Solution structure of homology region (HR) domain of type II secretion system

The type II secretion system of Gram-negative bacteria is important for bacterial pathogenesis and survival; it is composed of 12 mostly multimeric core proteins, which build a sophisticated secretion machine spanning both bacterial membranes. OutC is the core component of the inner membrane subcomplex thought to be involved in both recognition of substrate and interaction with the outer membrane secretin OutD. Here, we report the solution structure of the HR domain of OutC and explore its interaction with the secretin. The HR domain adopts a β-sandwich-like fold consisting of two β-sheets each composed of three anti-parallel β-strands. This structure is strikingly similar to the periplasmic region of PilP, an inner membrane lipoprotein from the type IV pilus system highlighting the common evolutionary origin of these two systems and showing that all the core components of the type II secretion system have a structural or sequence ortholog within the type IV pili system. The HR domain is shown to interact with the N0 domain of the secretin. The importance of this interaction is explored in the context of the functional secretion system.

Analysis of the interaction with the hepatitis C virus mRNA reveals an alternative mode of RNA recognition by the human La protein

Human La protein is an essential factor in the biology of both coding and non-coding RNAs. In the nucleus, La binds primarily to 3' oligoU containing RNAs, while in the cytoplasm La interacts with an array of different mRNAs lacking a 3' UUU(OH) trailer. An example of the latter is the binding of La to the IRES domain IV of the hepatitis C virus (HCV) RNA, which is associated with viral translation stimulation. By systematic biophysical investigations, we have found that La binds to domain IV using an RNA recognition that is quite distinct from its mode of binding to RNAs with a 3' UUU(OH) trailer: although the La motif and first RNA recognition motif (RRM1) are sufficient for high-affinity binding to 3' oligoU, recognition of HCV domain IV requires the La motif and RRM1 to work in concert with the atypical RRM2 which has not previously been shown to have a significant role in RNA binding. This new mode of binding does not appear sequence specific, but recognizes structural features of the RNA, in particular a double-stranded stem flanked by single-stranded extensions. These findings pave the way for a better understanding of the role of La in viral translation initiation.

Structural basis for increased toxicity of pathological aβ42:aβ40 ratios in Alzheimer disease

The β-amyloid peptide (Aβ) is directly related to neurotoxicity in Alzheimer disease (AD). The two most abundant alloforms of the peptide co-exist under normal physiological conditions in the brain in an Aβ(42):Aβ(40) ratio of ∼1:9. This ratio is often shifted to a higher percentage of Aβ(42) in brains of patients with familial AD and this has recently been shown to lead to increased synaptotoxicity. The molecular basis for this phenomenon is unclear. Although the aggregation characteristics of Aβ(40) and Aβ(42) individually are well established, little is known about the properties of mixtures. We have explored the biophysical and structural properties of physiologically relevant Aβ(42):Aβ(40) ratios by several techniques. We show that Aβ(40) and Aβ(42) directly interact as well as modify the behavior of the other. The structures of monomeric and fibrillar assemblies formed from Aβ(40) and Aβ(42) mixtures do not differ from those formed from either of these peptides alone. Instead, the co-assembly of Aβ(40) and Aβ(42) influences the aggregation kinetics by altering the pattern of oligomer formation as evidenced by a unique combination of solution nuclear magnetic resonance spectroscopy, high molecular weight mass spectrometry, and cross-seeding experiments. We relate these observations to the observed enhanced toxicity of relevant ratios of Aβ(42):Aβ(40) in synaptotoxicity assays and in AD patients.

