Phaser crystallographic software

Integrating immune library probing with structure-based computational design to develop potent neutralizing nanobodies against emerging SARS-CoV-2 variants

To generate antibodies (Abs) against SARS-CoV-2 emerging variants, we integrated multiple tools and engineered molecules with excellent neutralizing breadth and potency. Initially, the screening of an immune library identified a nanobody (Nb), termed Nb4, specific to the receptor-binding domain (RBD) of the Omicron BA.1 variant. A Nb4-derived heavy chain antibody (hcAb4) recognized the spike (S) of the Wuhan, Beta, Delta, Omicron BA.1, and BA.5 SARS-CoV-2 variants. A high-resolution crystal structure of the Nb4 variable (VHH) domain in complex with the SARS-CoV-2 RBD (Wuhan) defined the Nb4 binding mode and interface. The Nb4 VHH domain grasped the RBD and covered most of its outer face, including the core and the receptor-binding motif (RBM), which was consistent with hcAb4 blocking RBD binding to the SARS-CoV-2 receptor. In mouse models, a humanized hcAb4 showed therapeutic potential and prevented the replication of SARS-CoV-2 BA.1 virus in the lungs of the animals. In vitro, hcAb4 neutralized Wuhan, Beta, Delta, Omicron BA.1, and BA.5 viral variants, as well as the BQ.1.1 subvariant, but showed poor neutralization against the Omicron XBB.1.5. Structure-based computation of the RBD-Nb4 interface identified three Nb4 residues with a reduced contribution to the interaction with the XBB.1.5 RBD. Site-saturation mutagenesis of these residues resulted in two hcAb4 mutants with enhanced XBB.1.5 S binding and virus neutralization, further improved by mutant Nb4 trimers. This research highlights an approach that combines library screening, Nb engineering, and structure-based computational predictions for the generation of SARS-CoV-2 Omicron-specific Abs and their adaptation to emerging variants.

The crystal structure of the toxin EspC from enteropathogenic Escherichia coli reveals the mechanism that governs host cell entry and cytotoxicity

Enteropathogenic E. coli (EPEC) is a significant cause of diarrhea, leading to high infant mortality rates. A key toxin produced by EPEC is the EspC autotransporter, which is regulated alongside genes from the locus of enterocyte effacement (LEE), which collectively result in the characteristic attaching and effacing lesions on the intestinal epithelium. In this study, we present the crystal structure of the EspC passenger domain (αEspC) revealing a toxin comprised a serine protease attached to a large β-helix with additional subdomains. Using various modified EspC expression constructs, alongside type III secretion system-mediated cell internalization assays, we dissect how the αEspC structural features enable toxin entry into the intestinal epithelium to cause cell cytotoxicity.

Design of orthogonal constant domain interfaces to aid proper heavy/light chain pairing of bispecific antibodies

The correct pairing of cognate heavy and light chains is critical to the efficient manufacturing of IgG-like bispecific antibodies (bsAbs) from a single host cell. We present a general solution for the elimination of heavy chain (HC):light chain (LC) mispairs in bsAbs with κ LCs via the use of two orthogonal constant domain (CH1:Cκ ) interfaces comprising computationally designed amino acid substitutions. Substitutions were designed by Rosetta to introduce novel hydrogen bond (H-bond) networks at the CH1:Cκ interface, followed by Rosetta energy calculations to identify designs with enhanced pairing specificity and interface stability. Our final design, featuring a total of 11 amino acid substitutions across two Fab constant regions, was tested on a set of six IgG-like bsAbs featuring a diverse set of unmodified human antibody variable domains. Purity assessments showed near-complete elimination of LC mispairs, including in cases with high baseline mispairing with wild-type constant domains. The engineered bsAbs broadly recapitulated the antigen-binding and biophysical developability properties of their monospecific counterparts and no adverse immunogenicity signal was identified by an in vitro assay. Fab crystal structures containing engineered constant domain interfaces revealed no major perturbations relative to the wild-type coordinates and validated the presence of the designed hydrogen bond interactions. Our work enables the facile assembly of independently discovered IgG-like bispecific antibodies in a single-cell host and demonstrates a streamlined and generalizable computational and experimental workflow for redesigning conserved protein:protein interfaces.

Nipocalimab, an immunoselective FcRn blocker that lowers IgG and has unique molecular properties

Nipocalimab is a human immunoglobulin G (IgG)1 monoclonal antibody that binds to the neonatal Fc receptor (FcRn) with high specificity and high affinity at both neutral (extracellular) and acidic (intracellular) pH, resulting in the reduction of circulating IgG levels, including those of pathogenic IgG antibodies. Here, we present the molecular, cellular, and nonclinical characteristics of nipocalimab that support the reported clinical pharmacology and potential clinical application in IgG-driven, autoantibody- and alloantibody-mediated diseases. The crystal structure of the nipocalimab antigen binding fragment (Fab)/FcRn complex reveals its binding to a unique epitope on the IgG binding site of FcRn that supports the observed pH-independent high-binding affinity to FcRn. Cell-based and in vivo studies demonstrate concentration/dose- and time-dependent FcRn occupancy and IgG reduction. Nipocalimab selectively reduces circulating IgG levels without detectable effects on other adaptive and innate immune functions. In vitro experiments and in vivo studies in mice and cynomolgus monkeys generated data that align with observations from clinical studies of nipocalimab in IgG autoantibody- and alloantibody-mediated diseases.

Tension-induced suppression of allosteric conformational changes coordinates kinesin-1 stepping

Kinesin-1 walks along microtubules by alternating ATP hydrolysis and movement of its two motor domains ("head"). The detached head preferentially binds to the forward tubulin-binding site after ATP binds to the microtubule-bound head, but the mechanism preventing premature microtubule binding while the partner head awaits ATP remains unknown. Here, we examined the role of the neck linker, the segment connecting two heads, in this mechanism. Structural analyses of the nucleotide-free head revealed a bulge just ahead of the neck linker's base, creating an asymmetric constraint on its mobility. While the neck linker can stretch freely backward, it must navigate around this bulge to extend forward. We hypothesized that increased neck linker tension suppresses premature binding of the tethered head, which was supported by molecular dynamics simulations and single-molecule fluorescence assays. These findings demonstrate a tension-dependent allosteric mechanism that coordinates the movement of two heads, where neck linker tension modulates the allosteric conformational changes rather than directly affecting the nucleotide state.

Deep Mutational Scanning of an Engineered High-affinity Ligand of the poly(A) Binding Protein MLLE Domain

The MLLE domain is a peptide-binding domain found in the poly(A) binding protein (PABP) and the ubiquitin protein E3 ligase N-recognin 5 (UBR5) that recognizes a conserved motif, named PABP-interacting motif 2 (PAM2). The majority of PAM2 sequences bind to MLLE domains with low-micromolar affinity. Here, we designed a chimeric PAM2 peptide termed super PAM2 (sPAM2) by combining classical and trinucleotide repeat-containing 6 (TNRC6)-like binding modes to create a superior binder for the MLLE domain. The crystal structure of the PABPC1 MLLE-sPAM2 complex shows a crucial role of conserved sPAM2 leucine, phenylalanine and tryptophan residues in the interaction. We used deep mutational scanning (DMS) coupled with isothermal titration calorimetry (ITC) to characterize the specificity profiles for PABPC1 and UBR5 MLLE. The best sPAM2 sequence binds to PABPC1 MLLE with low-nanomolar affinity and nearly 20-fold more tightly than the best natural PAM2 sequence. This suggests that the affinities of natural PAM2 sequences are tuned to control their binding to PABPC1 and UBR5. Our study will aid in the discovery of new PAM2-containing proteins (PACs) and facilitate in vivo studies of PAM2-mediated cellular pathways.

