ABSTRACT
Transmembrane ß-barrels have considerable potential for a broad range of sensing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels, which provide suboptimal starting points. By contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to designing transmembrane ß-barrel pores with different diameters and pore geometries. Nuclear magnetic resonance and crystallographic characterization show that the designs are stably folded with structures resembling those of the design models. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 picosiemens (~0.5 nanometer pore diameter) to 430 picosiemens (~1.1 nanometer pore diameter). Our approach opens the door to the custom design of transmembrane nanopores for sensing and sequencing applications.
Subject(s)
Nanopores , Protein Engineering , Protein Folding , Crystallography, X-Ray , Nuclear Magnetic Resonance, Biomolecular , Protein Conformation, beta-Strand , Models, MolecularABSTRACT
BACKGROUND: Prediabetes management is a priority for policymakers globally, to avoid/delay type 2 diabetes (T2D) and reduce severe, costly health consequences. Countries moving from low to middle income are most at risk from the T2D "epidemic" and may find implementing preventative measures challenging; yet prevention has largely been evaluated in developed countries. METHODS: Markov cohort simulations explored costs and benefits of various prediabetes management approaches, expressed as "savings" to the public health care system, for three countries with high prediabetes prevalence and contrasting economic status (Poland, Saudi Arabia, Vietnam). Two scenarios were compared up to 15 y: "inaction" (no prediabetes intervention) and "intervention" with metformin extended release (ER), intensive lifestyle change (ILC), ILC with metformin (ER), or ILC with metformin (ER) "titration." RESULTS: T2D was the highest-cost health state at all time horizons due to resource use, and inaction produced the highest T2D costs, ranging from 9% to 34% of total health care resource costs. All interventions reduced T2D versus inaction, the most effective being ILC + metformin (ER) "titration" (39% reduction at 5 y). Metformin (ER) was the only strategy that produced net saving across the time horizon; however, relative total health care system costs of other interventions vs inaction declined over time up to 15 y. Viet Nam was most sensitive to cost and parameter changes via a one-way sensitivity analysis. CONCLUSIONS: Metformin (ER) and lifestyle interventions for prediabetes offer promise for reducing T2D incidence. Metformin (ER) could reduce T2D patient numbers and health care costs, given concerns regarding adherence in the context of funding/reimbursement challenges for lifestyle interventions.
Subject(s)
Diabetes Mellitus, Type 2 , Hypoglycemic Agents , Markov Chains , Metformin , Prediabetic State , Humans , Prediabetic State/economics , Prediabetic State/therapy , Prediabetic State/epidemiology , Diabetes Mellitus, Type 2/economics , Diabetes Mellitus, Type 2/epidemiology , Diabetes Mellitus, Type 2/prevention & control , Metformin/therapeutic use , Metformin/economics , Vietnam/epidemiology , Hypoglycemic Agents/therapeutic use , Hypoglycemic Agents/economics , Saudi Arabia/epidemiology , Cost-Benefit Analysis , Cost Savings , Male , Female , Middle Aged , Life Style , Health Care Costs/statistics & numerical dataABSTRACT
The ß-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E.â coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
Subject(s)
Escherichia coli Proteins , Escherichia coli , Escherichia coli/metabolism , Escherichia coli Proteins/chemistry , Bacterial Outer Membrane Proteins/metabolism , Electron Spin Resonance Spectroscopy , Protein FoldingABSTRACT
Transmembrane ß-barrels (TMBs) are widely used for single molecule DNA and RNA sequencing and have considerable potential for a broad range of sensing and sequencing applications. Current engineering approaches for nanopore sensors are limited to naturally occurring channels such as CsgG, which have evolved to carry out functions very different from sensing, and hence provide sub-optimal starting points. In contrast, de novo protein design can in principle create an unlimited number of new nanopores with any desired properties. Here we describe a general approach to the design of transmembrane ß-barrel pores with different diameter and pore geometry. NMR and crystallographic characterization shows that the designs are stably folded with structures close to the design models. We report the first examples of de novo designed TMBs with 10, 12 and 14 stranded ß-barrels. The designs have distinct conductances that correlate with their pore diameter, ranging from 110 pS (~0.5 nm pore diameter) to 430 pS (~1.1 nm pore diameter), and can be converted into sensitive small-molecule sensors with high signal to noise ratio. The capability to generate on demand ß-barrel pores of defined geometry opens up fundamentally new opportunities for custom engineering of sequencing and sensing technologies.
