Protein Interaction Kinetics Delimit the Performance of Phosphorylation-Driven Protein Switches.

Post-translational modifications (PTMs) such as phosphorylation and dephosphorylation can rapidly alter protein surface chemistry and structural conformation, which can switch protein-protein interactions (PPIs) within signaling networks. Recently, de novo-designed phosphorylation-responsive protein switches have been created that harness kinase- and phosphatase-mediated phosphorylation to modulate PPIs. PTM-driven protein switches are promising tools for investigating PTM dynamics in living cells, developing biocompatible nanodevices, and engineering signaling pathways to program cell behavior. However, little is known about the physical and kinetic constraints of PTM-driven protein switches, which limits their practical application. In this study, we present a framework to evaluate two-component PTM-driven protein switches based on four performance metrics: effective concentration, dynamic range, response time, and reversibility. Our computational models reveal an intricate relationship between the binding kinetics, phosphorylation kinetics, and switch concentration that governs the sensitivity and reversibility of PTM-driven protein switches. Building upon the insights of the interaction modeling, we built and evaluated novel phosphorylation-driven protein switches consisting of phosphorylation-sensitive coiled coils as sensor domains fused to fluorescent proteins as actuator domains. By modulating the phosphorylation state of the switches with a specific protein kinase and phosphatase, we demonstrate fast, reversible transitions between "on" and "off" states. The response of the switches linearly correlated to the kinase concentration, demonstrating its potential as a biosensor for kinase measurements in real time. As intended, the switches responded to specific kinase activity with an increase in the fluorescence signal and our model could be used to distinguish between two mechanisms of switch activation: dimerization or a structural rearrangement. The protein switch kinetics model developed here should enable PTM-driven switches to be designed with ideal performance for specific applications.

Tuning the stator subunit of the flagellar motor with coiled-coil engineering.

Many bacteria swim driven by an extracellular filament rotated by the bacterial flagellar motor. This motor is powered by the stator complex, MotA5 MotB2 , an heptameric complex which forms an ion channel which couples energy from the ion motive force to torque generation. Recent structural work revealed that stator complex consists of a ring of five MotA subunits which rotate around a central dimer of MotB subunits. Transmembrane (TM) domains TM3 and TM4 from MotA combine with the single TM domain from MotB to form two separate ion channels within this complex. Much is known about the ion binding site and ion specificity; however, to date, no modeling has been undertaken to explore the MotB-MotB dimer stability and the role of MotB conformational dynamics during rotation. Here, we modeled the central MotB dimer using coiled-coil engineering and modeling principles and calculated free energies to identify stable states in the operating cycle of the stator. We found three stable coiled-coil states with dimer interface angles of 28°, 56°, and 64°. We tested the effect of strategic mutagenesis on the comparative energy of the states and correlated motility with a specific hierarchy of stability between the three states. In general, our results indicate agreement with existing models describing a 36° rotation step of the MotA pentameric ring during the power stroke and provide an energetic basis for the coordinated rotation of the central MotB dimer based on coiled-coil modeling.

Effects of Phosphorylation on the Activity, Inhibition and Stability of Carbonic Anhydrases.

Carbonic anhydrases (CAs) are a metalloenzyme family that have important roles in cellular processes including pH homeostasis and have been implicated in multiple pathological conditions. Small molecule inhibitors have been developed to target carbonic anhydrases, but the effects of post-translational modifications (PTMs) on the activity and inhibition profiles of these enzymes remain unclear. Here, we investigate the effects of phosphorylation, the most prevalent carbonic anhydrase PTM, on the activities and drug-binding affinities of human CAI and CAII, two heavily modified active isozymes. Using serine to glutamic acid (S > E) mutations to mimic the effect of phosphorylation, we demonstrate that phosphomimics at a single site can significantly increase or decrease the catalytic efficiencies of CAs, depending on both the position of the modification and the CA isoform. We also show that the S > E mutation at Ser50 of hCAII decreases the binding affinities of hCAII with well-characterized sulphonamide inhibitors including by over 800-fold for acetazolamide. Our findings suggest that CA phosphorylation may serve as a regulatory mechanism for enzymatic activity, and affect the binding affinity and specificity of small, drug and drug-like molecules. This work should motivate future studies examining the PTM-modification forms of CAs and their distributions, which should provide insights into CA physiopathological functions and facilitate the development of 'modform-specific' carbonic anhydrase inhibitors.