Structure of the C-terminal domain of Neisseria heparin binding antigen (NHBA), one of the main antigens of a novel vaccine against Neisseria meningitidis

Neisseria heparin binding antigen (NHBA), also known as GNA2132 (genome-derived Neisseria antigen 2132), is a surface-exposed lipoprotein from Neisseria meningitidis that was originally identified by reverse vaccinology. It is one the three main antigens of a multicomponent vaccine against serogroup B meningitis (4CMenB), which has just completed phase III clinical trials in infants. In contrast to the other two main vaccine components, little is known about the origin of the immunogenicity of this antigen, and about its ability to induce a strong cross-bactericidal response in animals and humans. To characterize NHBA in terms of its structural/immunogenic properties, we have analyzed its sequence and identified a C-terminal region that is highly conserved in all strains. We demonstrate experimentally that this region is independently folded, and solved its three-dimensional structure by nuclear magnetic resonance. Notably, we need detergents to observe a single species in solution. The NHBA domain fold consists of an 8-strand β-barrel that closely resembles the C-terminal domains of N. meningitidis factor H-binding protein and transferrin-binding protein B. This common fold together with more subtle structural similarities suggest a common ancestor for these important antigens and a role of the β-barrel fold in inducing immunogenicity against N. meningitidis. Our data represent the first step toward understanding the relationship between structural, functional, and immunological properties of this important vaccine component.

Tracking microbial transport through four onsite wastewater treatment systems to receiving waters in eastern North Carolina

AIMS

To examine microbial transport through properly functioning and failing onsite wastewater treatment systems (OWTS) and its implication in surrounding water quality.

METHODS AND RESULTS

Water samples were collected from monitoring wells near leach lines of OWTS and nearby ditches and receiving surface waters to analyse for Escherichia coli and enterococci. Tracer studies with Rhodamine WT (RWT) and coliphage MS2 were also carried out to understand the fate and transport of contaminants through each OWTS. Escherichia coli and enterococci concentrations were higher around failing than properly functioning OWTS by as much as 85-fold. A storm event resulting in 9·5 cm of rainfall increased E. coli and enterococci concentrations by averages of 4·1 × 10³ and 7·9 × 10³ MPN per 100 ml, respectively, in wells close to the OWTS. MS2 persisted in the wastewater distribution boxes of the OWTS for several months and was detected in some outer perimeter wells.

CONCLUSIONS

Properly functioning OWTS in eastern North Carolina were effective in treating wastewater, whereas the failing OWTS affected the groundwater quality more adversely, especially after a rain storm, but had minor impact on the nearby coastal surface water.

SIGNIFICANCE AND IMPACT OF THE STUDY

The study is the first description of the microbial contaminant signature stemming from properly functioning and failing systems under regular use in a high-priority coastal area.

A natural and readily available crowding agent: NMR studies of proteins in hen egg white

In vitro studies of biological macromolecules are usually performed in dilute, buffered solutions containing one or just a few different biological macromolecules. Under these conditions, the interactions among molecules are diffusion limited. On the contrary, in living systems, macromolecules of a given type are surrounded by many others, at very high total concentrations. In the last few years, there has been an increasing effort to study biological macromolecules directly in natural crowded environments, as in intact bacterial cells or by mimicking natural crowding by adding proteins, polysaccharides, or even synthetic polymers. Here, we propose the use of hen egg white (HEW) as a simple natural medium, with all features of the media of crowded cells, that could be used by any researcher without difficulty and inexpensively. We present a study of the stability and dynamics behavior of model proteins in HEW, chosen as a prototypical, readily accessible natural medium that can mimic cytosol. We show that two typical globular proteins, dissolved in HEW, give NMR spectra very similar to those obtained in dilute buffers, although dynamic parameters are clearly affected by the crowded medium. The thermal stability of one of these proteins, measured in a range comprising both heat and cold denaturation, is also similar to that in buffer. Our data open new possibilities to the study of proteins in natural crowded media. Proteins 2011. © 2010 Wiley-Liss, Inc.

Are medical student results affected by allocation to different sites in a dispersed rural medical school?

INTRODUCTION

As medical education becomes more decentralised, and greater use is made of rural clinical schools and other dispersed sites, attention is being paid to the quality of the learning experiences across these sites. This article explores this issue by analysing the performance data of 4 cohorts of students in a dispersed clinical school model across 4 sites. The study is set in a newly established medical school in a regional area with a model of dispersed education, using data from the second to fifth cohorts to graduate from this school.

METHODS

Summative assessment results of 4 graduating cohorts were examined over the final 2 years of the course. Two analyses were conducted: an analysis of variance of mean scores in both years across the 4 sites; and an analysis of the effect of moving to different clinical schools on the students' rank order of performance by use of the Kruskal-Wallis test.

