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1. Segmented flow generator for serial crystallography at the European X-ray free electron laser

   https://doi.org/10.1038/s41467-020-18156-7  

   Echelmeier, Austin; Cruz_Villarreal, Jorvani; Messerschmidt, Marc; Kim, Daihyun; Coe, Jesse D; Thifault, Darren; Botha, Sabine; Egatz-Gomez, Ana; Gandhi, Sahir; Brehm, Gerrit; et al (December 2020, Nature Communications)

   Abstract Serial femtosecond crystallography (SFX) with X-ray free electron lasers (XFELs) allows structure determination of membrane proteins and time-resolved crystallography. Common liquid sample delivery continuously jets the protein crystal suspension into the path of the XFEL, wasting a vast amount of sample due to the pulsed nature of all current XFEL sources. The European XFEL (EuXFEL) delivers femtosecond (fs) X-ray pulses in trains spaced 100 ms apart whereas pulses within trains are currently separated by 889 ns. Therefore, continuous sample delivery via fast jets wastes >99% of sample. Here, we introduce a microfluidic device delivering crystal laden droplets segmented with an immiscible oil reducing sample waste and demonstrate droplet injection at the EuXFEL compatible with high pressure liquid delivery of an SFX experiment. While achieving ~60% reduction in sample waste, we determine the structure of the enzyme 3-deoxy-D-manno-octulosonate-8-phosphate synthase from microcrystals delivered in droplets revealing distinct structural features not previously reported. 

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2. Evidence for the chemical mechanism of RibB (3,4-dihydroxy-2-butanone 4-phosphate synthase) of riboflavin biosynthesis.

   Nikola Kenjić, Kathleen M. (July 2022, Journal of the American Chemical Society)

   RibB (3,4-dihydroxy-2-butanone 4-phosphate synthase) is a magnesium-dependent enzyme that excis-es the C4 of D-ribulose-5-phosphate (D-Ru5P) as formate. This chemistry forms the four-carbon sub-strate for RibE (lumazine synthase) that is incorporated into the xylene moiety of lumazine and ulti-mately the riboflavin isoalloxazine. The reaction was first identified in studies by Bacher and cowork-ers in the early 1990s and a chemical mechanism hypothesis offered by these researchers has become the consensus mechanism despite minimal direct evidence. In addition, X-ray crystal structures of RibB typically show two metal ions when solved in the presence of non-native metals and/or liganding non-substrate analogues and the concensus hypothetical mechanism has incorporated this cofactor set. We have used a variety of biochemical approaches to further characterize the chemistry catalyzed by RibB from Vibrio cholera (VcRibB). We show that full activity is achieved at metal ion concentra-tions equal to the enzyme concentration indicating that only one metal ion is required for catalysis. This was confirmed from EPR of the enzyme reconstituted with manganese and crystal structures ob-tained from soaking with the native substrate, D-Ru5P. These data definitively show the involvement of a single active site metal ion. The slow rate of turnover of VcRibB was used to identify two transient species prior to the formation of products using acid quench of single turnover reactions in combina-tion with NMR for singly and fully 13C-labelled D-Ru5P. The data indicate that dehydration of C1 forms the first transient species that then undergoes rearrangement by a 1,2 migration that fuses C5 to C3 and renders C4 hydrated as a gem diol that is poised for elimination as formate. Time-dependent Mn2+ soaks of VcRibB-D-Ru5P co-crystals provided structures that show accumulation in crystallo of the same intermediate states as observed with acid-quench and NMR. Collectively these data reveal for the first time crucial transient chemical states in the mechanism of RibB. 

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3. Capturing ribosomal structures in cellular extracts with cryoPRISM: A purification-free cryoEM approach reveals novel structural states

   https://doi.org/10.1073/pnas.2521210123  

   May, Mira B; Lopez-Perez, Gabriella S; Davis, Joseph H (March 2026, Proceedings of the National Academy of Sciences)

   Structural analyses of ribosomes by single particle cryogenic electron microscopy (cryoEM) have traditionally relied on purified or reconstituted samples, with particles often trapped in desired states using genetic, pharmacological, or biochemical perturbations. While informative, such in vitro methods often fail to capture the full diversity of structural states and associated protein factors present in cells. In contrast, in situ cryoelectron tomography preserves cellular context but is limited by low throughput and modest resolution. Here, we present cryoPRISM (purification-free ribosome imaging from subcellular mixtures), a rapid ex vivo workflow encompassing cell lysis, vitrification, and image analysis methods for high-resolution analyses of ribosomal structures directly from cell lysates. Applying cryoPRISM inEscherichia coli, we resolved more than 20 distinct ribosomal states spanning assembly, translation initiation, elongation, trans-translation, and quiescence, including a novel configuration of EF-G bound to idle ribosomes with the ribosome hibernation factor ribosome-associated inhibitor A. Given its speed, accessibility, and ability to preserve native interactions and structural heterogeneity, we anticipate that cryoPRISM will be broadly applicable for uncovering ribosomal biology across diverse organisms and conditions. 

