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Journal articleHeng JYY, 2022,
Emerging stars special issue
, CHEMICAL ENGINEERING RESEARCH & DESIGN, Vol: 188, Pages: 861-867, ISSN: 0263-8762 -
Journal articleFusco G, Biancaniello C, Vrettas MD, et al., 2022,
Thermal tuning of protein hydration in a hyperthermophilic enzyme
, FRONTIERS IN MOLECULAR BIOSCIENCES, Vol: 9 -
Journal articleFala AK, Alvarez-Ordonez A, Filloux A, et al., 2022,
Quorum sensing in human gut and food microbiomes: significance and potential for therapeutic targeting
, Frontiers in Microbiology, Vol: 13, ISSN: 1664-302XHuman gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.
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Journal articleKotta-Loizou I, Giuliano MG, Jovanovic M, et al., 2022,
The RNA repair proteins RtcAB regulate transcription activator RtcR via its CRISPR-associated Rossmann fold domain
, iScience, Vol: 25, ISSN: 2589-0042CRISPR-associated Rossmann fold (CARF) domain signaling underpins modulation of CRISPR-Cas nucleases; however, the RtcR CARF domain controls expression of two conserved RNA repair enzymes, cyclase RtcA and ligase RtcB. Here, we demonstrate that RtcAB are required for RtcR-dependent transcription activation and directly bind to RtcR CARF. RtcAB catalytic activity is not required for complex formation with CARF, but is essential yet not sufficient for RtcRAB-dependent transcription activation, implying the need for an additional RNA repair-dependent activating signal. This signal differs from oligoadenylates, a known ligand of CARF domains, and instead appears to originate from the translation apparatus: RtcB repairs a tmRNA that rescues stalled ribosomes and increases translation elongation speed. Taken together, our data provide evidence for an expanded range for CARF domain signaling, including the first evidence of its control via in trans protein-protein interactions, and a feed-forward mechanism to regulate RNA repair required for a functioning translation apparatus.
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Journal articleBaxter JM, Hutchison CDM, Maghlaoui K, et al., 2022,
Observation of Cation Chromophore Photoisomerization of a Fluorescent Protein Using Millisecond Synchrotron Serial Crystallography and Infrared Vibrational and Visible Spectroscopy
, JOURNAL OF PHYSICAL CHEMISTRY B, Vol: 126, Pages: 9288-9296, ISSN: 1520-6106 -
Journal articleBeattie JW, Istrate A, Lu A, et al., 2022,
Causes of industrial protein a column degradation, explored using Raman spectroscopy.
, Analytical Chemistry, Vol: 94, Pages: 15703-15710, ISSN: 0003-2700Monoclonal antibodies (mAbs) are used extensively as biotherapeutics for chronic and acute conditions. Production of mAbs is lengthy and expensive, with protein A affinity capture the most costly step, due both to the nature of the resin and its marked reduction in binding capacity with repeated use. Our previous studies using in situ ATR-FTIR spectroscopy indicated that loss in protein A binding capacity is not the result of leaching or degradation of protein A ligand, suggesting fouling is the principal cause. Here we explore binding behavior and resin capacity loss using Raman spectroscopy. Our data reveal a distinct Raman spectral fingerprint for mAb bound to the protein A ligand of MabSelect SuRe. The results show that the drop in static binding capacity (SBC) previously observed for used protein A resin is discernible by Raman spectroscopy in combination with partial least-squares regression. The SBC is lowest (35.76 mg mL-1) for used inlet resin compared to used outlet (40.17 mg mL-1) and unused resin samples (70.35 mg mL-1). Depth profiling by Raman spectroscopy indicates that at below saturating concentrations (∼18 mg mL-1), binding of mAb is not homogeneous through used resin beads with protein binding preferentially to the outer regions of the bead, in contrast to fully homogeneous distribution through unused control MabSelect SuRe resin beads. Analysis of the Raman spectra indicates that one foulant is irreversibly bound mAb. The presence of irreversibly bound mAb and host cell proteins was confirmed by mass spectrometric analysis of used resin beads.