ABSTRACT
The ß-barrel assembly machinery (BAM complex) is essential for outer membrane protein (OMP) folding in Gram-negative bacteria, and represents a promising antimicrobial target. Several conformational states of BAM have been reported, but all have been obtained under conditions which lack the unique features and complexity of the outer membrane (OM). Here, we use Pulsed Electron-Electron Double Resonance (PELDOR, or DEER) spectroscopy distance measurements to interrogate the conformational ensemble of the BAM complex in E.â coli cells. We show that BAM adopts a broad ensemble of conformations in the OM, while in the presence of the antibiotic darobactin B (DAR-B), BAM's conformational equilibrium shifts to a restricted ensemble consistent with the lateral closed state. Our in-cell PELDOR findings are supported by new cryoEM structures of BAM in the presence and absence of DAR-B. This work demonstrates the utility of PELDOR to map conformational changes in BAM within its native cellular environment.
ABSTRACT
The outer membrane of Gram-negative bacteria presents a robust physicochemical barrier protecting the cell from both the natural environment and acting as the first line of defense against antimicrobial materials. The proteins situated within the outer membrane are responsible for a range of biological functions including controlling influx and efflux. These outer membrane proteins (OMPs) are ultimately inserted and folded within the membrane by the ß-barrel assembly machine (Bam) complex. The precise mechanism by which the Bam complex folds and inserts OMPs remains unclear. Here, we have developed a platform for investigating Bam-mediated OMP insertion. By derivatizing a gold surface with a copper-chelating self-assembled monolayer, we were able to assemble a planar system containing the complete Bam complex reconstituted within a phospholipid bilayer. Structural characterization of this interfacial protein-tethered bilayer by polarized neutron reflectometry revealed distinct regions consistent with known high-resolution models of the Bam complex. Additionally, by monitoring changes of mass associated with OMP insertion by quartz crystal microbalance with dissipation monitoring, we were able to demonstrate the functionality of this system by inserting two diverse OMPs within the membrane, pertactin, and OmpT. This platform has promising application in investigating the mechanism of Bam-mediated OMP insertion, in addition to OMP function and activity within a phospholipid bilayer environment.
Subject(s)
Escherichia coli Proteins , Bacterial Outer Membrane Proteins , Escherichia coli , Protein FoldingABSTRACT
The folding of ß-barrel outer membrane proteins (OMPs) in Gram-negative bacteria is catalysed by the ß-barrel assembly machinery (BAM). How lateral opening in the ß-barrel of the major subunit BamA assists in OMP folding, and the contribution of membrane disruption to BAM catalysis remain unresolved. Here, we use an anti-BamA monoclonal antibody fragment (Fab1) and two disulphide-crosslinked BAM variants (lid-locked (LL), and POTRA-5-locked (P5L)) to dissect these roles. Despite being lethal in vivo, we show that all complexes catalyse folding in vitro, albeit less efficiently than wild-type BAM. CryoEM reveals that while Fab1 and BAM-P5L trap an open-barrel state, BAM-LL contains a mixture of closed and contorted, partially-open structures. Finally, all three complexes globally destabilise the lipid bilayer, while BamA does not, revealing that the BAM lipoproteins are required for this function. Together the results provide insights into the role of BAM structure and lipid dynamics in OMP folding.
Subject(s)
Bacterial Outer Membrane Proteins/metabolism , Escherichia coli Proteins/metabolism , Hydrolases/metabolism , Liposomes/metabolism , Protein Folding , Bacterial Outer Membrane Proteins/genetics , Bacterial Outer Membrane Proteins/isolation & purification , Bacterial Outer Membrane Proteins/ultrastructure , Cryoelectron Microscopy , Dynamic Light Scattering , Escherichia coli Proteins/genetics , Escherichia coli Proteins/isolation & purification , Escherichia coli Proteins/ultrastructure , Hydrolases/genetics , Hydrolases/isolation & purification , Hydrolases/ultrastructure , Lipid Metabolism , Liposomes/ultrastructure , Molecular Dynamics Simulation , Protein Conformation, beta-Strand , Proteolipids/metabolism , Proteolipids/ultrastructure , Recombinant Proteins/genetics , Recombinant Proteins/isolation & purification , Recombinant Proteins/metabolism , Recombinant Proteins/ultrastructureABSTRACT
The purpose of this study was to produce two statistical survival models in those with cirrhosis utilising only routine parameters, including non-liver-related clinical factors that influence survival. The first model identified and utilised factors impacting short-term survival to 90-days post incident diagnosis, and a further model characterised factors that impacted survival following this acute phase. Data were from the Clinical Practice Research Datalink linked with Hospital Episode Statistics. Incident cases in patients ≥18 years were identified between 1998 and 2014. Patients that had prior history of cancer or had received liver transplants prior were excluded. Model-1 used a logistic regression model to predict mortality. Model-2 used data from those patients who survived 90 days, and used an extension of the Cox regression model, adjusting for time-dependent covariables. At 90 days, 23% of patients had died. Overall median survival was 3.7 years. Model-1: numerous predictors, prior comorbidities and decompensating events were incorporated. All comorbidities contributed to increased odds of death, with renal disease having the largest adjusted odds ratio (OR = 3.35, 95%CI 2.97-3.77). Model-2: covariables included cumulative admissions for liver disease-related events and admissions for infections. Significant covariates were renal disease (adjusted hazard ratio (HR = 2.89, 2.47-3.38)), elevated bilirubin levels (aHR = 1.38, 1.26-1.51) and low sodium levels (aHR = 2.26, 1.84-2.78). An internal validation demonstrated reliability of both models. In conclusion: two survival models that included parameters commonly recorded in routine clinical practice were generated that reliably forecast the risk of death in patients with cirrhosis: in the acute, post diagnosis phase, and following this critical, 90 day phase. This has implications for practice and helps better forecast the risk of mortality from cirrhosis using routinely recorded parameters without inputs from specialists.