A versatile multimodal chromatography strategy to rapidly purify protein nanostructures assembled in cell lysates.

BACKGROUND: Protein nanostructures produced through the self-assembly of individual subunits are attractive scaffolds to attach and position functional molecules for applications in biomaterials, metabolic engineering, tissue engineering, and a plethora of nanomaterials. However, the assembly of multicomponent protein nanomaterials is generally a laborious process that requires each protein component to be separately expressed and purified prior to assembly. Moreover, excess components not incorporated into the final assembly must be removed from the solution and thereby necessitate additional processing steps. RESULTS: We developed an efficient approach to purify functionalized protein nanostructures directly from bacterial lysates through a type of multimodal chromatography (MMC) that combines size-exclusion, hydrophilic interaction, and ion exchange to separate recombinant protein assemblies from excess free subunits and bacterial proteins. We employed the ultrastable filamentous protein gamma-prefoldin as a material scaffold that can be functionalized with a variety of protein domains through SpyTag/SpyCatcher conjugation chemistry. The purification of recombinant gamma-prefoldin filaments from bacterial lysates using MMC was tested across a wide range of salt concentrations and pH, demonstrating that the MMC resin is robust, however the optimal choice of salt species, salt concentration, and pH is likely dependent on the protein nanostructure to be purified. In addition, we show that pre-processing of the samples with tangential flow filtration to remove nucleotides and metabolites improves resin capacity, and that post-processing with Triton X-114 phase partitioning is useful to remove lipids and any remaining lipid-associated protein. Subsequently, functionalized protein filaments were purified from bacterial lysates using MMC and shown to be free of unincorporated subunits. The assembly and purification of protein filaments with varying amounts of functionalization was confirmed using polyacrylamide gel electrophoresis, Förster resonance energy transfer, and transmission electron microscopy. Finally, we compared our MMC workflow to anion exchange chromatography with the purification of encapsulin nanocompartments containing a fluorescent protein as a cargo, demonstrating the versatility of the protocol and that the purity of the assembly is comparable to more traditional procedures. CONCLUSIONS: We envision that the use of MMC will increase the throughput of protein nanostructure prototyping as well as enable the upscaling of the bioproduction of protein nanodevices.

Spraying Fluorinated Silicon Oxide Nanoparticles on CuONPs@CF-PVDF Membrane: A Simple Method to Achieve Superhydrophobic Surfaces and High Flux in Direct Contact Membrane Distillation.

Desalinization of seawater can be achieved by membrane distillation techniques (MD). In MD, the membranes should be resistant to fouling, robust for extended operating time, and preferably provide a superhydrophobic surface. In this work, we report the preparation and characterization of a robust and superhydrophobic polyvinylidene fluoride membrane containing fluoroalkyl-capped CuONPs (CuONPs@CF) in the inner and fluorinated capped silicon oxide nanoparticles (SiO2NPs@CF) on its surface. SiO2NPs@CF with a mean diameter of 225 ± 20 nm were prepared by the sol method using 1H,1H,2H,2H-perfluorodecyltriethoxysilane as a capping agent. Surface modification of the membrane was carried out by spraying SiO2NPs@CF (5% wt.) dispersed in a mixture of dimethyl formamide (DMF) and ethanol (EtOH) at different DMF/EtOH % v/v ratios (0, 5, 10, 20, and 50). While ethanol dispersed the nanoparticles in the spraying solution, DMF dissolved the PVDF on the surface and retained the sprayed nanoparticles. According to SEM micrographs and water contact angle measurements, the best results were achieved by depositing the nanoparticles at 10% v/v of DMF/EtOH. Under these conditions, a SiO2NPs covered surface was observed with a water contact angle of 168.5°. The water contact angle was retained after the sonication of the membrane, indicating that the modification was successfully achieved. The membrane with SiO2NPs@CF showed a flux of 14.3 kg(m2·h)-1, 3.4 times higher than the unmodified version. The method presented herein avoids the complicated modification procedure offered by chemical step modification and, due to its simplicity, could be scalable to a commercial membrane.

Recovery of Lithium Carbonate from Dilute Li-Rich Brine via Homogenous and Heterogeneous Precipitation.