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Journal articleCamara M, Filloux A, 2022,
Supporting the strategic pillars of translational research in biofilms
, NPJ BIOFILMS AND MICROBIOMES, Vol: 8 -
Journal articlePatchsung M, Homchan A, Aphicho K, et al., 2022,
A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance
, The CRISPR Journal, Vol: 6, Pages: 1-17, ISSN: 2573-1599Point-of-care (POC) nucleic acid detection technologies are poised to aid gold-standard technologies in controlling the COVID-19 pandemic, yet shortcomings in the capability to perform critically needed complex detection—such as multiplexed detection for viral variant surveillance—may limit their widespread adoption. Herein, we developed a robust multiplexed clustered regularly interspaced short palindromic repeats (CRISPR)-based detection using LwaCas13a and PsmCas13b to simultaneously diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and pinpoint the causative SARS-CoV-2 variant of concern (VOC)—including globally dominant VOCs Delta (B.1.617.2) and Omicron (B.1.1.529)—all the while maintaining high levels of accuracy upon the detection of multiple SARS-CoV-2 gene targets. The platform has several attributes suitable for POC use: premixed, freeze-dried reagents for easy use and storage; convenient direct-to-eye or smartphone-based readouts; and a one-pot variant of the multiplexed detection. To reduce reliance on proprietary reagents and enable sustainable use of such a technology in low- and middle-income countries, we locally produced and formulated our own recombinase polymerase amplification reaction and demonstrated its equivalent efficiency to commercial counterparts. Our tool—CRISPR-based detection for simultaneous COVID-19 diagnosis and variant surveillance that can be locally manufactured—may enable sustainable use of CRISPR diagnostics technologies for COVID-19 and other diseases in POC settings.
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Journal articleMathavan I, Liu LJ, Robinson SW, et al., 2022,
Identification of inhibitors of the Schistosoma mansoni VKR2 kinase domain
, ACS Medicinal Chemistry Letters, Vol: 13, Pages: 1715-1722, ISSN: 1948-5875Schistosomiasis is a neglected tropical disease caused by parasitic flatworms. Current treatment relies on just one partially effective drug, praziquantel (PZQ). Schistosoma mansoni Venus Kinase Receptors 1 and 2 (SmVKR1 and SmVKR2) are important for parasite growth and egg production, and are potential targets for combating schistosomiasis. VKRs consist of an extracellular Venus Flytrap Module (VFTM) linked via a transmembrane helix to a kinase domain. Here, we initiated a drug discovery effort to inhibit the activity of the SmVKR2 kinase domain (SmVKR2KD) by screening the GSK published kinase inhibitor set 2 (PKIS2). We identified several inhibitors, of which four were able to inhibit its enzymatic activity and induced phenotypic changes in ex vivoS. mansoni. Our crystal structure of the SmVKR2KD displays an active-like state that sheds light on the activation process of VKRs. Our data provide a basis for the further exploration of SmVKR2 as a possible drug target.
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Journal articleValsecchi M, Ramadani J, Williams D, et al., 2022,
Influence of Tie-Molecules and Microstructure on the Fluid Solubility in Semicrystalline Polymers.
