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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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723 records · Page 41
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Conformational flexibility is a critical factor in designing broad-spectrum human norovirus protease inhibitors

Human norovirus (HuNoV) is a leading cause of gastroenteritis worldwide and is associated with significant morbidity, mortality, and economic impact. There are currently no licensed antiviral drugs for the treatment of HuNoV-associated gastroenteritis. The HuNoV protease plays a critical role in the initiation of virus replication by cleaving the polyprotein. Thus, it is an ideal target for developing antiviral small-molecule inhibitors. While rupintrivir, a potent small-molecule inhibitor of several picornavirus proteases, effectively inhibits GI.1 protease, it is an order of magnitude less effective against GII protease. Other GI.1 protease inhibitors also tend to be less effective against GII proteases. To understand the structural basis for the potency difference, we determined the crystal structures of proteases of GI.1, pandemic GII.4 (Houston and Sydney), and GII.3 in complex with rupintrivir. These structures show that the open substrate pocket in GI protease binds rupintrivir without requiring significant conformational changes, whereas, in GII proteases, the closed pocket flexibly extends, reorienting arginine-112 in the BII-CII loop to accommodate rupintrivir. Structures of R112A protease mutants with rupintrivir, coupled with enzymatic and inhibition studies, suggest R112 is involved in displacing both substrate and ligands from the active site, implying a role in the release of cleaved products during polyprotein processing. Thus, the primary determinant for differential inhibitor potency between the GI and GII proteases is the increased flexibility in the BII-CII loop of the GII proteases caused by the H-G mutation in this loop. Therefore, the inherent flexibility of the BII-CII loop in GII proteases is a critical factor to consider when developing broad-spectrum inhibitors for HuNoV proteases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structural and Mechanistic Advances in the Chemistry of Methyl-Coenzyme M Reductase (MCR)

Methane represents 34% of U.S. energy consumption and is a major greenhouse gas related to the global carbon cycle and energy production. However, current industrial practices significantly increase atmospheric methane levels, necessitating a deeper understanding of its biosynthesis and oxidation. Methyl-coenzyme M reductase (MCR) is central to biological methane metabolism, catalyzing the final step of methanogenesis and the first step in anaerobic methane oxidation. It is also a key target for strategies to capture and transform methane into value-added chemicals.The active site of MCR is a buried Ni-based cofactor only accessible by the substrates via a 50 Å long tunnel. Although the Ni(I) state is required to initiate catalysis, capturing this state remains a challenge for the current structural techniques. Recent advances in structural biology using X-ray Free-Electron Laser serial crystallography have provided insights into MCR's inactive Ni(II) state at room temperature and show promise for capturing its active Ni(I) form.Our team has established several critical aspects of the MCR mechanism using a combination of experimental and computational studies. MCR uses CH 3 -SCoM and CoBSH as substrates, producing methane and a disulfide product CoMSSCoB. Kinetic analysis showed that productive substrate binding requires CH 3 -SCoM to bind first, inducing conformational changes that optimize the active site for subsequent CoBSH binding. Following substrate binding, four proposed methane production/oxidation mechanisms were examined, establishing whether the reaction proceeds through an organometallic methyl-nickel(III), methyl anion ion, or methyl radical intermediate. Experimental measurements using CoBSH analogs successfully slowed the reaction, allowing for mechanistic insight that demonstrated the methyl radical pathway, where the initial interactions involve homolytic cleavage of the methyl-sulfur bond, generating a methyl radical that quickly abstracts the thiol hydrogen atom of CoBSH to form methane. Computational studies further confirmed that, compared to other mechanisms, the methyl radical mechanism is thermodynamically more favorable and accessible under physiological conditions.Spectroscopic and computational studies challenged the conventional understanding of substrate binding in MCR by proposing an alternative positioning of CH 3 -SCoM and CoMSSCoB in the active site pocket. The research suggested that CH 3 -SCoM (substrate) and CoMSSCoB (product) bind via their sulfonate groups to the Ni(I) center of cofactor F 430 . This binding allows for the reaction without substrate reorganization in the pocket but would require a long-range electron transfer. Altogether, the work summarized in this review reflects our current understanding of the enzyme's catalytic mechanism and structural dynamics. This is essential for developing efficient methane conversion technologies that could mitigate its environmental impact while harnessing energy-storage properties.

03 NATURAL GAS↗
DOE OSTI2023

Chemical Insights into the Formation of Colloidal Iridium Nanoparticles from In Situ X-ray Total Scattering: Influence of Precursors and Cations on the Reaction Pathway

Iridium nanoparticles are important catalysts for several chemical and energy conversion reactions. Studies of iridium nanoparticles have also been a key for the development of kinetic models of nanomaterial formation. However, compared to other metals such as gold or platinum, knowledge on the nature of prenucleation species and structural insights into the resultant nanoparticles are missing, especially for nanoparticles obtained from Ir$_x$Cl$_y$ precursors investigated here. We use in situ X-ray total scattering (TS) experiments with pair distribution function (PDF) analysis to study a simple, surfactant-free synthesis of colloidal iridium nanoparticles. The reaction is performed in methanol at 50 °C with only a base and an iridium salt as precursor. From different precursor salts–IrCl 3 , IrCl 4 , H 2 IrCl 6 , or Na 2 IrCl 6 –colloidal nanoparticles as small as Ir ~55 are obtained as the final product. The nanoparticles do not show the bulk iridium face-centered cubic ($fcc$) structure but show decahedral and icosahedral structures. The formation route is highly dependent on the precursor salt used. Using IrCl 3 or IrCl 4 , metallic iridium nanoparticles form rapidly from Ir$_x$Cl$_y$$^{n–}$ complexes, whereas using H 2 IrCl 6 or Na 2 IrCl 6 , the iridium nanoparticle formation follows a sudden growth after an induction period and the brief appearance of a crystalline phase. With H 2 IrCl 6 , the formation of different Ir$_n$ ($n$ = 55, 55, 85, and 116) nanoparticles depends on the nature of the cation in the base (LiOH, NaOH, KOH, or CsOH, respectively) and larger particles are obtained with larger cations. As the particles grow, the nanoparticle structure changes from partly icosahedral to decahedral. In conclusion, the results show that the synthesis of iridium nanoparticles from Ir$_x$Cl$_y$ is a valuable iridium nanoparticle model system, which can provide new compositional and structural insights into iridium nanoparticle formation and growth.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