Structural insights into membrane remodeling by SNX1.

The sorting nexin (SNX) family of proteins deform the membrane to generate transport carriers in endosomal pathways. Here, we elucidate how a prototypic member, SNX1, acts in this process. Performing cryoelectron microscopy, we find that SNX1 assembles into a protein lattice that consists of helical rows of SNX1 dimers wrapped around tubular membranes in a crosslinked fashion. We also visualize the details of this structure, which provides a molecular understanding of how various parts of SNX1 contribute to its ability to deform the membrane. Moreover, we have compared the SNX1 structure with a previously elucidated structure of an endosomal coat complex formed by retromer coupled to a SNX, which reveals how the molecular organization of the SNX in this coat complex is affected by retromer. The comparison also suggests insight into intermediary stages of assembly that results in the formation of the retromer-SNX coat complex on the membrane.

The Unusual Homodimer of a Heme-Copper Terminal Oxidase Allows Itself to Utilize Two Electron Donors.

The heme-copper oxidase superfamily comprises cytochrome c and ubiquinol oxidases. These enzymes catalyze the transfer of electrons from different electron donors onto molecular oxygen. A B-family cytochrome c oxidase from the hyperthermophilic bacterium Aquifex aeolicus was discovered previously to be able to use both cytochrome c and naphthoquinol as electron donors. Its molecular mechanism as well as the evolutionary significance are yet unknown. Here we solved its 3.4 Šresolution electron cryo-microscopic structure and discovered a novel dimeric structure mediated by subunit I (CoxA2) that would be essential for naphthoquinol binding and oxidation. The unique structural features in both proton and oxygen pathways suggest an evolutionary adaptation of this oxidase to its hyperthermophilic environment. Our results add a new conceptual understanding of structural variation of cytochrome c oxidases in different species.

ACAP1 assembles into an unusual protein lattice for membrane deformation through multiple stages.

Studies on the Bin-Amphiphysin-Rvs (BAR) domain have advanced a fundamental understanding of how proteins deform membrane. We previously showed that a BAR domain in tandem with a Pleckstrin Homology (PH domain) underlies the assembly of ACAP1 (Arfgap with Coil-coil, Ankryin repeat, and PH domain I) into an unusual lattice structure that also uncovers a new paradigm for how a BAR protein deforms membrane. Here, we initially pursued computation-based refinement of the ACAP1 lattice to identify its critical protein contacts. Simulation studies then revealed how ACAP1, which dimerizes into a symmetrical structure in solution, is recruited asymmetrically to the membrane through dynamic behavior. We also pursued electron microscopy (EM)-based structural studies, which shed further insight into the dynamic nature of the ACAP1 lattice assembly. As ACAP1 is an unconventional BAR protein, our findings broaden the understanding of the mechanistic spectrum by which proteins assemble into higher-ordered structures to achieve membrane deformation.

Effectiveness of tigecycline in the treatment of infections caused by carbapenem-resistant gram-negative bacteria in pediatric liver transplant recipients: A retrospective study.

INTRODUCTION: Tigecycline (TGC) is effective for the infections caused by carbapenem-resistant gram-negative bacteria (CRGNB) in adults, but it is not investigated systematically in children because of concern about adverse effects. This study aimed to analyze the effectiveness of TGC in treating CRGNB infections in children after receiving liver transplant. METHODS: The subjects in this retrospective study were pediatric liver transplant recipients treated with TGC for at least 3 days to fight microbiologically verified CRGNB infection after initial antibiotic failure during the period from January 2014 to May 2018. Clinical and microbiological outcomes were reviewed to evaluate the efficacy and safety of TGC. RESULTS: Of the 1177 pediatric liver transplant recipients, 13 patients were eligible for inclusion in this analysis. All the patients received TGC at dose of 2 mg/kg every 12 hours for a duration of 10.1 ± 5.1 days on average to treat CRGNB infections, including complicated intra-abdominal infection, ventilator-associated pneumonia, and bloodstream infection. The isolates included Klebsiella pneumoniae (69.2%, 9/13) and Acinetobacter baumannii (30.8%, 4/13). Clinical efficacy was achieved in 84.6% (11/13) and pathogen eradicated in 69.2% (9/13) of the patients. The overall mortality rate was 15.4% (2/13). No TGC-related serious adverse event was reported. CONCLUSION: Tigecycline can be considered in combination antimicrobial regimen for treating CRGNB-related infections in pediatric liver transplant recipients.

A 3.3†Å-Resolution Structure of Hyperthermophilic Respiratory Complex†III Reveals the Mechanism of Its Thermal Stability.