, J Phys Chem B - Special Issue in Honor of Doros N. TheodorouPredicting the absorption of gases and liquids in semicrystalline polymers is of critical importance for numerous applications; the mechanical and transport properties of these materials are highly dependent on the amount of solutes dissolved in their bulk. For most semicrystalline polymers which are in contact with an external fluid, the observed uptake of the solute is found to be lower than that predicted by treating the amorphous domains of the polymer as subcooled polymer melts at the same thermodynamic state. This observation has recently led to the hypothesis that the amorphous domains effectively behave as polymer liquids subject to an additional "constraint pressure" which reduces the equilibrium solubility in the domains. We present a new statistical mechanical model of semicrystalline polymers. The constraint pressure emerges naturally from our treatment, as a property of the interlamellar amorphous domains caused by the stretching and localization in space of the tie-molecules (polymer chains linking different lamellae). By assuming that the interlamellar domains exchange monomers reversibly with the lamellae, the model allows one to simultaneously predict the increase of constraint pressure at low temperatures and the variation of the lamellar thickness as a function of temperature─a phenomenon known as premelting. The sorption isotherms of a range of fluids in different polyethylene and polypropylene samples are determined experimentally and the data is compared with calculations of the new model using the SAFT-VR Mie EoS. In order to accurately predict the absorption close to the vapor pressure of the penetrant, we find that it is essential to include the "free", unconstrained amorphous domains in the description, resulting in a multiscale model with two adjustable parameters (the fractions of tie-molecules and free amorphous domains) that characterize the morphology of a given semicrystalline polymer sample. The trends observed fo
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Journal articleMosscrop L, Watber P, Elliot P, et al., 2022,
Evaluation of the impact of pre-analytical conditions on sample stability for the detection of SARS-CoV-2 RNA
, Journal of Virological Methods, Vol: 309, Pages: 1-5, ISSN: 0166-0934Demand for accurate SARS-CoV-2 diagnostics is high. Most samples in the UK are collected in the community and rely on the postal service for delivery to the laboratories. The current recommendation remains that swabs should be collected in Viral Transport Media (VTM) and transported with a cold chain to the laboratory for RNA extraction and RT-qPCR. This is not always possible. We aimed to test the stability of SARS-CoV-2 RNA subjected to different pre-analytical conditions. Swabs were dipped into PBS containing cultured SARS-CoV-2 and placed in either a dry tube or a tube containing either normal saline or VTM. The tubes were then stored at different temperatures (20–50 °C) for variable periods (8 h to 5 days). Samples were tested by RT-qPCR targeting SARS-CoV-2 E gene. VTM outperformed swabs in saline and dry swabs in all conditions. Samples in VTM were stable, independent of a cold chain, for 5 days, with a maximum increase in cycle threshold (Ct) of 1.34 when held at 40 °C. Using normal saline as the transport media resulted in a loss of sensitivity (increased Ct) over time and with increasing temperature (up to 7.8 cycles compared to VTM). SARS-CoV-2 was not detected in 3/9 samples in normal saline when tested after 120 h incubation. Transportation of samples in VTM provides a high level of confidence in the results despite the potential for considerable, uncontrolled variation in temperature and longer transportation periods. False negative results may be seen after 96 h in saline and viral loads will appear lower.
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Journal articleHakki S, Zhou J, Jonnerby J, et al., 2022,
Onset and window of SARS-CoV-2 infectiousness and temporal correlation with symptom onset: a prospective, longitudinal, community cohort study
, The Lancet Respiratory Medicine, Vol: 10, Pages: 1061-1073, ISSN: 2213-2600BACKGROUND: Knowledge of the window of SARS-CoV-2 infectiousness is crucial in developing policies to curb transmission. Mathematical modelling based on scarce empirical evidence and key assumptions has driven isolation and testing policy, but real-world data are needed. We aimed to characterise infectiousness across the full course of infection in a real-world community setting. METHODS: The Assessment of Transmission and Contagiousness of COVID-19 in Contacts (ATACCC) study was a UK prospective, longitudinal, community cohort of contacts of newly diagnosed, PCR-confirmed SARS-CoV-2 index cases. Household and non-household exposed contacts aged 5 years or older were eligible for recruitment if they could provide informed consent and agree to self-swabbing of the upper respiratory tract. The primary objective was to define the window of SARS-CoV-2 infectiousness and its temporal correlation with symptom onset. We quantified viral RNA load by RT-PCR and infectious viral shedding by enumerating cultivable virus daily across the course of infection. Participants completed a daily diary to track the emergence of symptoms. Outcomes were assessed with empirical data and a phenomenological Bayesian hierarchical model. FINDINGS: Between Sept 13, 2020, and March 31, 2021, we enrolled 393 contacts from 327 households (the SARS-CoV-2 pre-alpha and alpha variant waves); and between May 24, 2021, and Oct 28, 2021, we enrolled 345 contacts from 215 households (the delta variant wave). 