Structure and dynamics of Proteus vulgaris tryptophan indole-lyase complexes with l-ethionine and l-alanine

Tryptophan indole-lyase (TIL; [E.C. 4.1.99.1]) is a pyridoxal-5'-phosphate (PLP) dependent enzyme that catalyzes the reversible β-elimination of indole from l-tryptophan. l-Alanine and l-ethionine are TIL competitive inhibitors that form stable quinonoid complexes with λmax ∼508 nm. We have now determined the X-ray crystal structure of the tetrameric TIL complexes with l-alanine and l-ethionine, with either K+ or Na+ in the cation binding site. For the K+-form, the structures show a mixture of external aldimine and quinonoid complexes, with both open and closed active site conformations. However, the Na+-form exhibits noncovalent and external aldimine complexes in only open active site conformations. Stopped-flow kinetics of l-ethionine binding show that the Na+-form of TIL reacts much more slowly than the K+-form. The l-alanine and l-ethionine complexes of TIL are affected by hydrostatic pressure, suggesting that solvation contributes to the reaction. As pressure increases, the peak at 508 nm decreases, and a new peak at 344 nm appears. These changes are reversible when pressure is released. The 344 nm species could be either a gem-diamine or an enolimine tautomer of the external aldimine. We measured the fluorescence spectrum of the complex under pressure to differentiate these structures. When excited at either 290 or 325 nm, the complex emits at 400 nm, establishing that it is a gem-diamine complex. This peak does not form when the Na+-form of TIL complexed with l-ethionine is subjected to high pressure. Pressure jumps for the TIL-K+-l-ethionine complex measured at 508 nm result in pressure dependent relaxation rate constants. The relaxations show a large activation volume in the direction of quinonoid intermediate formation, suggesting that it is coupled with a conformational change. These results provide new insights into the dynamics of ligand binding to TIL.

A high affinity Sybody blocks Cofilin-1 binding to F-actin in vitro and in cancer cells

Upregulation of the actin-severing protein Cofilin-1 is implicated in enhancing malignancy of various cancer types by promoting actin turnover and increasing cellular motility. Despite the importance of targeting Cofilin-1, currently there is a lack of inhibitors specifically targeting its actin-severing activity. To address this issue, we generated synthetic anti-Cofilin-1 nanobodies (Sybodies) that interfere with human Cofilin-1 binding to filamentous actin. We identified four high affinity Sybodies against human Cofilin-1 with dissociation constants (KD) in the nanomolar range that inhibited G-actin sequestration, and actin-severing activity of Cofilin-1 in vitro. Notably, Sybody B12, with the lowest KD of approximately 27 nM, competitively blocked actin binding to Cofilin-1, and also inhibited G-actin sequestration of murine Cofilin-1. The crystal structure of the Sybody-B12-Cofilin-1 complex, resolved at 1.8 Å, revealed that Sybody B12 binds to the G-actin binding site of Cofilin-1, showing that Sybody B12 engages the same binding site on Cofilin-1 as actin. Consistently, transient expression of mPlum-tagged Sybody B12 in human H1299 lung cancer cells inhibited the formation of enhanced green fluorescent protein (EGFP)-Cofilin-actin rods. Notably, stable expression of Sybody B12 did not affect viability of H1299 cells, and no compensatory up-regulation of Cofilin-2 or actin-depolymerization factor (ADF) mRNA were detectable in Sybody B12 expressing H1299 cells. Together, these findings suggest that Sybody B12 exhibits a strong potential as tool for inhibiting the interaction of Cofilin-1 with actin. In addition, it could serve as a promising lead structure for designing Cofilin-1 inhibitors in silico.

The RBR E3 ubiquitin ligase HOIL-1 can ubiquitinate diverse non-protein substrates in vitro

HOIL-1 is a RING-between-RING-family E3 ubiquitin ligase and a component of the linear ubiquitin chain assembly complex. Although most E3 ubiquitin ligases conjugate ubiquitin to protein lysine sidechains, HOIL-1 has also been reported to ubiquitinate hydroxyl groups in protein serine and threonine sidechains and glucosaccharides, such as glycogen and its building block maltose, in vitro. However, HOIL-1 substrate specificity is currently poorly defined. Here, we show that HOIL-1 is unable to ubiquitinate lysine but can efficiently ubiquitinate serine and a variety of model and physiologically relevant di- and monosaccharides in vitro. We identify a critical catalytic histidine residue, His510, in the flexible catalytic site of HOIL-1 that enables this O-linked ubiquitination and prohibits ubiquitin discharge onto lysine sidechains. We use HOIL-1's in vitro non-proteinaceous ubiquitination activity to produce preparative amounts of different ubiquitinated saccharides that can be used as tool compounds and standards in the rapidly emerging field of non-proteinaceous ubiquitination. Finally, we report an engineered, constitutively active HOIL-1 variant that simplifies in vitro generation of ubiquitinated saccharides.

Structural analysis of EPOP BC-box binding to the elongin BC complex

The elongin BC complex (ELOBC) interacts with BC-box-containing proteins and plays a role in various cellular processes, including transcriptional regulation and ubiquitination. Elongin BC and polycomb repressive complex 2-associated protein (EPOP) contains a BC-box motif in its N-terminal region and influences cancer cell proliferation and differentiation. A previous study showed that a BC-box containing an EPOP-derived peptide suppresses cancer cell growth and induces apoptosis by disrupting the interaction between the ELOBC and its partner proteins. Here, we report the crystal structure of the EPOP BC-box peptide bound to the ELOBC and compare it with the structures of other BC-box-containing proteins in complex with the ELOBC. The overall structure of interactions between the BC-box and the ELOC was similar across different complexes, indicating a conserved binding mode. Our structural analysis revealed that the strictly conserved leucine residue (Leu40) within the BC-box of EPOP, which was previously suggested to be critical for interactions between the BC-box and the ELOC, was deeply embedded in the hydrophobic pocket of the ELOC protein. This study provided structural insights into BC-box-mediated protein-protein interactions and may serve as a fundamental resource for developing small molecules that modulate the interactions between ELOBC and BC-box-containing proteins.

Structural insight into ligand interactions of thymidylate synthase from white spot syndrome virus

White spot syndrome virus (WSSV) is one of the deadliest crustacean pathogens, causing huge economic loss in global shrimp industry. WSSV encodes a thymidylate synthase (wTS) that is essential for DNA replication and viral proliferation, serving as a promising drug target against WSSV infections. To aid drug design, we solved wTS structures in complex with dUMP and dUMP/raltitrexed, at 2.28 Å and 1.43 Å resolutions, respectively. wTS forms a homodimer and each ligand-binding cavity is contributed by both monomers. In wTS-dUMP binary structure, the protein adopts an open conformation, with dUMP bound to the cavity through extensive hydrogen bonds and salt bridges. In wTS-dUMP-raltitrexed ternary structure, the protein exhibits a closed conformation; the TS inhibitor raltitrexed contacts intensively with the protein and dUMP via hydrogen bonding and hydrophobic interactions, resulting in the covalent bond formation between dUMP and the catalytic cysteine. Pairwise comparison of the structures of wTS and shrimp TS shows that they share similarity in the dUMP bound forms but differ significantly in the dUMP/raltitrexed bound forms: wTS presents a more tightly closed conformation than shrimp TS, showing more interactions with raltitrexed. As the ligand binding residues are conserved between the two proteins, the observed structural differences are supposed to originate from the variations in other vicinity residues. In sum, the comparative structural study on the homologous viral and host proteins would boost the opportunity to design wTS-specific inhibitors against WSSV infections.

Structural Plasticity of Plasmodium falciparum Plasmepsin X to Accommodate Binding of Potent Macrocyclic Hydroxyethylamine Inhibitors

Plasmodium falciparum plasmepsin X (PMX) has become a target of choice for the development of new antimalarial drugs due to its essential role across the parasite life cycle. Here we describe the 1.7 Å crystallographic structure of PMX noncovalently bound to a potent macrocyclic peptidomimetic inhibitor (7k) possessing a hydroxyethylamine (HEA) scaffold. Upon 7k binding, the enzyme adopts a novel conformation, with significant involvement of the S2'S2 loop (M526-H536) and the S2 flap (F311-G314). This results in partial closure of the active site with widespread interactions in both the prime (S') and the non-prime (S) sites of PMX. The catalytic aspartate residues D266 and D467 directly interact with the HEA pharmacophore. Docking of a 7k derivative, compound 7a, highlights a region in the S3 pocket near the S3 flexible loop (H242-F248) that may be key for ligand stabilisation. The dynamic nature of PMX and its propensity to undergo distinct types of induced fit upon inhibitor binding enables generation of potent inhibitors that target this essential malarial aspartic protease.