Respiratory chain complexes convert energy by coupling electron flow to transmembrane proton translocation. Owing to a lack of atomic structures of cytochrome bc1 complex (Complex III) from thermophilic bacteria, little is known about the adaptations of this macromolecular machine to hyperthermophilic environments. In this study, we purified the cytochrome bc1 complex of Aquifex aeolicus, one of the most extreme thermophilic bacteria known, and determined its structure with and without an inhibitor at 3.3 Šresolution. Several residues unique for thermophilic bacteria were detected that provide additional stabilization for the structure. An extra transmembrane helix at the N-terminus of cyt. c1 was found to greatly enhance the interaction between cyt. b and cyt. c1 , and to bind a phospholipid molecule to stabilize the complex in the membrane. These results provide the structural basis for the hyperstability of the cytochrome bc1 complex in an extreme thermal environment.

BrkAutoDisplay: functional display of multiple exogenous proteins on the surface of Escherichia coli by using BrkA autotransporter.

BACKGROUND: Bacterial surface display technique enables the exogenous proteins or polypeptides displayed on the bacterial surface, while maintaining their relatively independent spatial structures and biological activities. The technique makes recombinant bacteria possess the expectant functions, subsequently, directly used for many applications. Many proteins could be used to achieve bacterial surface display, among them, autotransporter, a member of the type V secretion system of gram-negative bacteria, has been extensively studied because of its modular structure and apparent simplicity. However, autotransporter has not been widely used at present due to lack of a convenient genetic vector system. With our recently characterized autotransporter BrkA (Bordetella serum-resistance killing protein A) from Bordetella pertussis, we are aiming to develop a new autotransporter-based surface display system for potential wide application. RESULTS: Here, we construct a bacterial surface display system named as BrkAutoDisplay, based on the structure of autotransporter BrkA. BrkAutoDisplay is a convenient system to host exogenous genes. In our test, this system is good to efficiently display various proteins on the outer membrane surface of Escherichia coli, including green fluorescent protein (GFP), various enzymes and single chain antibody. Moreover, the displayed GFP possesses green fluorescence, the enzymes CotA, EstPc and PalA exhibit catalytic activity 0.12, 6.88 and 0.32 mU (per 5.2 × 10(8) living bacteria cells) respectively, and the single chain antibody fragment (scFv) can bind with its antigen strongly. Finally, we showed that C41(DE3) is a good strain of E. coli for the successful functionality of BrkAutoDisplay. CONCLUSIONS: We designed a new bacterial display system called as BrkAutoDisplay and displayed various exogenous proteins on E. coli surface. Our results indicate that BrkAutoDisplay system is worthy of further study for industrial applications.

Mechanistic insights into regulated cargo binding by ACAP1 protein.

Coat complexes sort protein cargoes into vesicular transport pathways. An emerging class of coat components has been the GTPase-activating proteins (GAPs) that act on the ADP-ribosylation factor (ARF) family of small GTPases. ACAP1 (ArfGAP with coiled-coil, ankyrin repeat, and PH domains protein 1) is an ARF6 GAP that also acts as a key component of a recently defined clathrin complex for endocytic recycling. Phosphorylation by Akt has been shown to enhance cargo binding by ACAP1 in explaining how integrin recycling is an example of regulated transport. We now shed further mechanistic insights into how this regulation is achieved at the level of cargo binding by ACAP1. We initially defined a critical sequence in the cytoplasmic domain of integrin ß1 recognized by ACAP1 and showed that this sequence acts as a recycling sorting signal. We then pursued a combination of structural, modeling, and functional studies, which suggest that phosphorylation of ACAP1 relieves a localized mechanism of autoinhibition in regulating cargo binding. Thus, we have elucidated a key regulatory juncture that controls integrin recycling and also advanced the understanding of how regulated cargo binding can lead to regulated transport.

Structural elucidation of how ARF small GTPases induce membrane tubulation for vesicle fission.

The ADP-Ribosylation Factor (ARF) small GTPases have been found to act in vesicle fission through a direct ability to tubulate membrane. Here, we have used cryo-electron microscopy (EM) to solve the structure of an ARF6 protein lattice assembled on tubulated membrane to 3.9 Å resolution. ARF6 forms tetramers that polymerize into helical arrays to form this lattice. We identify, and confirm functionally, protein contacts critical for this lattice formation. The solved structure also suggests how the ARF amphipathic helix is positioned in the lattice for membrane insertion, and how a GTPase-activating protein (GAP) docks onto the lattice to catalyze ARF-GTP hydrolysis in completing membrane fission. As ARF1 and ARF6 are structurally conserved, we have also modeled ARF1 onto the ARF6 lattice, which has allowed us to pursue the reconstitution of Coat Protein I (COPI) vesicles to confirm more definitively that the ARF lattice acts in vesicle fission. Our findings are notable for having achieved the first detailed glimpse of how a small GTPase bends membrane and having provided a molecular understanding of how an ARF protein acts in vesicle fission.