173 of these 738 contacts were PCR positive for more than one timepoint, 57 of which were at the start of infection and comprised the final study population. The onset and end of infectious viral shedding were captured in 42 cases and the median duration of infectiousness was 5 (IQR 3-7) days. Although 24 (63%) of 38 cases had PCR-detectable virus before symptom onset, only seven (20%) of 35 shed infectious virus presymptomatically. Symptom onset was a median of 3 days before both peak viral RNA and
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Journal articleCordery R, Reeves L, Zhou J, et al., 2022,
Transmission of SARS-CoV-2 by children to contacts in schools and households: a prospective cohort and environmental sampling study in London
, The Lancet Microbe, Vol: 3, Pages: e814-e823, ISSN: 2666-5247Background: Assessing transmission of SARS-CoV-2 by children in schools is of critical importance to inform public health action. We assessed frequency of acquisition of SARS-CoV-2 by contacts of pupils with COVID-19 in schools and households, and quantified SARS-CoV-2 shed into air and onto fomites in both settings.Methods: Incidents involving exposure to at least one index pupil with COVID-19 in 8 schools were identified between October 2020-July 2021 (prevailing variants, original, alpha and delta). Weekly PCR testing for SARS-CoV-2 was undertaken on immediate classroom contacts (the “bubble”), non-bubble school contacts, and household contacts of index pupils, supported by genome sequencing, and on surface and air samples from school and home environments.Findings: Secondary transmission of SARS-CoV-2 was not detected in 28 bubble contacts, representing 10 bubble classes (participation rate 8.8%, IQR 4.6-15.3%). Across 8 non-bubble classes, 3/62 pupils tested positive but these were unrelated to the original index case (participation rate 22.5%, IQR 9.7-32.3%). All three were asymptomatic and tested positive in one setting on the same day. In contrast, secondary transmission to previously-negative household contacts from infected index pupils was 17.1% (6/35) rising to 27.7% (13/47) when considering all potentialinfections in household contacts. Environmental contamination with SARS-CoV-2 was rare in schools; fomite SARS-CoV-2 was identified in 4/189 (2.1%) samples in bubble classrooms, 2/127 (1.6%) samples in non-bubble classrooms, and 5/130 (3.8%) samples in washrooms. This contrasted with fomites in households, where SARS-CoV-2 was identified in 60/248 (24.2%) bedroom samples, 66/241 (27.4%) communal room samples, and 21/188 (11.2%) bathroom samples. Air sampling identified SARS-CoV-2 RNA in just 1/68 (1.5%) of school air samples, compared with 21/85 (24.7%) of air samples taken in homes.Interpretation: There was no evidence of large scale SARS-Co
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Journal articleReimer L, Gram H, Jensen NM, et al., 2022,
Protein kinase R dependent phosphorylation of α-synuclein regulates its membrane binding and aggregation
, PNAS NEXUS, Vol: 1- Author Web Link
- Cite
- Citations: 1
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Journal articleMercer T, Almond N, Crone MA, et al., 2022,
The Coronavirus Standards Working Group's roadmap for improved population testing
, NATURE BIOTECHNOLOGY, Vol: 40, Pages: 1563-1568, ISSN: 1087-0156- Cite
- Citations: 8
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Journal articleMiguel-Romero L, Alqasmi M, Bacarizo J, et al., 2022,
Non-canonical Staphylococcus aureus pathogenicity island repression
, Nucleic Acids Research, Vol: 50, Pages: 11109-11127, ISSN: 0305-1048Mobile genetic elements control their life cycles by the expression of a master repressor, whose function must be disabled to allow the spread of these elements in nature. Here we describe an unprecedented repression-derepression mechanism involved in the transfer of Staphylococcus aureus pathogenicity islands. Contrary to the classical phage and SaPI repressors, which are dimers, the SaPI1 repressor StlSaPI1 presents a unique tetramericconformation never seen before. Importantly, not just one but two tetramers are required for SaPI1 repression, which increases the novelty of the system. To derepress SaPI1, the phage-encoded protein Sri binds to and induces a conformational change in the DNA binding domains of StlSaPI1, preventing the binding of the repressor to its cognate StlSaPI1 sites. Finally, our findings demonstrate that this system is not exclusive to SaPI1 but widespread in nature. Overall, our results characterise a novel repression-induction system involved in the transfer of MGE-encoded virulence factors in nature.