An extensive experimental campaign on Li recovery from relatively dilute LiCl solutions (i.e., Li+ ∼ 4000 ppm) is presented to identify the best operating conditions for a Li2CO3 crystallization unit. Lithium is currently mainly produced via solar evaporation, purification, and precipitation from highly concentrated Li brines located in a few world areas. The process requires large surfaces and long times (18-24 months) to concentrate Li+ up to 20,000 ppm. The present work investigates two separation routes to extract Li+ from synthetic solutions, mimicking those obtained from low-content Li+ sources through selective Li+ separation and further concentration steps: (i) addition of Na2CO3 solution and (ii) addition of NaOH solution + CO2 insufflation. A Li recovery up to 80% and purities up to 99% at 80 °C and with high-ionic strength solutions was achieved employing NaOH solution + CO2 insufflation and an ethanol washing step.

Economic Benefits of Waste Pickling Solution Valorization.

An integrated hybrid membrane process, composed of a diffusion dialysis (DD), a membrane distillation (MD) and a reactive precipitation unit (CSTR), is proposed as a promising solution for the valorization and onsite recycling of pickling waste streams. An economic analysis was performed aiming to demonstrate the feasibility of the developed process with a NPV of about EUR 40,000 and a DPBP of 4 years. The investment and operating costs, as well as the avoided costs and the benefits for the company operating the plant, were analyzed with an extensive cost tracking exercise and through face-to-face contact with manufacturers and sector leaders. A mathematical model was implemented using the gPROMS modelling platform. It is able to simulate steady state operations and run optimization analysis of the process performance. The impact of key operating and design parameters, such as the set-point bath concentration and the DD and MD membrane areas, respectively, was investigated and the optimal arrangement was identified. Finally, operating variables and design parameters were optimized simultaneously in a nonlinear framework as a tradeoff between profitability and environmental impact. We show how the integration of new technologies into the traditional pickling industry could provide a significant benefit for the issues of process sustainability, which are currently pressing.

Multiplexed Screening of Thousands of Natural Products for Protein-Ligand Binding in Native Mass Spectrometry.

The structural diversity of natural products offers unique opportunities for drug discovery, but challenges associated with their isolation and screening can hinder the identification of drug-like molecules from complex natural product extracts. Here we introduce a mass spectrometry-based approach that integrates untargeted metabolomics with multistage, high-resolution native mass spectrometry to rapidly identify natural products that bind to therapeutically relevant protein targets. By directly screening crude natural product extracts containing thousands of drug-like small molecules using a single, rapid measurement, we could identify novel natural product ligands of human drug targets without fractionation. This method should significantly increase the efficiency of target-based natural product drug discovery workflows.

New Australian guidelines for the treatment of alcohol problems: an overview of recommendations.