RESULTS

Analysis revealed no significant difference in the mean scores of the students studying at each site, and no significant differences overall in the median ranking across the years. Some small changes in the relative ranking of students were noticed, and workplace-based assessment scores in the final year were higher than the examination-based scores in the previous year.

CONCLUSIONS

The choice of clinical school site for the final 2 years of an undergraduate rural medical school appears to have no effect on mean assessment scores and only a minor effect on the rank order of student scores. Workplace-based assessment produces higher scores but also has little effect on student rank order. Further studies are necessary to replicate these findings in other settings and demonstrate that student learning experiences in rural sites, while popular with students, translate into required learning outcomes, as measured by summative assessments.

Molecular basis of FIR-mediated c-myc transcriptional control

The far upstream element (FUSE) regulatory system promotes a peak in the concentration of c-Myc during cell cycle. First, the FBP transcriptional activator binds to the FUSE DNA element upstream of the c-myc promoter. Then, FBP recruits its specific repressor (FIR), which acts as an on/off transcriptional switch. Here we describe the molecular basis of FIR recruitment, showing that the tandem RNA recognition motifs of FIR provide a platform for independent FUSE DNA and FBP protein binding and explaining the structural basis of the reversibility of the FBP-FIR interaction. We also show that the physical coupling between FBP and FIR is modulated by a flexible linker positioned sequentially to the recruiting element. Our data explain how the FUSE system precisely regulates c-myc transcription and suggest that a small change in FBP-FIR affinity leads to a substantial effect on c-Myc concentration.

Orientation of the central domains of KSRP and its implications for the interaction with the RNA targets

KSRP is a multi-domain RNA-binding protein that recruits the exosome-containing mRNA degradation complex to mRNAs coding for cellular proliferation and inflammatory response factors. The selectivity of this mRNA degradation mechanism relies on KSRP recognition of AU-rich elements in the mRNA 3'UTR, that is mediated by KSRP's KH domains. Our structural analysis shows that the inter-domain linker orients the two central KH domains of KSRP-and their RNA-binding surfaces-creating a two-domain unit. We also show that this inter-domain arrangement is important to the interaction with KSRP's RNA targets.

NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor

Termination of translation in eukaryotes is triggered by two polypeptide chain release factors, eukaryotic class 1 polypeptide chain release factor (eRF1) and eukaryotic class 2 polypeptide chain release factor 3. eRF1 is a three-domain protein that interacts with eukaryotic class 2 polypeptide chain release factor 3 via its C-terminal domain (C-domain). The high-resolution NMR structure of the human C-domain (residues 277–437) has been determined in solution. The overall fold and the structure of the β-strand core of the protein in solution are similar to those found in the crystal structure. The structure of the minidomain (residues 329–372), which was ill-defined in the crystal structure, has been determined in solution. The protein backbone dynamics, studied using ¹⁵N-relaxation experiments, showed that the C-terminal tail 414–437 and the minidomain are the most flexible parts of the human C-domain. The minidomain exists in solution in two conformational states, slowly interconverting on the NMR timescale. Superposition of this NMR solution structure of the human C-domain onto the available crystal structure of full-length human eRF1 shows that the minidomain is close to the stop codon-recognizing N-terminal domain. Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor. The results provide new insights into the possible role of the C-domain in the process of translation termination.

Effects of imposed postfeedback delays in programmed instruction

Imposed postfeedback delays promote discrimination training; the present experiments determined whether they also improve performance in programmed instruction. In two experiments, college students completed 45 sets of Holland and Skinner's (1961) programmed text on behavior analysis in a computerized format in a three-component multiple schedule. In Experiment 1, the conditions were (a) no delay between questions, (b) a 10-s delay after each question (noncontingent delay), and (c) a 10-s delay after each question answered incorrectly (contingent delay). Noncontingent delay produced better performance than no delay and contingent delay. To determine whether performance increased in the noncontingent delay condition because subjects studied the material during delay periods, Experiment 2 tested three conditions: (a) no delay between questions, (b) a 10-s delay after each question (noncontingent delay), and (c) a 10-s delay after each question with the screen blank during the delay period. Noncontingent delay produced better performance than no delay, but there was no difference in performance between no delay and noncontingent delay with blank screen. Hence, noncontingent delay improved performance because students used delay periods to study. Furthermore, subjects preferred noncontingent delay to the other conditions, and session time increased only slightly.