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Journal articleChukhutsina VU, Baxter JM, Fadini A, et al., 2022,
Light activation of Orange Carotenoid Protein reveals bicycle-pedal single-bond isomerization
, Nature Communications, Vol: 13, Pages: 1-14, ISSN: 2041-1723Orange Carotenoid protein (OCP) is the only known photoreceptor which uses carotenoid for its activation. It is found exclusively in cyanobacteria, where it functions to control light-harvesting of the photosynthetic machinery. However, the photochemical reactions and structural dynamics of this unique photosensing process are not yet resolved. We present time-resolved crystal structures at second-to-minute delays under bright illumination, capturing the early photoproduct and structures of the subsequent reaction intermediates. The first stable photoproduct shows concerted isomerization of C9’-C8’ and C7’-C6’ single bonds in the bicycle-pedal (s-BP) manner and structural changes in the N-terminal domain with minute timescale kinetics. These are followed by a thermally-driven recovery of the s-BP isomer to the dark state carotenoid configuration. Structural changes propagate to the C-terminal domain, resulting, at later time, in the H-bond rupture of the carotenoid keto group with protein residues. Solution FTIR and UV/Vis spectroscopy support the single bond isomerization of the carotenoid in the s-BP manner and subsequent thermal structural reactions as the basis of OCP photoreception.
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Journal articleBenns HJ, Storch M, Falco JA, et al., 2022,
CRISPR-based oligo recombineering prioritizes apicomplexan cysteines for drug discovery.
, Nat MicrobiolNucleophilic amino acids are important in covalent drug development yet underutilized as anti-microbial targets. Chemoproteomic technologies have been developed to mine chemically accessible residues via their intrinsic reactivity towards electrophilic probes but cannot discern which chemically reactive sites contribute to protein function and should therefore be prioritized for drug discovery. To address this, we have developed a CRISPR-based oligo recombineering (CORe) platform to support the rapid identification, functional prioritization and rational targeting of chemically reactive sites in haploid systems. Our approach couples protein sequence and function with biological fitness of live cells. Here we profile the electrophile sensitivity of proteinogenic cysteines in the eukaryotic pathogen Toxoplasma gondii and prioritize functional sites using CORe. Electrophile-sensitive cysteines decorating the ribosome were found to be critical for parasite growth, with target-based screening identifying a parasite-selective anti-malarial lead molecule and validating the apicomplexan translation machinery as a target for ongoing covalent ligand development.
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Journal articleAlmusaimi O, Lombardi L, Williams D, et al., 2022,
Strategies for improving peptide stability and delivery
, Pharmaceuticals, Vol: 15, ISSN: 1424-8247Peptides play an important role in many fields, including immunology, medical diagnostics, and drug discovery, due to their high specificity and positive safety profile. However, for their delivery as active pharmaceutical ingredients, delivery vectors, or diagnostic imaging molecules, they suffer from two serious shortcomings: their poor metabolic stability and short half-life. Major research efforts are being invested to tackle those drawbacks, where structural modifications and novel delivery tactics have been developed to boost their ability to reach their targets as fully functional species. The benefit of selected technologies for enhancing the resistance of peptides against enzymatic degradation pathways and maximizing their therapeutic impact are also reviewed. Special note of cell-penetrating peptides as delivery vectors, as well as stapled modified peptides, which have demonstrated superior stability from their parent peptides, are reported.