OF RECOMMENDATIONS AND LEVELS OF EVIDENCE: Chapter 2: Screening and assessment for unhealthy alcohol use Screening Screening for unhealthy alcohol use and appropriate interventions should be implemented in general practice (Level A), hospitals (Level B), emergency departments and community health and welfare settings (Level C). Quantity-frequency measures can detect consumption that exceeds levels in the current Australian guidelines (Level B). The Alcohol Use Disorders Identification Test (AUDIT) is the most effective screening tool and is recommended for use in primary care and hospital settings. For screening in the general community, the AUDIT-C is a suitable alternative (Level A). Indirect biological markers should be used as an adjunct to screening (Level A), and direct measures of alcohol in breath and/or blood can be useful markers of recent use (Level B). Assessment Assessment should include evaluation of alcohol use and its effects, physical examination, clinical investigations and collateral history taking (Level C). Assessment for alcohol-related physical problems, mental health problems and social support should be undertaken routinely (GPP). Where there are concerns regarding the safety of the patient or others, specialist consultation is recommended (Level C). Assessment should lead to a clear, mutually acceptable treatment plan which specifies interventions to meet the patient's needs (Level D). Sustained abstinence is the optimal outcome for most patients with alcohol dependence (Level C). Chapter 3: Caring for and managing patients with alcohol problems: interventions, treatments, relapse prevention, aftercare, and long term follow-up Brief interventions Brief motivational interviewing interventions are more effective than no treatment for people who consume alcohol at risky levels (Level A). Their effectiveness compared with standard care or alternative psychosocial interventions varies by treatment setting. They are most effective in primary care settings (Level A). Psychosocial interventions Cognitive behaviour therapy should be a first-line psychosocial intervention for alcohol dependence. Its clinical benefit is enhanced when it is combined with pharmacotherapy for alcohol dependence or an additional psychosocial intervention (eg, motivational interviewing) (Level A). Motivational interviewing is effective in the short term and in patients with less severe alcohol dependence (Level A). Residential rehabilitation may be of benefit to patients who have moderate-to-severe alcohol dependence and require a structured residential treatment setting (Level D). Alcohol withdrawal management Most cases of withdrawal can be managed in an ambulatory setting with appropriate support (Level B). Tapering diazepam regimens (Level A) with daily staged supply from a pharmacy or clinic are recommended (GPP). Pharmacotherapies for alcohol dependence Acamprosate is recommended to help maintain abstinence from alcohol (Level A). Naltrexone is recommended for prevention of relapse to heavy drinking (Level A). Disulfiram is only recommended in close supervision settings where patients are motivated for abstinence (Level A). Some evidence for off-label therapies baclofen and topiramate exists, but their side effect profiles are complex and neither should be a first-line medication (Level B). Peer support programs Peer-led support programs such as Alcoholics Anonymous and SMART Recovery are effective at maintaining abstinence or reductions in drinking (Level A). Relapse prevention, aftercare and long-term follow-up Return to problematic drinking is common and aftercare should focus on addressing factors that contribute to relapse (GPP). A harm-minimisation approach should be considered for patients who are unable to reduce their drinking (GPP). Chapter 4: Providing appropriate treatment and care to people with alcohol problems: a summary for key specific populations Gender-specific issues Screen women and men for domestic abuse (Level C). Consider child protection assessments for caregivers with alcohol use disorder (GPP). Explore contraceptive options with women of reproductive age who regularly consume alcohol (Level B). Pregnant and breastfeeding women Advise pregnant and breastfeeding women that there is no safe level of alcohol consumption (Level B). Pregnant women who are alcohol dependent should be admitted to hospital for treatment in an appropriate maternity unit that has an addiction specialist (GPP). Young people Perform a comprehensive HEEADSSS assessment for young people with alcohol problems (Level B). Treatment should focus on tangible benefits of reducing drinking through psychotherapy and engagement of family and peer networks (Level B). Aboriginal and Torres Strait Islander peoples Collaborate with Aboriginal or Torres Strait Islander health workers, organisations and communities, and seek guidance on patient engagement approaches (GPP). Use validated screening tools and consider integrated mainstream and Aboriginal or Torres Strait Islander-specific approaches to care (Level B). Culturally and linguistically diverse groups Use an appropriate method, such as the "teach-back" technique, to assess the need for language and health literacy support (Level C). Engage with culture-specific agencies as this can improve treatment access and success (Level C). Sexually diverse and gender diverse populations Be mindful that sexually diverse and gender diverse populations experience lower levels of satisfaction, connection and treatment completion (Level C). Seek to incorporate LGBTQ-specific treatment and agencies (Level C). Older people All new patients aged over 50 years should be screened for harmful alcohol use (Level D). Consider alcohol as a possible cause for older patients presenting with unexplained physical or psychological symptoms (Level D). Consider shorter acting benzodiazepines for withdrawal management (Level D). Cognitive impairment Cognitive impairment may impair engagement with treatment (Level A). Perform cognitive screening for patients who have alcohol problems and refer them for neuropsychological assessment if significant impairment is suspected (Level A). SUMMARY OF KEY RECOMMENDATIONS AND LEVELS OF EVIDENCE: Chapter 5: Understanding and managing comorbidities for people with alcohol problems: polydrug use and dependence, co-occurring mental disorders, and physical comorbidities Polydrug use and dependence Active alcohol use disorder, including dependence, significantly increases the risk of overdose associated with the administration of opioid drugs. Specialist advice is recommended before treatment of people dependent on both alcohol and opioid drugs (GPP). Older patients requiring management of alcohol withdrawal should have their use of pharmaceutical medications reviewed, given the prevalence of polypharmacy in this age group (GPP). Smoking cessation can be undertaken in patients with alcohol dependence and/or polydrug use problems; some evidence suggests varenicline may help support reduction of both tobacco and alcohol consumption (Level C). Co-occurring mental disorders More intensive interventions are needed for people with comorbid conditions, as this population tends to have more severe problems and carries a worse prognosis than those with single pathology (GPP). The Kessler Psychological Distress Scale (K10 or K6) is recommended for screening for comorbid mental disorders in people presenting for alcohol use disorders (Level A). People with alcohol use disorder and comorbid mental disorders should be offered treatment for both disorders; care should be taken to coordinate intervention (Level C). Physical comorbidities Patients should be advised that alcohol use has no beneficial health effects. There is no clear risk-free threshold for alcohol intake. The safe dose for alcohol intake is dependent on many factors such as underlying liver disease, comorbidities, age and sex (Level A). In patients with alcohol use disorder, early recognition of the risk for liver cirrhosis is critical. Patients with cirrhosis should abstain from alcohol and should be offered referral to a hepatologist for liver disease management and to an addiction physician for management of alcohol use disorder (Level A). Alcohol abstinence reduces the risk of cancer and improves outcomes after a diagnosis of cancer (Level A).