Subject(s)
Liver Cirrhosis/mortality , Models, Theoretical , Female , Humans , Incidence , Kaplan-Meier Estimate , Liver Cirrhosis/diagnosis , Logistic Models , Male , Middle Aged , Proportional Hazards Models , Reproducibility of ResultsABSTRACT
BACKGROUND: Hepatic encephalopathy (HE) is one of the most important severe complications of liver cirrhosis. Thought to be caused by elevated blood levels of gut-derived neurotoxins (particularly ammonia) entering the brain, HE manifests as a wide range of neurological or psychiatric abnormalities, which increase the risk of mortality, result in substantial morbidity and negatively affect the quality of life (QoL) of both patients and their caregivers. HE is also associated with a substantial economic burden. Rifaximin-α 550 mg is a locally acting oral antibiotic that reduces the effects of ammonia-producing intestinal flora, and which is used to help reduce the recurrence of overt HE. The efficacy of rifaximin-α 550 mg was established in a randomised controlled trial and long-term extension study. However, 'real-world' evidence is also required to assess how this efficacy may translate into effectiveness in clinical practice, including the potential impact of treatment on healthcare resource utilisation. METHODS: The Prospective Real-world Outcomes Study of HE Patients' Experience on Rifaximin-α 550 mg (PROSPER) is a multinational, multicentre, observational study that will be conducted under real-world clinical practice conditions. Comprising a retrospective phase (up to 12 months) and a prospective phase (up to 24 months), and employing a robust statistical methodology, PROSPER has been specifically designed to minimise the bias associated with observational studies. The primary endpoint will be the effect of rifaximin-α 550 mg treatment on HE- and liver-related hospitalisation rate and duration of hospitalisation. Secondary endpoints will include comprehensive assessments of the impact of treatment on the QoL and workplace productivity of patients and caregivers, a global assessment of treatment effectiveness and safety/tolerability. Approximately 550 patients will be enrolled. CONCLUSIONS: PROSPER will provide valuable real-world information on the effectiveness of rifaximin-α 550 mg in reducing the recurrence of HE, and its impact on the QoL and work productivity of patients and their caregivers. By providing data on both the direct costs (e.g., hospitalisation rate, duration of hospitalisation) and indirect costs (such as work productivity) of HE, PROSPER should help confirm whether rifaximin-α 550 mg treatment represents a good use of economic resources. TRIAL REGISTRATION: ClinicalTrials.gov identifier NCT02488993.
