficacy of these small molecule GuaB inhibitors in a model ofA. baumanniiinfection validates GuaB as an essential antibiotic target. IMPORTANCE The emergence of multidrug-resistant bacteria worldwide has renewed interest in discovering antibiotics with novel mechanism of action. For the first time ever, we demonstrate that pharmacological inhibition ofde novoguanine biosynthesis is bactericidal in a mouse model ofAcinetobacter baumanniiinfection. Structural analyses of novel inhibitors explain differences in biochemical and whole-cell activity across bacterial clades and underscore why this discovery may have broad translational impact on treatment of the most recalcitrant bacterial infections.
Microbiology↗
Ca2+-dependent dephosphorylation of kinesin heavy chain on beta-granules in pancreatic beta-cells. Implications for regulated beta-granule transport and insulin exocytosis
The specific biochemical steps required for glucose-regulated insulin exocytosis from beta-cells are not well defined. Elevation of glucose leads to increases in cytosolic [Ca2+]i and biphasic release of insulin from both a readily releasable and a storage pool of beta-granules. The effect of elevated [Ca2+]i on phosphorylation of isolated beta-granule membrane proteins was evaluated, and the phosphorylation of four proteins was found to be altered by [Ca2+]i. One (a 18/20-kDa doublet) was a Ca2+-dependent increase in phosphorylation, and, surprisingly, three others (138, 42, and 36 kDa) were Ca2+-dependent dephosphorylations. The 138-kDa beta-granule phosphoprotein was found to be kinesin heavy chain (KHC). At low levels of [Ca2+]i KHC was phosphorylated by casein kinase 2, but KHC was rapidly dephosphorylated by protein phosphatase 2B beta (PP2Bbeta) as [Ca2+]i increased. Inhibitors of PP2B specifically reduced the second, microtubule-dependent, phase of insulin secretion, suggesting that dephosphorylation of KHC was required for transport of beta-granules from the storage pool to replenish the readily releasable pool of beta-granules. This is distinct from synaptic vesicle exocytosis, because neurotransmitter release from synaptosomes did not require a Ca2+-dependent KHC dephosphorylation. These results suggest a novel mechanism for regulating KHC function and beta-granule transport in beta-cells that is mediated by casein kinase 2 and PP2B. They also implicate a novel regulatory role for PP2B/calcineurin in the control of insulin secretion downstream of a rise in [Ca2+]i.
NASA Discipline Neuroscience↗