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Journal articleGovada L, Rubio N, Saridakis E, et al., 2022,
Graphene-based nucleants for protein crystallization
, Advanced Functional Materials, Vol: 32, ISSN: 1616-301XProtein crystallization remains a major bottleneck for the determination of high resolution structures. Nucleants can accelerate the process but should ideally be compatible with high throughput robotic screening. Polyethylene glycol grafted (PEGylated) graphenes can be stabilized in water providing dispensable, nucleant systems. Two graphitic feedstocks are exfoliated and functionalized with PEG using a non-destructive, scalable, chemical reduction method, delivering good water dispersibility (80 and 750 µg mL−1 for large and small layers, respectively). The wide utility of these nucleants has been established across five proteins and three different screens, each of 96 conditions, demonstrating greater effectiveness of the dispersed PEGylated graphenes. Smaller numbers of larger, more crystalline flakes consistently act as better protein nucleants. The delivered nucleant concentration is optimized (0.1 mg mL−1 in the condition), and the performance benchmarked against existing state of the art, molecularly imprinted polymer nucleants. Strikingly, graphene nucleants are effective even when decreasing both the nucleant and protein concentration to unusually low concentrations. The set-up to scale-up nucleant production to liter volumes can provide sufficient material for wide implementation. Together with the optimized crystallization conditions, the results are a step forward toward practical synthesis of a readily accessible “universal” nucleant.
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Journal articleBubeck D, Jin Y, Fyfe PK, et al., 2022,
Structural insights into the assembly and activation of the IL-27 signalling complex
, EMBO Reports, Vol: 23, ISSN: 1469-221XInterleukin 27 (IL-27) is a heterodimeric cytokine that elicits potent immuno-suppressive responses. Comprised of EBI3 and p28 subunits, IL-27 binds GP130 and IL-27Rα receptor chains to activate the JAK/STAT signalling cascade. However, how these receptors recognize IL-27 and form a complex capable of phosphorylating JAK proteins remains unclear. Here, we used cryo electron microscopy (cryoEM) and AlphaFold2 modelling to solve the structure of the IL-27 receptor recognition complex. Our data show how IL-27 serves as a bridge connecting IL-27Rα (domains 1-2) with GP130 (domains 1-3) to initiate signalling. While both receptors contact the p28 component of the heterodimeric cytokine, EBI3 stabilizes the complex by binding a positively charged surface of IL-27Rα and Domain 1 of GP130. We find that assembly of the IL-27 receptor recognition complex is distinct from both IL-12 and IL-6 cytokine families and provides a mechanistic blueprint for tuning IL-27 pleiotropic actions.
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Journal articleLangley J, Purchase R, Viola S, et al., 2022,
Simulating the low-temperature, metastable electrochromism of Photosystem I: Applications to <i>Thermosynechococcus vulcanus</i> and <i>Chroococcidiopsis thermalis</i>
, JOURNAL OF CHEMICAL PHYSICS, Vol: 157, ISSN: 0021-9606 -
Journal articleNajer A, Blight J, Ducker CB, et al., 2022,
Potent virustatic polymer-lipid nanomimics block viral entry and inhibit malaria parasites in vivo
, ACS Central Science, Vol: 8, Pages: 1238-1257, ISSN: 2374-7943Infectious diseases continue to pose a substantial burden on global populations, requiring innovative broad-spectrum prophylactic and treatment alternatives. Here, we have designed modular synthetic polymer nanoparticles that mimic functional components of host cell membranes, yielding multivalent nanomimics that act by directly binding to varied pathogens. Nanomimic blood circulation time was prolonged by reformulating polymer–lipid hybrids. Femtomolar concentrations of the polymer nanomimics were sufficient to inhibit herpes simplex virus type 2 (HSV-2) entry into epithelial cells, while higher doses were needed against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Given their observed virustatic mode of action, the nanomimics were also tested with malaria parasite blood-stage merozoites, which lose their invasive capacity after a few minutes. Efficient inhibition of merozoite invasion of red blood cells was demonstrated both in vitro and in vivo using a preclinical rodent malaria model. We envision these nanomimics forming an adaptable platform for developing pathogen entry inhibitors and as immunomodulators, wherein nanomimic-inhibited pathogens can be secondarily targeted to sites of immune recognition.