ABSTRACT
OBJECTIVE: Rifaximin-α 550 mg twice daily plus lactulose has demonstrated efficacy in reducing recurrence of episodes of overt hepatic encephalopathy (OHE) and the risk of hepatic encephalopathy (HE)-related hospitalizations compared with lactulose alone. This analysis estimated the cost effectiveness of rifaximin-α 550 mg twice daily plus lactulose versus lactulose alone in United Kingdom (UK) cirrhotic patients with OHE. METHOD: A Markov model was built to estimate the incremental cost-effectiveness ratio (ICER). The perspective was that of the UK National Health Service (NHS). Clinical data was sourced from a randomized controlled trial (RCT) and an open-label maintenance study in cirrhotic patients in remission from recurrent episodes of OHE. Health-related utility was estimated indirectly from disease-specific quality of life RCT data. Resource use data describing the impact of rifaximin-α on hospital admissions and length of stay for cirrhotic patients with OHE was from four single-center UK audits. Costs (2012) were derived from published sources; costs and benefits were discounted at 3.5%. The base-case time horizon was 5 years. RESULTS: The average cost per patient was £22,971 in the rifaximin-α plus lactulose arm and £23,545 in the lactulose arm, a saving of £573. The corresponding values for benefit were 2.35 quality adjusted life years (QALYs) and 1.83 QALYs per person, a difference of 0.52 QALYs. This translated into a dominant base-case ICER. Key parameters that impacted the ICER included number of hospital admissions and length of stay. CONCLUSION: Rifaximin-α 550 mg twice daily in patients with recurrent episodes of OHE was estimated to generate cost savings and improved clinical outcomes compared to standard care over 5 years.
Subject(s)
Hepatic Encephalopathy , Lactulose , Quality of Life , Rifaximin , Cost Savings , Cost-Benefit Analysis , Female , Gastrointestinal Agents/economics , Gastrointestinal Agents/therapeutic use , Hepatic Encephalopathy/drug therapy , Hepatic Encephalopathy/epidemiology , Hepatic Encephalopathy/psychology , Humans , Lactulose/economics , Lactulose/therapeutic use , Male , Middle Aged , Quality-Adjusted Life Years , Rifaximin/economics , Rifaximin/therapeutic use , Secondary Prevention/methods , Secondary Prevention/statistics & numerical data , United Kingdom/epidemiologyABSTRACT
AIM: To compare treatment costs with alternative luteinizing hormone-releasing hormone (LHRH) agonist preparations and determine whether a leuprorelin solid implant is associated with potential cost savings. PATIENTS & METHODS: A hypothetical population of 1000 prostate cancer patients was apportioned between the three most commonly-prescribed LHRH agonist preparations. Differentiated annual costs for 1- and 3-monthly formulations were calculated for France, Germany, Italy, Spain, the UK (EU5) and Sweden, and compared with the leuprorelin solid implant. RESULTS: Compared with alternative formulations, leuprorelin solid implants had potential annual cost savings/1000 patients of 353,000 (EU5) and 699,000 (Sweden; 1-month formulations), and 259,000 (EU5) and 300,000 (Sweden; 3-month formulations). CONCLUSION: The leuprorelin solid implant was associated with potential cost savings compared with the most commonly used LHRH agonist preparations.
Subject(s)
Antineoplastic Agents, Hormonal/economics , Antineoplastic Agents, Hormonal/therapeutic use , Leuprolide/economics , Leuprolide/therapeutic use , Prostatic Neoplasms/drug therapy , Prostatic Neoplasms/economics , Drug Implants , Humans , Internationality , MaleABSTRACT
OBJECTIVE: To measure the impact of orthopedic surgical-site infections (SSIs) on quality of life, length of hospitalization, and cost. DESIGN: A pairwise-matched (1:1) case-control study within a cohort. SETTING: A tertiary-care university medical center and a community hospital. PATIENTS: Cases of orthopedic SSIs were prospectively identified by infection control professionals. Matched controls were selected from the entire cohort of patients undergoing orthopedic surgery who did not have an SSI. Matching variables included type of surgical procedure, National Nosocomial Infections Surveillance risk index, age, date of surgery, and surgeon. MAIN OUTCOME MEASURES: Quality of life, duration of postoperative hospital stay, frequency of hospital readmission, overall direct medical costs, and mortality rate. RESULTS: Fifty-nine SSIs were identified. Each orthopedic SSI accounted for a median of 1 extra day of stay during the initial hospitalization (P = .001) and a median of 14 extra days of hospitalization during the follow-up period (P = .0001). Patients with SSI required more rehospitalizations (median, 2 vs 1; P = .0001) and more total surgical procedures (median, 2 vs 1; P = .0001). The median total direct cost of hospitalizations per infected patient was $24,344, compared with $6,636 per uninfected patient (P = .0001). Mortality rates were similar for cases and controls. Quality of life was adversely affected for patients with SSI. The largest decrements in scores on the Medical Outcome Study Short Form 36 questionnaire were seen in the physical functioning and role-physical domains. CONCLUSIONS: Orthopedic SSIs prolong total hospital stays by a median of 2 weeks per patient, approximately double rehospitalization rates, and increase healthcare costs by more than 300%. Moreover, patients with orthopedic SSIs have substantially greater physical limitations and significant reductions in their health-related quality of life.