Mechanism and application of thiol-disulfide redox biosensors with a fluorescence-lifetime readout

Genetically encoded biosensors with changes in fluorescence lifetime (as opposed to fluorescence intensity) can quantify small molecules in complex contexts, even in vivo. However, lifetime-readout sensors are poorly understood at a molecular level, complicating their development. Although there are many sensors that have fluorescence-intensity changes, there are currently only a few with fluorescence-lifetime changes. Here, we optimized two biosensors for thiol-disulfide redox (RoTq-Off and RoTq-On) with opposite changes in fluorescence lifetime in response to oxidation. Using biophysical approaches, we showed that the high-lifetime states of these sensors lock the chromophore more firmly in place than their low-lifetime states do. Two-photon fluorescence lifetime imaging of RoTq-On fused to a glutaredoxin (Grx1) enabled robust, straightforward monitoring of cytosolic glutathione redox state in acute mouse brain slices. The motional mechanism described here is probably common and may inform the design of other lifetime-readout sensors; the Grx1-RoTq-On fusion sensor will be useful for studying glutathione redox in physiology.

Architecture of Pseudomonas aeruginosa glutamyl-tRNA synthetase defines a subfamily of dimeric class Ib aminoacyl-tRNA synthetases

The aminoacyl-tRNA synthetases (AaRSs) are an ancient family of structurally diverse enzymes that are divided into two major classes. The functionalities of most AaRSs are inextricably linked to their oligomeric states. While GluRSs were previously classified as monomers, the current investigation reveals that the form expressed in Pseudomonas aeruginosa is a rotationally pseudosymmetrical homodimer featuring intersubunit tRNA binding sites. Both subunits display a highly bent, "pipe strap" conformation, with the anticodon binding domain directed toward the active site. The tRNA binding sites are similar in shape to those of the monomeric GluRSs, but are formed through an approximately 180-degree rotation of the anticodon binding domains and dimerization via the anticodon and D-arm binding domains. As a result, each anticodon binding domain is poised to recognize the anticodon loop of a tRNA bound to the adjacent protomer. Additionally, the anticodon binding domain has an α-helical C-terminal extension containing a conserved lysine-rich consensus motif positioned near the predicted location of the acceptor arm, suggesting dual functions in tRNA recognition. The unique architecture of PaGluRS broadens the structural diversity of the GluRS family, and member synthetases of all bacterial AaRS subclasses have now been identified that exhibit oligomerization.

Enzymatic combinatorial synthesis of E-64 and related cysteine protease inhibitors

E-64 is an irreversible cysteine protease inhibitor prominently used in chemical biology and drug discovery. Here we uncover a nonribosomal peptide synthetase-independent biosynthetic pathway for E-64, which is widely conserved in fungi. The pathway starts with epoxidation of fumaric acid to the warhead (2S,3S)-trans-epoxysuccinic acid with an Fe(II)/α-ketoglutarate-dependent oxygenase, followed by successive condensation with an L-amino acid by an adenosine triphosphate grasp enzyme and with an amine by the fungal example of amide bond synthetase. Both amide bond-forming enzymes display notable biocatalytic potential, including scalability, stereoselectivity toward the warhead and broader substrate scopes in forming the amide bonds. Biocatalytic cascade with these amide bond-forming enzymes generated a library of cysteine protease inhibitors, leading to more potent cathepsin inhibitors. Additionally, one-pot reactions enabled the preparative synthesis of clinically relevant inhibitors. Our work highlights the importance of biosynthetic investigation for enzyme discovery and the potential of amide bond-forming enzymes in synthesizing small-molecule libraries.

Discovery of ATX968: An Orally Available Allosteric Inhibitor of DHX9

DHX9 is an RNA/DNA helicase integral in the maintenance of genome stability that has emerged as an attractive target for oncology drug discovery. Disclosed herein is the discovery and optimization of a series of DHX9 inhibitors. Compound 1 was identified as a partial inhibitor of DHX9 ATPase activity but a full inhibitor of unwinding activity. Binding of 1 to a pocket distinct from the ATP binding site was confirmed by X-ray crystallography, enabling structure-based drug optimization. During this optimization, a sulfur-halogen bond was identified that increased on-target residence time without impacting equilibrium binding affinity. Analysis shows that cell potency more closely correlates with residence time than with equilibrium measurements of binding affinity or biochemical potency. Further optimization of potency and ADME properties led to the identification of ATX968, a potent and selective DHX9 inhibitor that is efficacious in a tumor xenograft model of microsatellite instability-high (MSI-H) colorectal cancer.

Derivatives of the Clinically Used HIF Prolyl Hydroxylase Inhibitor Desidustat Are Efficient Inhibitors of Human γ-Butyrobetaine Hydroxylase

The 2-oxoglutarate (2OG)/Fe(II)-dependent γ-butyrobetaine hydroxylase (BBOX) catalyzes the final step in l-carnitine biosynthesis, i.e., stereoselective C-3 oxidation of γ-butyrobetaine (GBB). BBOX inhibition is a validated clinical strategy to modulate l-carnitine levels and to enhance cardiovascular efficiency. Reported BBOX inhibitors, including the clinically used cardioprotective agent Mildronate, manifest moderate inhibitory activity in vitro, limited selectivity, and/or unfavorable physicochemical properties, indicating a need for improved BBOX inhibitors. We report that the clinically used hypoxia-inducible factor-α prolyl residue hydroxylase (PHD) inhibitors Desidustat, Enarodustat, and Vadadustat efficiently inhibit isolated recombinant BBOX, suggesting that BBOX inhibition by clinically used PHD inhibitors should be considered as a possible off-target effect. Structure-activity relationship studies on the Desidustat scaffold enabled development of potent BBOX inhibitors that manifest high levels of selectivity for BBOX inhibition over representative human 2OG oxygenases, including PHD2. The Desidustat derivatives will help to enable investigations into the biological roles of l-carnitine and the therapeutic potential of BBOX inhibition.

Structure-Guided Design of ISOX-DUAL-Based Degraders Targeting BRD4 and CBP/EP300: A Case of Degrader Collapse

Degraders with dual activity against BRD4 and CBP/EP300 were designed. A structure-guided design approach was taken to assess and test potential exit vectors on the dual BRD4 and CBP/EP300 inhibitor, ISOX-DUAL. Candidate degrader panels revealed that VHL-recruiting moieties could mediate dose-responsive ubiquitination of BRD4. A panel of CRBN-recruiting thalidomide-based degraders was unable to induce ubiquitination or degradation of target proteins. High-resolution protein cocrystal structures revealed an unexpected interaction between the thalidomide moiety and Trp81 on the first bromodomain of BRD4. The inability to form a ternary complex provides a potential rationale for the lack of degrader activity with these compounds, some of which have remarkable affinities close to those of (+)-JQ1, as low as 65 nM in a biochemical assay, vs 1.5 μM for their POI ligand, ISOX-DUAL. Such a "degrader collapse" may represent an under-reported mechanism by which some putative degrader molecules are inactive with respect to target protein degradation.

The disease-linked R336C mutation in cystathionine β-synthase disrupts communication with the PLP cofactor, yet maintains the enzyme's overall structural integrity

Cystathionine β-synthase (CBS) is a pyridoxal-phosphate (PLP)-dependent enzyme essential for the reverse transsulfuration pathway, where homocysteine and serine combine to form cystathionine, the immediate precursor of cysteine. Mutations in the CBS gene cause homocystinuria, a disorder associated with intellectual disability, multisystem complications, and reduced life expectancy. The CBS p.R336C mutation, linked to severe pyridoxine non-responsiveness, results in reduced enzyme activity, previously attributed to protein instability and weakened substrate and PLP binding. To clarify the effects of the pathological R336C mutation, we performed biochemical, biophysical, and crystallographic analyses, as well as molecular dynamics simulations. Our findings show that the R336C mutation minimally impacts the structural environment around residue 336, does not cause enzyme misfolding, and does not impair the binding of PLP or the allosteric activator S-adenosylmethionine (AdoMet) binding. Instead, the mutation induces subtle reorientations in nearby hydrophobic residues, including F185 and Y381, altering intramolecular contacts that perturb the interaction between asparagine 149 and the O3 oxygen of PLP. This alteration is known to potentially shift the tautomeric equilibrium of the PLP Schiff base from its catalytically active ketoenamine form to the inactive enolimine form, which aligns with the reduced activity of the R336C variant. Additionally, the R336C mutation disrupts intermolecular contacts between the catalytic core and Bateman module, altering the Bateman module's intrinsic mobility in the enzyme's basal state and potentially affecting the cavity opening required for catalysis. Importantly, the R336C variant retains the native enzyme's ability to assemble into polymeric chains in crystals, preserving its filament formation capacity.

