CIISB Research Highlights Archive

The mechanism of Renilla-type luciferase reaction and its inhibition.

Martin Marek and Zbyněk Prokop Research Group

Significance

The widely used coelenterazine-powered Renilla luciferase was discovered over 40 years ago, but the oxidative mechanism by which it generates blue photons remains unclear. Here we decipher Renilla-type catalysis through crystallographic, spectroscopic and computational experiments. Structures of ancestral and extant luciferases complexed with the substrate-like analogue azacoelenterazine or a reaction product were obtained, providing molecular snapshots of coelenterazine-to-coelenteramide oxidation. Bound coelenterazine adopts a Y-shaped conformation, enabling the deprotonated imidazopyrazinone component to attack O₂ via a radical charge-transfer mechanism. A high emission intensity is secured by an aspartate from a conserved proton-relay system, which protonates the excited coelenteramide product. Another aspartate on the rim of the catalytic pocket fine-tunes the electronic state of coelenteramide and promotes the formation of the blue light-emitting phenolate anion. The results obtained also reveal structural features distinguishing flash-type from glow-type bioluminescence, providing insights that will guide the engineering of next-generation luciferase‒luciferin pairs for ultrasensitive optical bioassays.

Schenkmayerova, A., Toul, M., Pluskal, D., Baatallah, R., Gagnot, G., Pinto, G.P., Santana, V.T., Stuchla, M., Neugebauer, P., Chaiyen, P., Damborsky, J., Bednar, D., Janin, Y.L., Prokop, Z. & Marek, M.: Catalytic mechanism for Renilla-type luciferases, Nat. Catal. (2023). https://doi.org/10.1038/s41929-022-00895-z

A new technique for the digital mapping of biomarkers in tissues based on desorption and counting intact gold nanoparticle (Au NP) tags using infrared laser ablation single - particle inductively coupled plasma mass spectrometry (IR LA SP ICP MS).

Jan Preisler Research Group

Significance

In contrast to conventional UV laser ablation, Au NPs are not disintegrated during the desorption process due to their low absorption at 2940 nm. A mass spectrometer detects up to 83% of Au NPs. The technique is demonstrated on mapping a proliferation marker, nuclear protein Ki-67, in three-dimensional (3D) aggregates of colorectal carcinoma cells, and the results are compared with confocal fluorescence microscopy and UV LA ICP MS. Precise counting of 20 nm Au NPs with a single-particle detection limit in each pixel by the new approach generates sharp distribution maps of a specific biomarker in the tissue. Advantageously, the desorption of Au NPs from regions outside the tissue is strongly suppressed. The developed methodology promises multiplex mapping of low-abundant biomarkers in numerous biological and medical applications using multielemental mass spectrometers.

Stiborek, M., Jindřichová, L., Meliorisová, S., Bednařík, A., Prysiazhnyi, V., Kroupa, J., Houška, P., Adamová, B., Navrátilová, J., Kanický, V., and Preisler, J.:

Infrared Laser Desorption of Intact Nanoparticles for Digital Tissue Imaging

Anal. Chem. 2022 94, 51, 18114 – 18121, https://doi.org/10.1021/acs.analchem.2c05216

Labdane-type terpenes are a large family of bioactive natural products. Their often-complex structures present challenges to semisynthesis and de novo chemical synthesis in search of analogs with improved properties. To enable new modifications of the well-known tricyclic terpene forskolin, we have developed a distinct and potentially general synthetic scheme for the preparation of analogs of complex labdanes.

Jakub Švenda Research Group

Significance

We report a new synthetic strategy for the flexible preparation of forskolin-like molecules. The approach is different from the previously published works and employs a convergent assembly of the tricyclic labdane-type core from pre-functionalized cyclic building blocks. Stereoselective Michael addition enabled the fragment coupling with excellent control over three newly created contiguous stereocenters, all-carbon quaternary centers included. Silyl enol ether-promoted ring-opening metathesis paired with ring closure were the other key steps enabling concise assembly of the tricyclic core. Late-stage functionalization sequences transformed the tricyclic intermediates into a set of different forskolin-like molecules. The modular nature of the synthetic scheme described herein has the potential to become a general platform for the preparation of analogs of forskolin and other complex tricyclic labdanes.

Szczepanik, P. M., Mikhaylov, A. A., Hylse, O., Kučera, R., Daďová, P., Nečas, M., Kubala, L., Paruch, K., and Švenda, J.:

Convergent Assembly of the Tricyclic Labdane Core Enables Synthesis of Diverse Forskolin-like Molecules, Angew. Chem. Int. Ed. 2022, on-line version e202213183, https://doi.org/10.1002/anie.202213183

Tau cooperativity by local microtubule lattice compaction

a, Schematics of the assay geometry. b, Quantification of cooperative binding of tau to taxol-lattice microtubules (mean ± s.d., n = 652 microtubules, 60 experiments, 95% confidence bounds, r² = 0.9633, gray), Hill–Langmuir equation fit (green). AU, arbitrary units. c, Fluorescence time-lapse micrographs showing microtubule lattice straightening (yellow arrow) upon formation of tau envelopes (green). Twenty nanomolar tau-mCherry was added at t = 0 s. Scale bar, 2 μm.