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Journal articleMartinez-Ahumada E, Kim DW, Wahiduzzaman M, et al., 2022,
Capture and detection of SO<sub>2</sub> using a chemically stable Mg(ii)-MOF
, JOURNAL OF MATERIALS CHEMISTRY A, Vol: 10, Pages: 18636-18643, ISSN: 2050-7488- Cite
- Citations: 3
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Journal articleKlitou P, Rosbottom I, Karde V, et al., 2022,
Relating crystal structure to surface properties: a study on quercetin solid forms
, Crystal Growth and Design, Vol: 22, Pages: 6103-6113, ISSN: 1528-7483The surface energy and surface chemistry of a crystal are of great importance when designing particles for a specific application, as these will impact both downstream manufacturing processes as well as final product quality. In this work, the surface properties of two different quercetin solvates (quercetin dihydrate and quercetin DMSO solvate) were studied using molecular (synthonic) modeling and experimental techniques, including inverse gas chromatography (IGC) and contact angle measurements, to establish a relationship between crystal structure and surface properties. The attachment energy model was used to predict morphologies and calculate surface properties through the study of their growth synthons. The modeling results confirmed the surface chemistry anisotropy for the two forms. For quercetin dihydrate, the {010} facets were found to grow mainly by nonpolar offset quercetin–quercetin stacking interactions, thus being hydrophobic, while the {100} facets were expected to be hydrophilic, growing by a polar quercetin–water hydrogen bond. For QDMSO, the dominant facet {002} grows by a strong polar quercetin–quercetin hydrogen bonding interaction, while the second most dominant facet {011} grows by nonpolar π–π stacking interactions. Water contact angle measurements and IGC confirmed a greater overall surface hydrophilicity for QDMSO compared to QDH and demonstrated surface energy heterogeneity for both structures. This work shows how synthonic modeling can help in the prediction of the surface nature of crystalline particles and guide the choice of parameters that will determine the optimal crystal form and final morphology for targeted surface properties, for example, the choice of crystallization conditions, choice of solvent, or presence of additives or impurities, which can direct the crystallization of a specific crystal form or crystal shape.
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Journal articleThabet MA, Penadés JR, Haag AF, 2022,
The ClpX protease is essential for removing the CI master repressor and completing prophage induction in <i>Staphylococcus aureus</i>
<jats:title>Abstract</jats:title> <jats:p>Bacteriophages (phages) are the predominant biological entities on the planet and play an important role in the spread of bacterial virulence, pathogenicity, and antimicrobial resistance. After infection, temperate phages can integrate in the bacterial chromosome thanks to the expression of the prophage-encoded CI master repressor. Upon SOS induction, and promoted by RecA*, CI auto-cleaves generating two fragments, one containing the N-terminal domain (NTD), which retains strong DNA-binding capacity, and other corresponding to the C-terminal part of the protein. However, it is unknown how the CI NTD is removed, a process that is essential to allow prophage induction. Here we identify for the first time that the specific interaction of the ClpX protease with the CI NTD repressor fragment is essential and sufficient for prophage activation after SOS-mediated CI autocleavage, defining the final stage in the prophage induction cascade. Our results provide unexpected roles for the bacterial protease ClpX in phage biology.</jats:p>
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Journal articleCrone M, MacDonald J, Freemont P, et al., 2022,
gDesigner: computational design of synthetic gRNAs for Cas12a-based transcriptional repression in mammalian cells
, npj Systems Biology and Applications, Vol: 8, Pages: 1-7, ISSN: 2056-7189Synthetic networks require complex intertwined genetic regulation often relying on transcriptional activation or repression of target genes. CRISPRi-based transcription factors facilitate the programmable modulation of endogenous or synthetic promoter activity and can be aided by using software to select appropriate gRNAs and limit non-specific gene modulation. Here, we develop a computational software pipeline, gDesigner, that enables the automated selection of orthogonal gRNAs with minimized off-target effects and promoter crosstalk. We next engineered a Lachnospiraceae bacterium Cas12a (dLbCas12a)-based repression system that downregulates target gene expression by means of steric hindrance of the cognate promoter. Finally, we generated a library of orthogonal synthetic dCas12a-repressed promoters and experimentally demonstrated it in HEK293FT, U2OS and H1299 cells lines. Our system expands the toolkit of mammalian synthetic promoters with a new complementary and orthogonal CRISPRi-based system, ultimately enabling the design of synthetic promoter libraries for multiplex gene perturbation that facilitate the understanding of complex cellular phenotypes.