Solid-state NMR of membrane peptides and proteins in the lipid cubic phase

Solid-state nuclear magnetic resonance (ssNMR) is a powerful technique for studying membrane protein structure and dynamics. Ideally, measurements are performed with the protein in a lipid bilayer. However, homogenous reconstitution of functional protein into intact bilayers at sufficiently high concentrations is often difficult to achieve. In this work, we investigate the suitability of the lipid cubic phase (LCP), which incorporates a lipid bilayer, as an alternative medium for ssNMR of integral membrane peptides and proteins. The cubic mesophase has long been used to generate membrane protein crystals for use in X-ray crystallographic structure determination by the so-called in meso method and for protein functional and biophysical characterization. Preparing and handling protein-laden LCP is straightforward. LCP may therefore provide a valuable alternative to native membranes and other membrane mimetics for ssNMR. We tested this idea by conducting standard magic-angle spinning ssNMR experiments on LCP into which gramicidin, a ∼4-kDa transmembrane peptide, or bacterial lipoprotein signal peptidase II (LspA), a ∼20-kDa integral membrane enzyme, had been reconstituted. We report one- and two-dimensional ssNMR spectra for both gramicidin and LspA and the parameters for optimizing spectral quality. The high protein-carrying capacity of the cubic phase facilitated 13C ssNMR at natural abundance. Lowering temperature and raising magic-angle spinning frequency enabled significant improvements in spectral quality. One-dimensional 13C and 15N spectra were collected for LspA. Two-dimensional ssNMR experiments provided information on LspA dynamics and its interaction with the water and lipid components of the cubic phase. Solution NMR measurements carried out in parallel yielded information on the effect of the antibiotic, globomycin, on LspA structure and dynamics.

A potent protective bispecific nanobody targeting Herpes simplex virus gD reveals vulnerable epitope for neutralizing

Herpes simplex virus (HSV) causes significant health burden worldwide. Currently used antiviral drugs are effective but resistance can occur. Here, we report two high-affinity neutralizing nanobodies, namely Nb14 and Nb32, that target non-overlapping epitopes in HSV gD. Nb14 binds a neutralization epitope located in the N-A' interloop, which prevents the interaction between gD and gH/gL during the second step of conformational changes during membrane fusion after virus attachment. The bispecific nanobody dimer (Nb14-32-Fc) exhibits high potency in vitro and in vivo. Mechanistically, Nb14-32-Fc neutralizes HSVs at both the pre-and post-attachment stages and prevents cell-to-cell spread in vitro. Administration of Nb14-32-Fc at low dosage of 1 mg/kg provides 100% protection in an HSV-1 infection male mouse model and an HSV-2 infection female mouse model. Our results demonstrate that Nb14-32-Fc could serve as a promising drug candidate for treatment of HSV infection, especially in the cases of antiviral drug resistance and severe herpes encephalitis.

Beyond the β-α-β Fold: Characterization of a SnoaL Domain in the Tautomerase Superfamily

Tautomerase superfamily (TSF) members are constructed from a single β-α-β unit or two consecutively joined β-α-β units, and most have a catalytic Pro1. This pattern prevails throughout the superfamily consisting of more than 11,000 members where homo- or heterohexamers are localized in the 4-oxalocrotonate tautomerase (4OT)-like subgroup and trimers are found in the other four subgroups except for a small subset of 4OT trimers, symmetric and asymmetric, that are found in the 4OT-like subgroup. During a sequence similarity network (SSN) update, a small cluster of sequences (117 sequences) was discovered in the 4OT-like subgroup that begins with Pro1. These sequences consist of a 4OT-like domain fused to a SnoaL domain at the C-terminus (except for one), as annotated in the UniProt database. The Pseudooceanicola atlanticus one (designated "4OT-SnoaL") was chosen for kinetic, mechanistic, and crystallographic analysis. 4OT-SnoaL did not display detectable activity with known TSF substrates, suggesting a new activity. A genome neighborhood diagram (GND) places 4OT-SnoaL in an operon for a hydantoin degradation/utilization pathway. Treatment of 4OT-SnoaL with 3-bromopropiolate results in covalent modification of Pro1 by a 3-oxopropanoate adduct. Crystallographic analysis of the apo and modified enzymes shows that the 4OT domain is a hexamer of six identical subunits (a trimer of dimers), where each dimer consists of two β-α-β building blocks. Each C-terminus is attached to a SnoaL-like domain that displays a distorted α + β-barrel. The motif is a new one in the TSF and adds structural diversity to the TSF by using a SnoaL-like domain.

A hidden cysteine in Fis1 targeted to prevent excessive mitochondrial fission and dysfunction under oxidative stress

Fis1-mediated mitochondrial localization of Drp1 and excessive mitochondrial fission occur in human pathologies associated with oxidative stress. However, it is not known how Fis1 detects oxidative stress and what structural changes in Fis1 enable mitochondrial recruitment of Drp1. We find that conformational change involving α1 helix in Fis1 exposes its only cysteine, Cys41. In the presence of oxidative stress, the exposed Cys41 in activated Fis1 forms a disulfide bridge and the Fis1 covalent homodimers cause increased mitochondrial fission through increased Drp1 recruitment to mitochondria. Our discovery of a small molecule, SP11, that binds only to activated Fis1 by engaging Cys41, and data from genetically engineered cell lines lacking Cys41 strongly suggest a role of Fis1 homodimerization in Drp1 recruitment to mitochondria and excessive mitochondrial fission. The structure of activated Fis1-SP11 complex further confirms these insights related to Cys41 being the sensor for oxidative stress. Importantly, SP11 preserves mitochondrial integrity and function in cells during oxidative stress and thus may serve as a candidate molecule for the development of treatment for diseases with underlying Fis1-mediated mitochondrial fragmentation and dysfunction.

Structure of an unfavorable de novo DNA methylation complex of plant methyltransferase ZMET2

DNA methylation is an important epigenetic mechanism that controls the assembly of heterochromatin and gene expression. In plants, DNA methylation occurs in both CG and non-CG contexts, with non-CG methylation showing notable substrate sequence dependence. The plant DNA methyltransferase CMT3 mediates maintenance of CHG (H = A, C, or T) DNA methylation, with a strong substrate preference for the hemimethylated CWG (W= A, T) motif. Yet, the underlying mechanism remains elusive. Here we present a crystal structure of ZMET2, the CMT3 ortholog from Zea mays (maize), in complex with a DNA substrate containing an unmethylated CTG motif and a histone peptide carrying a mimic of the histone H3K9me2 modification. Structural comparison of the ZMET2-CTG complex with the previously reported structure of ZMET2 bound to hemimethylated CAG DNA reveals similar but distinct protein-DNA interactions centered on the CWG motif, providing insight into the methylation state- and substrate sequence-specific ZMET2/CMT3-substrate interaction. Furthermore, our combined structural and biochemical analysis reveals a role for the +3-flanking base of the target cytosine in fine-tuning ZMET2-mediated DNA methylation and its functional interplay with the +1- and +2-flanking sites. Together, these results provide deep mechanistic insights into the substrate specificity of CMT3 DNA methyltransferases in plants.