Autotransporter passenger domain secretion requires a hydrophobic cavity at the extracellular entrance of the ß-domain pore.

Whooping cough (pertussis) is a highly contagious acute respiratory illness of humans caused by the Gram-negative bacterial pathogen Bordetella pertussis. The AT (autotransporter) BrkA (Bordetella serum-resistance killing protein A) is an important B. pertussis virulence factor that confers serum resistance and mediates adherence. In the present study, we have solved the crystal structure of the BrkA ß-domain at 3 Å (1 Å=0.1 nm) resolution. Special features are a hairpin-like structure formed by the external loop L4, which is observed fortuitously sitting inside the pore of the crystallographic adjacent ß-domain, and a previously undiscovered hydrophobic cavity formed by patches on loop L4 and ß-strands S5 and S6. This adopts a ubiquitous structure characteristic of all AT ß-domains. Mutagenesis studies have demonstrated that the hairpin-like structure and hydrophobic cavity are crucial for BrkA passenger domain (virulence effector) translocation. This structure helps in understanding the molecular mechanism of AT assembly and secretion and provides a potential target for anti-pertussis drug design.

Kinetics of low radioactive wastewater imbibition and radionuclides sorption in partially saturated ternary-binder mortar.

This study seeks to assess the imbibition kinetics of low radioactive wastewater (from the DayaBay nuclear power plant) into a partially saturated ternary-binder mortar, as well as the sorption kinetics of 60Co and 137Cs from the water. Mortar samples with the initial saturation degrees of 0, 0.4, 0.6, 0.8 and 1.0 were prepared for the wastewater treatment. Pore structure of the mortar was characterized using water vapor sorption isotherm and mercury intrusion porosimetry tests interpreted by the Guggenheim-Anderson-de Boer isothermal equilibrium, and volume- and energy-based fractal models. Results show that the mortar has consistent fractal pore structure between the models, and the liquid imbibitions follow the fractal imbibition kinetics, in which the parameters are non-linearly impacted by the initial saturation degrees. The sorption rate and retention capacity of 137Cs are much lower than those of 60Co, and both follow the Brouers-Sotolongo fractional kinetics. The findings uncover the complex liquid imbibition and radionuclides sorption kinetics in cement-based porous materials, and the in-situ data would contribute to the material designs and sorption controls for large scale in-situ treatments of wastewater from nuclear power plant.

Expression, purification and preliminary biochemical studies of the N-terminal domain of leucine-rich repeat kinase 2.

Leucine-rich repeat kinase 2 gene is a key factor for Parkinson's disease and encodes for a large protein kinase LRRK2 (280kDa) with multiple domains, including the different repeat sequences at the N-terminus such as ankyrin domain. Here, we successfully expressed and purified two kinds of LRRK2's N-terminal fragments N1 (aa12-320) and N2 (aa12-860). The purified N2 protein was identified by mass spectrometry and N1's molecular weight was determined to be 33.23kDa. Gel filtration revealed that N1 exhibits as monomer, dimer and tetramer and N2 as oligomer in solution. N1's multiple oligomeric states were further proved by native-page and cross-linking gel experiments. Circular dichroism spectrum indicated that N1 and N2 contain both alpha helixes and beta sheets. The polymerization character of LRRK2 N-terminal region would be speculated to relate with its biological function.

A bibliometric analysis of infectious diseases in patients with liver transplantation in the last decade.