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4. Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase

   https://doi.org/10.1021/jacsau.5c00756  

   Yehorova, Dariia; Alansson, Nikolas; Shen, Ruidan; Denson, Joshua M; Robinson, Michael; Risso, Valeria A; Ramirez_Molina, Nuria; Loria, J Patrick; Gaucher, Eric A; Sanchez-Ruiz, Jose M; et al (December 2025, JACS Au)

   Protein tyrosine phosphatases (PTPs) are a family of enzymes that play important roles in regulating cellular signaling pathways. The activity of these enzymes is regulated by the motion of a catalytic loop that places a critical conserved aspartic acid side chain into the active site for acid–base catalysis upon loop closure. These enzymes also have a conserved phosphate-binding loop that is typically highly rigid and forms a well-defined anion-binding nest. The intimate links between loop dynamics and chemistry in these enzymes make PTPs an excellent model system for understanding the role of loop dynamics in protein function and evolution. In this context, archaeal PTPs, which have often evolved in extremophilic organisms, are highly understudied, despite their unusual biophysical properties. We present here an engineered chimeric PTP (ShufPTP) generated by shuffling the amino acid sequence of five extant hyperthermophilic archaeal PTPs. Despite ShufPTP’s high sequence similarity to its natural counterparts, it presents a suite of unique properties, including high flexibility of the phosphate binding P-loop, facile oxidation of the active-site cysteine, mechanistic promiscuity, and, most notably, hyperthermostability, with a denaturation temperature likely >130 °C (>8 °C higher than the highest recorded growth temperature of any archaeal strain). Our combined structural, biochemical, biophysical, and computational analysis provides insight both into how small steps in evolutionary space can radically modulate the biophysical properties of an enzyme and showcases the tremendous potential of archaeal enzymes for biotechnology, to generate novel enzymes capable of operating under extreme conditions. 

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5. Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis

   https://doi.org/10.1021/jacs.2c03376  

   Kenjić, Nikola; Meneely, Kathleen M.; Wherritt, Daniel J.; Denler, Melissa C.; Jackson, Timothy A.; Moran, Graham R.; Lamb, Audrey L. (July 2022, Journal of the American Chemical Society)

   RibB (3,4-dihydroxy-2-butanone 4-phosphate synthase) is a magnesium-dependent enzyme that excises the C4 of d-ribulose-5-phosphate (d-Ru5P) as formate. RibB generates the four-carbon substrate for lumazine synthase that is incorporated into the xylene moiety of lumazine and ultimately the riboflavin isoalloxazine. The reaction was first identified by Bacher and co-workers in the 1990s, and their chemical mechanism hypothesis became canonical despite minimal direct evidence. X-ray crystal structures of RibB typically show two metal ions when solved in the presence of non-native metals and/or liganding non-substrate analogues, and the consensus hypothetical mechanism has incorporated this cofactor set. We have used a variety of biochemical approaches to further characterize the chemistry catalyzed by RibB from Vibrio cholera (VcRibB). We show that full activity is achieved at metal ion concentrations equal to the enzyme concentration. This was confirmed by electron paramagnetic resonance of the enzyme reconstituted with manganese and crystal structures liganded with Mn2+ and a variety of sugar phosphates. Two transient species prior to the formation of products were identified using acid quench of single turnover reactions in combination with NMR for singly and fully 13C-labeled d-Ru5P. These data indicate that dehydration of C1 forms the first transient species, which undergoes rearrangement by a 1,2 migration, fusing C5 to C3 and generating a hydrated C4 that is poised for elimination as formate. Structures determined from time-dependent Mn2+ soaks of VcRibB-d-Ru5P crystals show accumulation in crystallo of the same intermediates. Collectively, these data reveal for the first time crucial transient chemical states in the mechanism of RibB. 

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