From discovery to potential application: engineering a novel M23 peptidase to combat Listeria monocytogenes

Peptidoglycan hydrolases are promising alternatives for combating pathogens due to their specificity and potent bacteriolytic activity. In this study, a novel M23 peptidase from Streptococcus thermophilus NCTC10353, designated StM23, was discovered and characterized. It exhibited antibacterial activity against Listeria monocytogenes and other Gram-positive bacteria with meso-DAP-type peptidoglycan, including Bacillus subtilis and Bacillus cereus. To enhance StM23's efficacy and specificity, a chimeric enzyme, StM23_CWT, was engineered by fusing its catalytic domain with a cell wall-targeting domain (CWT) from SpM23B, a peptidoglycan hydrolase found in Staphylococcus pettenkoferi. The engineered chimera demonstrated expanded specificity, showing activity against Staphylococcus aureus and Enterococcus faecium. Its ability to disrupt L. monocytogenes cells was visualized by electron microscopy. The enzyme effectively disrupted biofilm structures and decontaminated surfaces like glass, stainless steel, and silicone, showcasing its industrial potential. Safety evaluations using zebrafish, moth larvae, and human cell models confirmed its non-toxic profile, supporting its broad applicability. Based on these findings, StM23_CWT is a novel and potent antimicrobial agent with significant potential to reduce the risk of listeriosis and control persistent pathogens.

Chimeric deubiquitinase engineering reveals structural basis for specific inhibition of the mitophagy regulator USP30

The mitochondrial deubiquitinase ubiquitin-specific protease (USP) 30 negatively regulates PINK1-parkin-driven mitophagy. Whether enhanced mitochondrial quality control through inhibition of USP30 can protect dopaminergic neurons is currently being explored in a clinical trial for Parkinson's disease. However, the molecular basis for specific inhibition of USP30 by small molecules has remained elusive. Here we report the crystal structure of human USP30 in complex with a specific inhibitor, enabled by chimeric protein engineering. Our study uncovers how the inhibitor extends into a cryptic pocket facilitated by a compound-induced conformation of the USP30 switching loop. Our work underscores the potential of exploring induced pockets and conformational dynamics to obtain deubiquitinase inhibitors and identifies residues facilitating specific inhibition of USP30. More broadly, we delineate a conceptual framework for specific USP deubiquitinase inhibition based on a common ligandability hotspot in the Leu73 ubiquitin binding site and on diverse compound extensions. Collectively, our work establishes a generalizable chimeric protein-engineering strategy to aid deubiquitinase crystallization and enables structure-based drug design with relevance to neurodegeneration.

Leveraging relaxation-optimized 1H-13CF correlations in 4-19F-phenylalanine as atomic beacons for probing structure and dynamics of large proteins

NMR spectroscopy of biomolecules provides atomic level information into their structure, dynamics and interactions with their binding partners. However, signal attenuation from line broadening caused by fast relaxation and signal overlap often limits the application of NMR to large macromolecular systems. Here we leverage the slow relaxation properties of 13C nuclei attached to 19F in aromatic 19F-13C spin pairs as well as the spin-spin coupling between the fluorinated 13C nucleus and the hydrogen atom at the meta-position to record two-dimensional 1H-13CF correlation spectra with transverse relaxation-optimized spectroscopy selection on 13CF. To accomplish this, we synthesized [4-19F13Cζ; 3,5-2H2ε] Phe, engineered for optimal relaxation properties, and adapted a residue-specific route to incorporate this residue globally into proteins and a site-specific 4-19F Phe encoding strategy. This approach resulted in narrow linewidths for proteins ranging from 30 kDa to 180 kDa, enabling interaction studies with small-molecule ligands without requiring specialized 19F-compatible probes.

Structural comparison of three MoaE proteins in Mycobacterium tuberculosis: Insights into molybdopterin synthase assembly and specificity

Molybdoenzymes are essential for the survival and pathogenicity of Mycobacterium tuberculosis and require the molybdenum cofactor (MoCo). The biosynthesis of MoCo involves the molybdopterin (MPT) synthase complex, which is composed of the MoaD and MoaE subunits. The genome of M. tuberculosis encodes three homologs of MoaE: MoaE1, MoaE2, and MoaXE (the latter being a MoaE component of a MoaD-MoaE fusion protein known as MoaX), as well as three MoaD proteins. However, the structural basis for their functional specificity and interaction with MoaD partners remains unclear. We determined the crystal structures of all three MoaE proteins, revealing a conserved α/β hammerhead fold with distinct binding interface features resulting from minor sequence variations. Pull-down assays demonstrate that MoaE2 and MoaXE selectively interact with their cognate MoaD partners, while MoaE1 exhibits promiscuous binding to all MoaD forms. Although the structural plasticity of MoaE1 enables binding to three MoaD forms, it suggests that not all MoaE-MoaD combinations yield functional MPT synthase complexes, as structural rearrangements can lead to enzymatic inactivation. Our findings provide detailed insights into the molecular determinants that govern the assembly and specificity of MPT synthase in M. tuberculosis.

Vaccination of nonhuman primates elicits a broadly neutralizing antibody lineage targeting a quaternary epitope on the HIV-1 Env trimer

The elicitation of cross-neutralizing antibodies to the HIV-1 envelope glycoprotein (Env) by vaccination remains a major challenge. Here, we immunized previously Env-immunized nonhuman primates with a series of near-native trimers that possessed N-glycan deletions proximal to the conserved CD4 binding site (CD4bs) to focus B cells to this region. Following heterologous boosting with fully glycosylated trimers, we detected tier 2 cross-neutralizing activity in the serum of several animals. Isolation of 185 matched heavy- and light-chain sequences from Env-binding memory B cells from an early responder identified a broadly neutralizing antibody lineage, LJF-0034, which neutralized nearly 70% of an 84-member HIV-1 global panel. High-resolution cryoelectron microscopy (cryo-EM) structures revealed a bifurcated binding mode that bridged the CD4bs to V3 across the gp120:120 interface on two adjacent protomers, evading the proximal N276 glycan impediment to the CD4bs, allowing neutralization breadth. This quaternary epitope defines a potential target for future HIV-1 vaccine development.

A F420-dependent single domain chemogenetic tool for protein de-dimerization

Protein-protein interactions (PPIs) mediate many fundamental cellular processes. Control of PPIs through optically or chemically responsive protein domains has had a profound impact on basic research and some clinical applications. Most chemogenetic methods induce the association, i.e., dimerization or oligomerization, of target proteins, whilst the few available dissociation approaches either break large oligomeric protein clusters or heteromeric complexes. Here, we have exploited the controlled dissociation of a homodimeric oxidoreductase from mycobacteria (MSMEG_2027) by its native cofactor, F420, which is not present in mammals, as a bioorthogonal monomerization switch. Using X-ray crystallography, we found that in the absence of F420, MSMEG_2027 forms a unique domain-swapped dimer that occludes the cofactor binding site. Rearrangement of the N-terminal helix upon F420 binding results in the dissolution of the dimer. We then showed that MSMEG_2027 can be fused to proteins of interest in human cells and applied it as a tool to induce and release MAPK/ERK signalling downstream of a chimeric fibroblast growth factor receptor 1 (FGFR1) tyrosine kinase. This F420-dependent chemogenetic de-homodimerization tool is stoichiometric and based on a single domain and thus represents a novel mechanism to investigate protein complexes in situ.

Biochemical and structural insights into position 97 micropolymorphisms in human leukocyte antigen (HLA)-C*12 allotypes and their differential disease associations

Micropolymorphisms drastically shape the antigen presentation characteristics of human leukocyte antigen class I (HLA-I) molecules, with profound implications for immune responses and disease susceptibility. HLA-C*12:02 and HLA-C*12:03 are closely related HLA-I allotypes that differ by a single amino acid substitution (R97W) but exhibit distinct associations with disease. HLA-C*12:02 has been shown to provide protective effects against HIV infection, playing a crucial role in controlling viral replication and slowing disease progression, whereas HLA-C*12:03 is associated with increased susceptibility to psoriasis. We determined the X-ray crystal structures of the two allotypes presenting MARELHPEY (MY9) and RAFPGLRYV (RV9). Peptide residues that function as anchors, as well as those accessible for T-cell antigen receptor (TCR) contact, were identified. Our results, combined with those of biochemical studies, demonstrated that the R97W variation alters the peptide-binding groove (PBG) volume and charge, leading to conformational and stability changes in pHLA-C*12 complexes and ultimately affecting peptide-binding preferences for the two HLA-C*12 allotypes. This research not only advances our understanding of the impact of HLA-I micropolymorphisms but also offers clues for the use of structure-guided therapeutics to interfere with peptide binding.