PVDF Composite Membranes with Hydrophobically-Capped CuONPs for Direct-Contact Membrane Distillation.

Water scarcity is an imminent problem that humanity is beginning to attempt to solve. Among the several technologies that have been developed to mitigate water scarcity, membrane distillation is of particular note. In the present work, CuO nanoparticles capped with 1-octanethiol (CuONPs@CH) or 1H,1H,2H,2H-perfluorodecanethiol (CuONPs@CF) are prepared. The nanoparticles are characterized by FT-IR and TGA methods. Two weight losses are observed in both cases, with the decomposition of the organic fragments beginning at 158 °C and 230 °C for CuONPs@CF and CuONPs@CH, respectively. Flat sheet PVDF composite membranes containing nanoparticles are prepared by the casting solution method using nanoparticle concentrations that ranged between 2-20% with a non-woven polyester fabric as support. The obtained membranes showed a thickness of 240 ± 40 µm. According to water contact angle (87° for CuONPs@CH and 95° for CuONPs@CF, both at 10% w.t) and roughness (12 pixel for CuONPs@CH and 14 pixels for CuONPs@CF, both at 10% w.t) determinations, the hydrophobicity of membranes changed due to a decrease in surface energy, while, for naked CuONPs, the roughness factor represents the main role. Membranes prepared with capped nanoparticles showed similar porosity (60-64%). SEM micrographs show asymmetric porous membranes with a 200-nm surface pore diameter. The largest finger-like pores in the membranes prepared with CuONPs, CuONPs@CH and CuONPs@CF had values of 63 ± 10 µm, 32 ± 8 µm, and 45 ± 10 µm, respectively. These membranes were submitted to a direct contact membrane distillation module and flux values of 1.8, 2.7, and 3.9 kg(m2·h)-1 at ΔT = 30 °C were obtained for the CuONPs, CuONPs@CH, and CuONPs@CF, respectively. The membranes showed 100% salt rejection during the testing time (240 min).

Are bottle shops using Twitter to increase advertising or encourage drinking during COVID-19?

OBJECTIVE: Preliminary reports suggested that liquor retailers used COVID-19 to promote alcohol through sponsored posts on Facebook and Instagram. To further understand the advertising practices during this period, we aimed to determine whether packaged liquor retailers increased their posts during COVID-19 or used COVID-19 to promote alcohol on Twitter. METHODS: 'Tweets' (Twitter posts) from all packaged liquor retailers in NSW written since 2018 were collected. Tweets written during the first COVID-19 lockdown period were coded for: references of COVID-19, types of marketing message, use of links to online stores and use of an alcohol-related 'meme'. RESULTS: There was no evidence of increased tweet frequency, however, some COVID-specific alcohol advertising was detected that leveraged the pandemic (4.0%) or referencing the pandemic without explicitly promoting alcohol (12.0%). The most popular market messages used in the tweets were encouraging alcohol use (15.4%) and easy access to alcohol at home (9.5%). CONCLUSIONS: At least on Twitter, there was no marked increase in posts from packaged liquor retailers in NSW and only some tweets used COVID-19 to promote alcohol. Implications for public health: The use of COVID-specific alcohol marketing on social media raises important considerations for legislative and regulatory requirements, particularly during major health events such as a pandemic.