BACKGROUND: A bibliometric analysis was performed to reveal the current status of investigations in infectious diseases in patients with liver transplantation (LT) and to prioritize future research needs. METHODS: The present study comprehensively retrieved publications relevant to infectious diseases in LT recipients published between 2010 and 2020. The search was conducted on the Web of Science (WoS) database. A bibliometric analysis was conducted through machine learning and visualization tools, including VOSviewer, Bibliographic Item Co-Occurrence Matrix Builder, and Graphical Clustering Toolkit. Research hotspots and trends in the field were assessed, while the contributions and collaborations of countries, institutions, and authors were documented. RESULTS: A total of 691 publications were analyzed. Research output sharply increased in 2015, with a fast drop afterward. "Liver transplantation" was the most frequent keyword, with strong links to "hepatitis C virus" and "infection". Study areas included risk factors of infectious diseases in LT recipients, pathogens causing post-transplantation infections, antibacterial therapy and prophylaxis for peritransplant infection complications, living donor LT, and pediatric LT. The efficacy and safety of direct-acting antivirals (DAAs) for hepatitis C virus (HCV) infection among liver transplant recipients has attracted recent research interest. Didier Samuel was the most productive author, while Xavier Forns was the top-cited author. Shanghai Jiao Tong University was the most productive contributor, and Gilead Sciences was the most cited organization. Moreover, the USA was the greatest contributor. Gastroenterology was the most cited journal, while Liver Transplantation was the most prolific journal. CONCLUSIONS: This bibliometric analysis will better understand the research status of infectious complications in LT recipients and forecast future research trends. Priority should be given to identifying risk factors for peritransplantation infections and effective treatments against infectious complications in the coming years.

Cryo-EM structures of S-OPA1 reveal its interactions with membrane and changes upon nucleotide binding.

Mammalian mitochondrial inner membrane fusion is mediated by optic atrophy 1 (OPA1). Under physiological conditions, OPA1 undergoes proteolytic processing to form a membrane-anchored long isoform (L-OPA1) and a soluble short isoform (S-OPA1). A combination of L-OPA1 and S-OPA1 is essential for efficient membrane fusion; however, the relevant mechanism is not well understood. In this study, we investigate the cryo-electron microscopic structures of S-OPA1-coated liposomes in nucleotide-free and GTPγS-bound states. S-OPA1 exhibits a general dynamin-like structure and can assemble onto membranes in a helical array with a dimer building block. We reveal that hydrophobic residues in its extended membrane-binding domain are critical for its tubulation activity. The binding of GTPγS triggers a conformational change and results in a rearrangement of the helical lattice and tube expansion similar to that of S-Mgm1. These observations indicate that S-OPA1 adopts a dynamin-like power stroke membrane remodeling mechanism during mitochondrial inner membrane fusion.

High mortality associated with gram-negative bacterial bloodstream infection in liver transplant recipients undergoing immunosuppression reduction.

BACKGROUND: Immunosuppression is an important factor in the incidence of infections in transplant recipient. Few studies are available on the management of immunosuppression (IS) treatment in the liver transplant (LT) recipients complicated with infection. The aim of this study is to describe our experience in the management of IS treatment during bacterial bloodstream infection (BSI) in LT recipients and assess the effect of temporary IS withdrawal on 30 d mortality of recipients presenting with severe infection. AIM: To assess the effect of temporary IS withdrawal on 30 d mortality of LT recipients presenting with severe infection. METHODS: A retrospective study was conducted with patients diagnosed with BSI after LT in the Department of Liver Surgery, Renji Hospital from January 1, 2016 through December 31, 2017. All recipients diagnosed with BSI after LT were included. Univariate and multivariate Cox regression analysis of risk factors for 30 d mortality was conducted in the LT recipients with Gram-negative bacterial (GNB) infection. RESULTS: Seventy-four episodes of BSI were identified in 70 LT recipients, including 45 episodes of Gram-positive bacterial (GPB) infections in 42 patients and 29 episodes of GNB infections in 28 patients. Overall, IS reduction (at least 50% dose reduction or cessation of one or more immunosuppressive agent) was made in 28 (41.2%) cases, specifically, in 5 (11.9%) cases with GPB infections and 23 (82.1%) cases with GNB infections. The 180 d all-cause mortality rate was 18.5% (13/70). The mortality rate in GNB group (39.3%, 11/28) was significantly higher than that in GPB group (4.8%, 2/42) (P = 0.001). All the deaths in GNB group were attributed to worsening infection secondary to IS withdrawal, but the deaths in GPB group were all due to graft-versus-host disease. GNB group was associated with significantly higher incidence of intra-abdominal infection, IS reduction, and complete IS withdrawal than GPB group (P < 0.05). Cox regression showed that rejection (adjusted hazard ratio 7.021, P = 0.001) and complete IS withdrawal (adjusted hazard ratio 12.65, P = 0.019) were independent risk factors for 30 d mortality in patients with GNB infections after LT. CONCLUSION: IS reduction is more frequently associated with GNB infection than GPB infection in LT recipients. Complete IS withdrawal should be cautious due to increased risk of mortality in LT recipients complicated with BSI.

New interfaces on MiD51 for Drp1 recruitment and regulation.