Structure of a putative terminal amidation domain in natural product biosynthesis

Bacteria are rich sources of pharmaceutically valuable natural products, many crafted by modular polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). PKS and NRPS systems typically contain a thioesterase (TE) to offload a linear or cyclized product from a carrier protein, but alternative chemistry is needed for products with a terminal amide. Several pathways with amidated products also possess an uncharacterized 400-amino acid terminal domain. We present the characterization and structure of this putative terminal amidation domain (TAD). TAD binds NAD with the nicotinamide near an invariant cysteine that is also accessible to an intermediate on a carrier protein, indicating a catalytic role. The TAD structure resembles cyanobacterial acyl-ACP reductase (AAR), which binds NADPH near an analogous catalytic cysteine. Bioinformatic analysis reveals that TADs are broadly distributed across bacterial phyla and often occur at the end of terminal NRPS modules, suggesting many amidated products may yet be discovered.

Crystal structure of Anopheles gambiae actin depolymerizing factor explains high affinity to monomeric actin

Actin is an intrinsically dynamic protein, the function and state of which are modulated by actin-binding proteins. Actin-depolymerizing factors (ADF)/cofilins are ubiquitous actin-binding proteins that accelerate actin turnover. Malaria is an infectious disease caused by parasites of the genus Plasmodium, which belong to the phylum Apicomplexa. The parasites require two hosts to complete their life cycle: the definitive host, or the vector, an Anopheles spp. mosquito, and a vertebrate intermediate host, such as humans. Here, the malaria vector Anopheles gambiae ADF (AgADF) crystal structure is reported. AgADF has a conserved ADF/cofilin fold with six central β-strands surrounded by five α-helices with a long β-hairpin loop protruding out of the structure. The G- and F-actin-binding sites of AgADF are conserved, and the structure shows features of potential importance for regulation by membrane binding and redox state. AgADF binds monomeric ATP- and ADP-actin with a high affinity, having a nanomolar Kd, and binds effectively also to actin filaments.

Cytotoxicity and Binding to DNA, Lysozyme, Ribonuclease A, and Human Serum Albumin of the Diiodido Analog of Picoplatin

Here we investigated cytotoxicity and DNA and protein binding of an iodido analog of picoplatin, the cis-ammine-diiodido(2-methylpyridine)platinum(II) complex (I-picoplatin). I-picoplatin (IC50 = 3.7-12.4 μM) outperforms picoplatin (IC50 = 11.8-22.6 μM) in the human cancer cell lines used and shows a greater ability to overcome the cisplatin resistance of A2780 ovarian cancer cells than does picoplatin. I-picoplatin also induces different cell cycle changes (reduced S-phase fraction and an increase in the G2/M phase arrest) in HeLa cervical carcinoma cells compared to both picoplatin and cisplatin. Binding of the metal compound to DNA model systems was investigated by ethidium bromide displacement assay and circular dichroism. Its reactivity with lysozyme (HEWL) and pancreatic RNase A was studied by X-ray diffraction and mass spectrometry experiments. I-picoplatin binds the DNA double helix and is able to retain the 2-methylpyridine ligand and at least one of the two iodido ligands when bound to the two proteins. Various Pt-containing moieties, including one based on the isomerized structure of I-picoplatin, coordinate the His and Met residues. A low-resolution structure of the I-picoplatin/human serum albumin (HSA) adduct has also been solved. The side chains of His146, Met289, and Met329 are the primary binding sites of the I-picoplatin moieties on HSA.

ZBP1 senses spliceosome stress through Z-RNA:DNA hybrid recognition

Z-DNA-binding protein 1 (ZBP1; also known as DAI or DLM-1) regulates cell death and inflammation by sensing left-handed double-helical nucleic acids, including Z-RNA and Z-DNA. However, the physiological conditions that generate Z-form nucleic acids (Z-NAs) and activate ZBP1-dependent signaling pathways remain largely elusive. In this study, we developed a probe, Zα-mFc, that specifically detected both Z-DNA and Z-RNA. Utilizing this probe, we discovered that inhibiting spliceosome causes nuclear accumulation of Z-RNA:DNA hybrids, which are sensed by ZBP1 via its Zα domains, triggering apoptosis and necroptosis in mammalian cells. Furthermore, we solved crystal structures of the human or mouse Zα1 domain complexed with a 6-bp RNA:DNA hybrid, revealing that the RNA:DNA hybrid adopts a left-handed conformation. Our findings demonstrate that the spliceosome acts as a checkpoint preventing accumulation of Z-RNA:DNA hybrids, which potentially function as endogenous ligands activating ZBP1-dependent cell death pathways.

Discovery and mechanism of K63-linkage-directed deubiquitinase activity in USP53

Ubiquitin-specific proteases (USPs) represent the largest class of human deubiquitinases (DUBs) and comprise its phylogenetically most distant members USP53 and USP54, which are annotated as catalytically inactive pseudoenzymes. Conspicuously, mutations within the USP domain of USP53 cause progressive familial intrahepatic cholestasis. Here, we report the discovery that USP53 and USP54 are active DUBs with high specificity for K63-linked polyubiquitin. We demonstrate how USP53 mutations abrogate catalytic activity, implicating loss of DUB activity in USP53-mediated pathology. Depletion of USP53 increases K63-linked ubiquitination of tricellular junction components. Assays with substrate-bound polyubiquitin reveal that USP54 cleaves within K63-linked chains, whereas USP53 can en bloc deubiquitinate substrate proteins in a K63-linkage-dependent manner. Biochemical and structural analyses uncover underlying K63-specific S2 ubiquitin-binding sites within their catalytic domains. Collectively, our work revises the annotation of USP53 and USP54, provides reagents and a mechanistic framework to investigate K63-linked polyubiquitin decoding and establishes K63-linkage-directed deubiquitination as a new DUB activity.

B, Hsiao Y, Van Oers TJ, Lemieux MJ, Vederas JC. Structure and inhibition of diaminopimelic acid epimerase by slow-binding α-methyl amino acids

Cofactor-independent racemases and epimerases produce D-amino acids from their L-isomers for a variety of biological processes. These enzymes operate via an unusual mechanism that relies on an active site cysteine thiolate (pKa ~ 8.5) to deprotonate an amino acid α-carbon (pKa ~ 29) and are of interest not only because of their biocatalytic potential for D-amino acid production, but also because many play key roles in biology and are antibiotic targets. However, obtaining crystal structures of these enzymes, especially in their closed, substrate- or inhibitor-bound conformations, is difficult. In this work, we characterized diaminopimelic acid (DAP) epimerase from the cyanobacterium Anabaena. DAP epimerase has long been of interest as an antibiotic target as it converts L,L-DAP to D,L-DAP for lysine and peptidoglycan biosynthesis. We solved three crystal structures of this enzyme in its closed, inhibitor-bound conformation, up to a resolution of 1.5 Å. Two structures show the enzyme covalently bound through its catalytic cysteine residues to previously reported aziridine-based inhibitors. One structure unexpectedly shows the enzyme bound to a different compound, D,L-α-methylDAP, presumably produced as a synthetic byproduct. Stereoselective synthesis of L,L- and D,L-α-methylDAP followed by inhibition assays shows that these compounds are slow-binding inhibitors of DAP epimerase. α-MethylDAP inhibitors provide a more accessible alternative to aziridine-based inhibitors to obtain crystal structures of DAP epimerase in its closed conformation. Comparisons of bacterial, cyanobacterial, and plant DAP epimerases provided here offer new insights into functional and structural differences between these enzymes.

Unravelling the amyloid aggregation mechanism of the sweet protein Monellin: Insights from circular permutated mutants

Protein amyloid aggregates, once regarded solely as pathological hallmarks of human neurodegenerative diseases, have recently gained attention for their potential in biotechnological applications. Among others, MNEI and its variants, initially developed as single-chain derivatives of the sweet protein monellin, also serve as valuable models for studying protein fibrillary aggregation. In this work, we have characterized three circular permutated mutants of MNEI obtained joining the N- and C-termini of MNEI with linkers of different length and restoring the splitting of the polypeptide chain of native monellin. All proteins are well folded but have a different propensity to form oligomeric structures in solution and aggregation rates comparable to or faster than MNEI, as indicated by Thioflavin-T binding assays. Transmission Electron Microscopy (TEM) studies indicate that only Perm1, the mutant with the longest linker, forms fibrillar aggregates. X-ray structures of the mutants show that they crystallize as domain-swapped dimers. Molecular dynamics study highlights potential hot spots controlling the ordered aggregation process of Perm1. Our data support the idea that the formation of a domain-swapped dimer does not favour the formation of fibrillar aggregates and highlight circular permutation as a valuable tool to build nanostructured biomaterials.