Zdeněk Lánský Research Group

Significance

Tau is an intrinsically disordered microtubule-associated protein (MAP) implicated in neurodegenerative disease. On microtubules, tau molecules segregate into two kinetically distinct phases, consisting of either independently diffusing molecules or interacting molecules that form cohesive ‘envelopes’ around microtubules. Envelopes differentially regulate lattice accessibility for other MAPs, but the mechanism of envelope formation remains unclear. Here we find that tau envelopes form cooperatively, locally altering the spacing of tubulin dimers within the microtubule lattice. Envelope formation compacted the underlying lattice, whereas lattice extension induced tau envelope disassembly. Investigating other members of the tau family, we find that MAP2 similarly forms envelopes governed by lattice spacing, whereas MAP4 cannot. Envelopes differentially biased motor protein movement, suggesting that tau family members could spatially divide the microtubule surface into functionally distinct regions. We conclude that the interdependent allostery between lattice spacing and cooperative envelope formation provides the molecular basis for spatial regulation of microtubule-based processes by tau and MAP2.

Valerie Siahaan, Ruensern Tan, Tereza Humhalova, Lenka Libusova, Samuel E. Lacey, Tracy Tan, Mariah Dacy, Kassandra M. Ori-McKenney, Richard J. McKenney, Marcus Braun & Zdenek Lansky

Microtubule lattice spacing governs cohesive envelope formation of tau family proteins

Na.t Chem. Biol., 18, 1224-1235 (2022): | https://doi.org/10.1038/s41589-022-01096-2

a Front and side views of the composite model with both monomers in rotational state 1. The two F₁/c₁₀-ring complexes, each augmented by three copies of the phylum-specific p18 subunit, are tied together at a 60°-angle. The membrane-bound F_o region displays a unique architecture and is composed of both conserved and phylum-specific subunits.
b Side view of the F_o region showing the lumenal interaction of the ten-stranded β-barrel of the c-ring (grey) with ATPTB12 (pale blue). The lipid-filled peripheral F_o cavity is indicated.
c Close-up view of the bound lipids within the peripheral F_o cavity with cryo-EM density shown.
d Top view into the decameric c-ring with a bound pyrimidine ribonucleoside triphosphate, assigned as UTP, although not experimentally detected. Map density shown in transparent blue, interacting residues shown.

Alena Zíková and Alexey Amunts Research Group

Significance

Mitochondrial ATP synthase forms stable dimers arranged into oligomeric assemblies that generate the inner-membrane curvature essential for efficient energy conversion. Here, we report cryo-EM structures of the intact ATP synthase dimer from Trypanosoma brucei in ten different rotational states. The model consists of 25 subunits, including nine lineage-specific, as well as 36 lipids. The rotary mechanism is influenced by the divergent peripheral stalk, conferring a greater conformational flexibility. Proton transfer in the lumenal half-channel occurs via a chain of five ordered water molecules. The dimerization interface is formed by subunit-g that is critical for interactions but not for the catalytic activity. Although overall dimer architecture varies among eukaryotes, we find that subunit-g together with subunit-eform an ancestral oligomerization motif, which is shared between the trypanosomal and mammalian lineages. Therefore, our data defines the subunit-g/e module as a structural component determining ATP synthase oligomeric assemblies.

Gahura, O., Mühleip, A., Hierro-Yap, C., Panicucci, B, Jain, M., Hollaus, D., Slapničková, M., Zíková, A. & Amunts, A.: An ancestral interaction module promotes oligomerization in divergent mitochondrial ATP synthases, Nature Comm. (2022) 13:5989,https://doi.org/10.1038/s41467-022-33588-z

Cryo-EM structures of mouse full-length Dicer alone and in complex with Dicerdpre-miRNA reveal the molecular basis of locking Dicer in the closed state
(A) Domain architecture of full-length mouse Dicer numbered at boundaries.
(B) Overall structure of the full-length mouse Dicer, shown as 3.8-A ̊ cryo-EM density map and ribbon representations in two orthogonal views. Interface between the HEL1 and RNase IIIb domains is highlighted by a box.
(C) Overall structure of the full-length mouse Dicer-RNA complex, shown as 4.2-A ̊ cryo-EM density map and ribbon representations in two orthogonal views.

Richard Štefl and Petr Svoboda Research Groups

Significance

MicroRNA (miRNA) and RNA interference (RNAi) pathways rely on small RNAs produced by Dicer endonucle- ases. Mammalian Dicer primarily supports the essential gene-regulating miRNA pathway, but how it is spe- cifically adapted to miRNA biogenesis is unknown. We show that the adaptation entails a unique structural role of Dicer’s DExD/H helicase domain. Although mice tolerate loss of its putative ATPase function, the com- plete absence of the domain is lethal because it assures high-fidelity miRNA biogenesis. Structures of murine Dicerd–miRNA precursor complexes revealed that the DExD/H domain has a helicase-unrelated structural function. It locks Dicer in a closed state, which facilitates miRNA precursor selection. Transition to a cleav- age-competent open state is stimulated by Dicer-binding protein TARBP2. Absence of the DExD/H domain or its mutations unlocks the closed state, reduces substrate selectivity, and activates RNAi. Thus, the DExD/H domain structurally contributes to mammalian miRNA biogenesis and underlies mechanistical partitioning of miRNA and RNAi pathways.

Zapletal, D., Taborska, E., Pasulka, J., Malik, R., Kubicek, K., Zanova, M., Much, Ch., Sebesta, M. Buccheri, V., Horvat, F., Jenickova, I., Prochazkova, M., Prochazka, J., Pinkas, M., Novacek, J., Joseph, D. F., Sedlacek R., Bernecky C., O’Carrol, D., Stefl. R., and Svoboda, P.: Structural and functional basis of mammalian microRNA biogenesis by Dicer

Mol. Cell 2022, 82, 4064–4079, https://doi.org/10.1016/j.molcel.2022.10.010