Mitochondrial fission is facilitated by dynamin-related protein Drp1 and a variety of its receptors. However, the molecular mechanism of how Drp1 is recruited to the mitochondrial surface by receptors MiD49 and MiD51 remains elusive. Here, we showed that the interaction between Drp1 and MiD51 is regulated by GTP binding and depends on the polymerization of Drp1. We identified two regions on MiD51 that directly bind to Drp1, and found that dimerization of MiD51, relevant to residue C452, is required for mitochondrial dynamics regulation. Our Results have suggested a multi-faceted regulatory mechanism for the interaction between Drp1 and MiD51 that illustrates the potentially complicated and tight regulation of mitochondrial fission.

Correction: New interfaces on MiD51 for Drp1 recruitment and regulation.

[This corrects the article DOI: 10.1371/journal.pone.0211459.].

Minimal change disease induced by tiopronin: a rare case report and a review of the literature.

Tiopronin (TP), a glycine derivative with a free thiol, is extensively used for the treatment of cystinuria. Moreover, TP is usually prescribed as hepatoprotective medicine in China. In the present case, a 36-year-old female who presented with foamy urine and general edema was admitted to the hospital. She had been taking TP for six months to treat drug-induced liver injury due to anti-tuberculosis drugs including isoniazid, rifampicin and pyrazinamide. The urine tests at admission revealed nephritic-range proteinuria with a daily urinary protein level of 8,024 mg. Meanwhile, albumin and cholesterol levels were abnormal. The light microscopy was negative and electron microscopy showed foot process effacement. Thus, minimal change disease (MCD) was diagnosed, and TP was consequently discontinued. Finally, the patient accomplished complete remission within five weeks after the cessation of TP without undergoing glucocorticoid therapy. TP was speculated to play an antigenic role in this adverse effect. To date, there are only two similar cases documented in the literature. Herein, we first report a case of a Chinese patient who generated MCD after prolonged TP administration. Clinicians should be wary of the occurrence of MCD due to TP when administering long-term therapy of TP. A weekly urinalysis may be useful for early identification of TP-induced MCD.

Purification, crystallization and preliminary crystallographic analysis of CYP 195A2, a P450 enzyme from Rhodopseudomonas palustris.

Cytochrome P450 monooxygenases are a superfamily of heme-thiolate proteins involved in the metabolism of a wide variety of endogenous and xenobiotic compounds. The P450 enzyme CYP195A2 from Rhodopseudomonas palustris CGA009, a metabolically versatile bacterium, was overproduced in E. coli and purified. Two distinct crystal forms were obtained under separately optimized conditions by the hanging-drop vapor-diffusion method. Native data sets extending to resolutions of 2.3 A and 2.8 A have been collected and processed in space groups P222 and C2221 respectively.

Phase I safety and pharmacokinetic study of magnesium isoglycyrrhizinate after single and multiple intravenous doses in chinese healthy volunteers.

The safety and pharmacokinetics of magnesium isoglycyrrhizinate were assessed in healthy Chinese volunteers. In the single-dose format of this pharmacokinetic study, 100-, 200-, and 300-mg doses of magnesium isoglycyrrhizinate were given by intravenous infusion. The results indicated that the plasma levels were directly proportional to the administered dose, with the mean C(max) and AUC(0-72) ranging from approximately 28.79 to 99.28 mg x L(-1) and 448.68 to 1688.42 mg x h x L(-1) over the dose range. In the multiple-dose format of this pharmacokinetic study, 100 mg magnesium isoglycyrrhizinate was administrated once daily for 9 days. Moderate drug accumulation was noted, which was attributable to the drug's long terminal half-life of 19 to 31 hours. The distribution and elimination rate of magnesium isoglycyrrhizinate had no changes. It had a favorable pharmacokinetics and safety profile that enables the drug to be explored in future clinical studies that target patients with hepatic impairment.

Purification, crystallization and preliminary crystallographic analysis of cytochrome P450 203A1 from Rhodopseudomonas palustris.

Cytochrome P450 enzymes constitute a large family of haemoproteins that catalyze the monooxygenation of a great variety of endogenous and exogenous organic compounds. Cytochrome P450 203A1 (CYP203A1, RPA1009) from the metabolically versatile organism Rhodopseudomonas palustris binds a broad range of substrates, in particular substituted aromatic compounds. Crystals of CYP203A1 suitable for X-ray crystallography have been obtained and diffraction data were collected in-house to 2.0 A resolution from a single crystal. The crystals belong to space group P222, with unit-cell parameters a = 40.1, b = 95.1, c = 99.0 A, alpha = beta = gamma = 90 degrees. There is one protein molecule per asymmetric unit.