Micropolymorphism outside the peptide-binding groove of human leukocyte antigen (HLA)-C*14 modulates structural stability and shapes immune responses

Micropolymorphisms in human leukocyte antigen class I (HLA-I) molecules critically influence antigen presentation and immune recognition. Most studies have focused on variations within the peptide-binding groove (PBG), neglecting the potential impact of residues located outside this region. HLA-C*14:02 and HLA-C*14:03 differ only at position 21 (R21 and H21, respectively), which is situated outside the PBG, yet these two allotypes exhibit distinct clinical associations with HIV control in the context of KIR2DL2, an inhibitory killer cell immunoglobulin-like receptor that modulates natural killer (NK) cell activity. Here, we investigated the molecular mechanisms by which the R21H micropolymorphism shapes immune responses. Structural and biochemical analyses revealed that position 21 indirectly regulates the conformation of the B pocket within the PBG, significantly affecting HLA-C*14 stability and altering the composition of its peptide repertoire, while preserving core peptide motifs and recognition by KIR2DL2. Notably, the R21H variation is evolutionarily conserved across various HLA-I molecules and exhibits similar interactions with neighboring residues, suggesting a broadly conserved role in structural stability and immune regulation. These findings suggest that the stability differences between HLA-C*14 allotypes may influence their differential clinical associations, highlighting the previously underappreciated role of micropolymorphisms outside the PBG in modulating immune responses.

Structure of the Saccharolobus solfataricus GINS tetramer

DNA replication is tightly regulated to ensure genomic stability and prevent several diseases, including cancers. Eukaryotes and archaea partly achieve this regulation by strictly controlling the activation of hexameric minichromosome maintenance (MCM) helicase rings that unwind DNA during its replication. In eukaryotes, MCM activation critically relies on the sequential recruitment of the essential factors Cdc45 and a tetrameric GINS complex at the onset of the S-phase to generate a larger CMG complex. We present the crystal structure of the tetrameric GINS complex from the archaeal organism Saccharolobus solfataricus (Sso) to reveal a core structure that is highly similar to the previously determined GINS core structures of other eukaryotes and archaea. Using molecular modeling, we illustrate that a subdomain of SsoGINS would need to move to accommodate known interactions of the archaeal GINS complex and to generate a SsoCMG complex analogous to that of eukaryotes.

Structure of the Fab fragment of a humanized 5E5 antibody to a cancer-specific Tn-MUC1 epitope

The structure of the humanized Fab from murine monoclonal antibody 5E5 specific for tumor antigen Tn-MUC1 has been determined to 1.57 Å resolution. Despite undertaking thousands of crystallization trials of the humanized 5E5 (h-5E5) Fab in the presence of either the singly or doubly glycosylated peptide antigens corresponding to Tn-MUC1, the Fab is only observed unliganded in the crystal. The conformations of the complementarity-determining regions (CDRs) of the combining site on the h-5E5 Fab do not differ significantly from those reported for liganded murine scFv at 3.0 Å resolution. While the affinity of the murine 5E5 has previously been reported as KD = 1.7 nM for the 24-mer Tn-MUC1 peptide PPAHGVT*SAPDTRPAPGS*T*APPAH prepared by in vitro glycosylation of a synthetic 24-mer MUC1 peptide, the KD of the h-5E5 Fab for the shorter doubly glycosylated glycopeptide antigens PAPGS*T*AP and APGS*T*AP was measured here as only 41 and 61 µM, respectively. Interestingly, the single Fab molecule in the asymmetric unit of space group C2 is observed packed head-to-head with a symmetry-related Fab across a crystallographic twofold axis such that a polypeptide loop from the light chain of each Fab is observed to insert into the antigen-binding pocket of the symmetry-related Fab. While this might suggest that binding of the Tn-MUC1 peptides may have been inhibited by a homophilic association, none was detected. The humanization process has imposed changes in the framework regions of the Fv which may have affected the Vh-Vl interface.

Robust error calibration for serial crystallography

Serial crystallography is an important technique with unique abilities to resolve enzymatic transition states, minimize radiation damage to sensitive metalloenzymes and perform de novo structure determination from micrometre-sized crystals. This technique requires the merging of data from thousands of crystals, making manual identification of errant crystals unfeasible. cctbx.xfel.merge uses filtering to remove problematic data. However, this process is imperfect, and data reduction must be robust to outliers. We add robustness to cctbx.xfel.merge at the step of uncertainty determination for reflection intensities. This step is a critical point for robustness because it is the first step where the data sets are considered as a whole, as opposed to individual lattices. Robustness is conferred by reformulating the error-calibration procedure to have fewer and less stringent statistical assumptions and incorporating the ability to down-weight low-quality lattices. We then apply this method to five macromolecular XFEL data sets and observe the improvements to each. The appropriateness of the intensity uncertainties is demonstrated through internal consistency. This is performed through theoretical CC1/2 and I/σ relationships and by weighted second moments, which use Wilson's prior to connect intensity uncertainties with their expected distribution. This work presents new mathematical tools to analyze intensity statistics and demonstrates their effectiveness through the often underappreciated process of uncertainty analysis.

Interface integrity in septin protofilaments is maintained by an arginine residue conserved from yeast to man

The septins are conserved, filament-forming, guanine nucleotide binding cytoskeletal proteins. They assemble into palindromic protofilaments which polymerize further into higher-ordered structures that participate in essential intracellular processes such as cytokinesis or polarity establishment. Septins belong structurally to the P-Loop NTPases but, unlike their relatives Ras or Rho, do not mediate signals to effectors through GTP binding and hydrolysis. Biochemical approaches addressing how and why septins utilize nucleotides are hampered by the lack of nucleotide-free complexes. Using molecular dynamics simulations, we determined structural alterations and intersubunit binding free energies in human and yeast septin dimer structures and in their in silico generated apo forms. An interchain salt bridge network around the septin unique β-meander, conserved across all kingdoms of septin containing species, is destabilized upon nucleotide removal, concomitant with disruption of the entire G-interface. Within this network, we confirmed a conserved arginine residue, which coordinates the guanine base of the nucleotide, as the central interaction hub. The essential role of this arginine for interface integrity was experimentally confirmed to be conserved in septins from yeast to human.

Stepwise neofunctionalization of the NF-κB family member Rel during vertebrate evolution

Adaptive immunity and the five vertebrate NF-κB family members first emerged in cartilaginous fish, suggesting that NF-κB family divergence helped to facilitate adaptive immunity. One specialized function of the NF-κB Rel protein in macrophages is activation of Il12b, which encodes a key regulator of T cell development. We found that Il12b exhibits much greater Rel dependence than inducible innate immunity genes in macrophages, with the unique function of Rel dimers depending on a heightened intrinsic DNA-binding affinity. Chromatin immunoprecipitation followed by sequencing experiments defined differential DNA-binding preferences of NF-κB family members genome-wide, and X-ray crystallography revealed a key residue that supports the heightened DNA-binding affinity of Rel dimers. Unexpectedly, this residue, the heightened affinity of Rel dimers, and the portion of the Il12b promoter bound by Rel dimers were largely restricted to mammals. Our findings reveal major structural transitions in an NF-κB family member and one of its key target promoters at a late stage of vertebrate evolution that apparently contributed to immunoregulatory rewiring in mammalian species.

SAMD12 as a Master Regulator of MAP4Ks by Decoupling Kinases From the CNKSR2 Scaffold

The MAP4K member TNIK and the multi-domain scaffold protein CNKSR2, both of which are clustered at neuronal synapses, interact with each other and are closely associated with neurodevelopmental disorders, although the mechanism underlying their interaction is unclear. In this study, we characterized the interaction mechanisms between MAP4K kinases (MAP4K4, MINK1 and TNIK) and the CNKSR1/2/3 scaffold proteins, and discovered that SAMD12, a familial adult myoclonic epilepsy disease gene product, or its close homolog SAMD10, binds to CNKSR1/2/3 with exceptionally strong affinities and can quantitatively displace MAP4K from CNKSR1/2/3 scaffolds. Additionally, we demonstrated that CNKSR2 acts as both a scaffold and an activator of TNIK during neuronal synapse development. Ectopic expression of SAMD12 can effectively alter synapse development, likely by inhibiting TNIK activity through the dissociation of the kinase from CNKSR2. Our findings may have broad implications on the roles of MAP4Ks and CNKSR1/2/3 in the nervous system and in other tissues under physiological and pathophysiological processes.