Ageusia and anosmia, a common sign of COVID-19? A case series from four countries.

Over the course of the pandemic due to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), multiple new clinical manifestations, as the consequence of the tropism of the virus, have been recognized. That includes now the neurological manifestations and conditions, such as headache, encephalitis, as well as olfactory and taste disorders. We present a series of ten cases of RT-PCR-confirmed SARS-CoV-2-infected patients diagnosed with viral-associated olfactory and taste loss from four different countries.

Design of Tunable Protein Interfaces Controlled by Post-Translational Modifications.

The design of protein interaction interfaces is a cornerstone of synthetic biology, where they can be used to promote the association of protein subunits into active molecular complexes or into protein nanostructures. In nature, protein interactions can be modulated by post-translational modifications (PTMs) that modify the protein interfaces with the addition and removal of various chemical groups. PTMs thus represent a means to gain control over protein interactions, yet they have seldom been considered in the design of synthetic proteins. Here, we explore the potential of a reversible PTM, serine phosphorylation, to modulate the interactions between peptides. We designed a series of interacting peptide pairs, including heterodimeric coiled coils, that contained one or more protein kinase A (PKA) recognition motifs. Our set of peptide pairs comprised interactions ranging from nanomolar to micromolar affinities. Mass spectrometry analyses showed that all peptides were excellent phosphorylation substrates of PKA, and subsequent phosphate removal could be catalyzed by lambda protein phosphatase. Binding kinetics measurements performed before and after treatment of the peptides with PKA revealed that phosphorylation of the target serines affected both the association and dissociation rates of the interacting peptides. We observed both the strengthening of interactions (up to an 11-fold decrease in Kd) and the weakening of interactions (up to a 180-fold increase in Kd). De novo-designed PTM-modulated interfaces will be useful to control the association of proteins in biological systems using protein-modifying enzymes, expanding the paradigm of self-assembly to encompass controlled assembly of engineerable protein complexes.

Bacteriophage genotyping using BOXA repetitive-PCR.

BACKGROUND: Repetitive-PCR (rep-PCR) using BOXA1R and BOXA2R as single primers was investigated for its potential to genotype bacteriophage. Previously, this technique has been primarily used for the discrimination of bacterial strains. Reproducible DNA fingerprint patterns for various phage types were generated using either of the two primers. RESULTS: The similarity index of replicates ranged from 89.4-100% for BOXA2R-PCR, and from 90 to 100% for BOXA1R-PCR. The method of DNA isolation (p = 0.08) and the phage propagation conditions at two different temperatures (p = 0.527) had no significant influence on generated patterns. Rep-PCR amplification products were generated from different templates including purified phage DNA, phage lysates and phage plaques. The use of this method enabled comparisons of phage genetic profiles to establish their similarity to related or unrelated phages and their bacterial hosts. CONCLUSION: The findings suggest that repetitive-PCR could be used as a rapid and inexpensive method to preliminary screen phage isolates prior to their selection for more comprehensive studies. The adoption of this rapid, simple and reproducible technique could facilitate preliminary characterisation of a large number of phage isolates and the investigation of genetic relationship between phage genotypes.

Structural Determination of a Filamentous Chaperone to Fabricate Electronically Conductive Metalloprotein Nanowires.

The transfer of electrons through protein complexes is central to cellular respiration. Exploiting proteins for charge transfer in a controllable fashion has the potential to revolutionize the integration of biological systems and electronic devices. Here we characterize the structure of an ultrastable protein filament and engineer the filament subunits to create electronically conductive nanowires under aqueous conditions. Cryoelectron microscopy was used to resolve the helical structure of gamma-prefoldin, a filamentous protein from a hyperthermophilic archaeon. Conjugation of tetra-heme c3-type cytochromes along the longitudinal axis of the filament created nanowires capable of long-range electron transfer. Electrochemical transport measurements indicated networks of the nanowires capable of conducting current between electrodes at the redox potential of the cytochromes. Functionalization of these highly engineerable nanowires with other molecules, such as redox enzymes, may be useful for bioelectronic applications.