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Journal articleKreutzberger MAB, Sonani RR, Liu J, et al., 2022,
Convergent evolution in the supercoiling of prokaryotic flagellar filaments
, CELL, Vol: 185, Pages: 3487-+, ISSN: 0092-8674- Cite
- Citations: 38
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Journal articleBullen NP, Sychantha D, Thang SS, et al., 2022,
An ADP-ribosyltransferase toxin kills bacterial cells by modifying structured non-coding RNAs
, Molecular Cell, Vol: 82, Pages: 3484-3498.e11, ISSN: 1097-2765ADP-ribosyltransferases (ARTs) were among the first identified bacterial virulence factors. Canonical ART toxins are delivered into host cells where they modify essential proteins, thereby inactivating cellular processes and promoting pathogenesis. Our understanding of ARTs has since expanded beyond protein-targeting toxins to include antibiotic inactivation and DNA damage repair. Here, we report the discovery of RhsP2 as an ART toxin delivered between competing bacteria by a type VI secretion system of Pseudomonas aeruginosa. A structure of RhsP2 reveals that it resembles protein-targeting ARTs such as diphtheria toxin. Remarkably, however, RhsP2 ADP-ribosylates 2'-hydroxyl groups of double-stranded RNA, and thus, its activity is highly promiscuous with identified cellular targets including the tRNA pool and the RNA-processing ribozyme, ribonuclease P. Consequently, cell death arises from the inhibition of translation and disruption of tRNA processing. Overall, our data demonstrate a previously undescribed mechanism of bacterial antagonism and uncover an unprecedented activity catalyzed by ART enzymes.
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Journal articleNanev CN, Saridakis E, Govada L, et al., 2022,
Protein crystals nucleated and grown by means of porous materials display improved X-ray diffraction quality
, International Journal of Molecular Sciences, Vol: 23, Pages: 1-13, ISSN: 1422-0067Well-diffracting protein crystals are indispensable for X-ray diffraction analysis, which is still the most powerful method for structure-function studies of biomolecules. A promising approach to growing such crystals is the use of porous nucleation-inducing materials. However, while protein crystal nucleation in pores has been thoroughly considered, little attention has been paid to the subsequent growth of crystals. Although the nucleation stage is decisive, it is the subsequent growth of crystals outside the pore that determines their diffraction quality. The molecular-scale mechanism of growth of protein crystals in and outside pores is theoretically considered. Due to the low degree of metastability, the crystals that emerge from the pores grow slowly, which is a prerequisite for better diffraction. This expectation has been corroborated by experiments carried out with several types of porous material, such as bioglass (“Naomi’s Nucleant”), buckypaper, porous gold and porous silicon. Protein crystals grown with the aid of bioglass and buckypaper yield significantly better diffraction quality compared with crystals grown conventionally. In all cases, visually superior crystals are usually obtained. Our theoretical conclusion is that heterogeneous nucleation of a crystal outside the pore is an exceptional case. Rather, the protein crystals nucleating inside the pores continue growing outside them.
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