Understanding the molecular mechanism of fumonisin esterases by kinetic and structural studies

Fumonisins are sphingolipid-like mycotoxins that cause serious damage by contaminating food and feed. The tricarballylic acid (TCA) units of fumonisin B1 (FB1; accounting for 70 % of fumonisin contamination) can be removed by fumonisin B1 esterase (FE, EC 3.1.1.87) providing a biotechnological FB1 detoxification possibility. Here, we report the regioselective cleavage of the TCA ester at C6 in the first step of FB1 hydrolysis and kinetic characterization for two FEs. The low KM values (4.76-44.3 μM) are comparable to concentrations of environmental contaminations, and the high catalytic efficiencies are promising for practical applications. The X-ray structure of one of the FEs enabled the understanding of the FB1 hydrolysis at molecular level and revealed an arginine pocket key for substrate binding, and the catalytic role of the glutamate preceding the catalytic serine. Computations showed that this FE is likely capable of detoxifying any fumonisin indicating its potential applicability in food and feed products.

Structures of Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in substrate-bound forms

We report structures of the Mycobacterium tuberculosis isoprenyl diphosphate synthase Rv2173 in three forms: apo and two substrate-bound forms [isoprenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP)]. The protein possesses a canonical all-α-helical trans-isoprenyl diphosphate synthase fold that is dimeric in each form. There are some differences between the structures: the IPP-bound form shows IPP bound in the DMAPP/allylic substrate-binding site with three divalent metal ions bound around the IPP and the complete C-terminus closing around the active site, while the apo and DMAPP-bound forms are more open, with some of the C-terminal region disordered, supporting suggestions that the C-terminus is important in substrate entry/product exit. In the DMAPP form DMAPP occupies the expected allylic substrate site, but only two metal ions are associated with the binding, with the DMAPP diphosphates adopting a slightly different binding pose compared with IPP in the same site, and the third metal-binding site is unoccupied. In no case is the IPP binding site occupied by IPP. There has been some uncertainty regarding product length for Rv2173, with variable lengths being reported. In the structures reported here, the `capping' residue at the bottom of the binding cavity is tryptophan and comparison with other IPP synthases suggests that the structure of Rv2173 is most consistent with a C10-C15 final product size.

Structural analysis of the ribosome assembly factor Nep1, an N1-specific pseudouridine methyltransferase, reveals mechanistic insights

Nucleolar essential protein 1 (Nep1; also known as ribosomal RNA small subunit methyltransferase Nep1) is a crucial factor in forming small ribosomal subunits in eukaryotes and archaea. Nep1 possesses an S-adenosyl-L-methionine (SAM)-dependent SpoU-TrmD (SPOUT) ribosomal RNA (rRNA) methyltransferase (MTase) fold and catalyzes pseudouridine (Ψ) methylation at specific sites of the small subunit (SSU) rRNA. Mutations in Nep1 proteins result in a severe developmental disorder in humans and reduced growth in yeast, suggesting its role in ribosome biogenesis. In this study, the crystal structures of Nep1 from the archaebacterium Pyrococcus horikoshii (PhNep1), both in its apo and holo (adenosine or 5-methylthioadenosine bound) forms have been reported. The structural analysis of PhNep1 revealed an α/β fold featuring a deep trefoil knot akin to the SPOUT domain, with two novel extensions-a globular loop and a β-α-β extension. Moreover, the cofactor-binding site of PhNep1 exhibits a preformed pocket, topologically similar to that of other SPOUT-class MTases. Further, structural analysis of PhNep1 revealed that it forms a homodimer coordinated by inter-subunit hydrogen bonds and hydrophobic interactions. Moreover, the results of this study indicate that PhNep1 can specifically methylate consensus RNAs, having a pseudouridine (ψ) located at position 926 of helix 35 (h35) of 16S rRNA in P. horikoshii. The stability of the Nep1-RNA complex seems to be primarily assisted by the conserved arginine residues located at the dimeric interface.

Antibody-secreting cell repertoires hold high-affinity anti-rocuronium specificities that can induce anaphylaxis in vivo

BACKGROUND

Neuromuscular blocking agents (NMBAs) are muscle relaxants used to assist mechanical ventilation but lead in 1 per 10,000 anesthesia cases to severe acute hypersensitivity reactions-that is, anaphylaxis. Incidences vary between types of NMBAs. Rocuronium, a widely used nondepolarizing aminosteroid NMBA, induces among the highest anaphylaxis rates. Rocuronium-induced anaphylaxis is proposed to rely on preexisting rocuronium-binding antibodies, but no such antibodies have ever been identified.

OBJECTIVES

We sought to identify rocuronium-specific antibody repertoires from plasma cells or plasmablasts of rocuronium-immunized mice to determine the affinities, structures, and anaphylactogenic potential of these antibodies for rocuronium.

METHODS

We engrafted rocuronium onto carrier proteins allowing immunization of mice against rocuronium, screening for rocuronium-specific antibody responses, and sorting of rocuronium-specific plasma cells using droplet microfluids coupled to single-cell antibody gene (variable heavy chain [VH] and variable light chain [VL]) sequencing.

RESULTS

The 2 different repertoires of >500 VH-VL pairs were oligoclonal, comprised 3 major clonal families, and displayed convergence. Expressed as human IgG1, these antibodies demonstrated subnanomolar affinities for rocuronium with families either monospecific for rocuronium or cross-reactive only for closely related NMBAs. Expressed as human IgE, they triggered human mast cell and basophil activation, and severe passive systemic anaphylaxis in mice humanized for the IgE receptor FcεRI. Cocrystal structures between rocuronium and antibody representatives of 3 different VH-VL families revealed distinct interaction modes, with the ammonium group involved systematically in the binding interface.

CONCLUSIONS

This work identifies the epitopes of antibody reactivity to rocuronium, demonstrates anaphylactogenic potential of anti-rocuronium IgE, and establishes the first mouse model of NMBA anaphylaxis.

Unique double-helical packing of protein molecules in the crystal of potassium-independent L-asparaginase from common bean

Common bean (Phaseolus vulgaris) encodes three class 2 L-asparaginase enzymes: two potassium-dependent enzymes [PvAIII(K)-1 and PvAIII(K)-2] and a potassium-independent enzyme (PvAIII). Here, we present the crystal structure of PvAIII, which displays a rare P2 space-group symmetry and a unique pseudosymmetric 41-like double-helical packing. The asymmetric unit contains 32 protein chains (16 αβ units labeled A-P) organized into two right-handed coiled arrangements, each consisting of four PvAIII (αβ)2 dimers. Detailed analysis of the crystal structure revealed that this unusual packing originates from three factors: (i) the ability of the PvAIII molecules to form extended intermolecular β-sheets, a feature enabled by the PvAIII sequence and secondary structure, (ii) incomplete degradation of the flexible linker remaining at the C-terminus of α subunits of protein chain C after the autoproteolytic cleavage (maturation) of the PvAIII precursor and (iii) intermolecular entanglement between protein chains from the two helices to create `hydrogen-bond linchpins' that connect adjacent protein chains. The Km value of PvAIII for L-asparagine is approximately five times higher than for β-peptides, suggesting that the physiological role of PvAIII may be more related to the removal of toxic β-peptides than to basic L-asparagine metabolism. A comparison of the active sites of PvAIII and PvAIII(K)-1 shows that the proteins have nearly identical residues in the catalytic center, except for Thr219, which is unique to PvAIII. To test whether the residue type at position 219 affects the enzymatic activity of PvAIII, we designed and produced a T219S mutant. The kinetic parameters determined for L-asparagine hydrolysis indicate that the T/S residue type at position 219 does not affect the L-asparaginase activity of PvAIII.