NMR solution structure and function of the C-terminal domain of eukaryotic class 1 polypeptide chain release factor

Termination of translation in eukaryotes is triggered by two polypeptide chain release factors, eukaryotic class 1 polypeptide chain release factor (eRF1) and eukaryotic class 2 polypeptide chain release factor 3. eRF1 is a three-domain protein that interacts with eukaryotic class 2 polypeptide chain release factor 3 via its C-terminal domain (C-domain). The high-resolution NMR structure of the human C-domain (residues 277-437) has been determined in solution. The overall fold and the structure of the beta-strand core of the protein in solution are similar to those found in the crystal structure. The structure of the minidomain (residues 329-372), which was ill-defined in the crystal structure, has been determined in solution. The protein backbone dynamics, studied using (15)N-relaxation experiments, showed that the C-terminal tail 414-437 and the minidomain are the most flexible parts of the human C-domain. The minidomain exists in solution in two conformational states, slowly interconverting on the NMR timescale. Superposition of this NMR solution structure of the human C-domain onto the available crystal structure of full-length human eRF1 shows that the minidomain is close to the stop codon-recognizing N-terminal domain. Mutations in the tip of the minidomain were found to affect the stop codon specificity of the factor. The results provide new insights into the possible role of the C-domain in the process of translation termination.

Letter to the Editor: resonance assignment of SlyD from E. coli

SlyD from Escherichia coli is a peptidyl-prolyl cis-trans isomerase involved in [Ni-Fe] hydrogenase metallocentre assembly in bacteria. We present here the backbone and side chain assignments for E. coli SlyD.

Solution structure and dynamics of ERp18, a small endoplasmic reticulum resident oxidoreductase

Here we report the solution structure of oxidized ERp18 as determined using NMR spectroscopy. ERp18 is the smallest member of the protein disulfide isomerase (PDI) family of proteins to contain a Cys-Xxx-Xxx-Cys active site motif. It is an 18 kDa endoplasmic reticulum resident protein with unknown function although sequence similarity to individual domains of the thiol-disulfide oxidoreductase PDI suggests ERp18 may have a similar structure and function. Like the catalytic domains of PDI, ERp18 adopts a thioredoxin fold with a thioredoxin-like active site located at the N-terminus of a long kinked helix that spans the length of the protein. Comparison of backbone chemical shifts for oxidized and reduced ERp18 shows the majority of residues possess the same backbone conformation in both states, with differences limited to the active site and regions in close proximity. S(2) order parameters from NMR backbone dynamics were found to be 0.81 for oxidized and 0.91 for reduced ERp18, and these observations, in combination with amide hydrogen exchange rates, imply a more rigid and compact backbone for the reduced structure. These observations support a putative role for ERp18 within the cell as an oxidase, introducing disulfide bonds to substrate proteins, providing structural confirmation of ERp18's role as a thiol-disulfide oxidoreductase.

The interaction of the Escherichia coli protein SlyD with nickel ions illuminates the mechanism of regulation of its peptidyl-prolyl isomerase activity

The sensitive to lysis D (SlyD) protein from Escherichia coli is related to the FK506-binding protein family, and it harbours both peptidyl-prolyl cis-trans isomerase (PPIase) and chaperone-like activity, preventing aggregation and promoting the correct folding of other proteins. Whereas a functional role of SlyD as a protein-folding catalyst in vivo remains unclear, SlyD has been shown to be an essential component for [Ni-Fe]-hydrogenase metallocentre assembly in bacteria. Interestingly, the isomerase activity of SlyD is uniquely modulated by nickel ions, which possibly regulate its functions in response to external stimuli. In this work, we investigated the solution structure of SlyD and its interaction with nickel ions, enabling us to gain insights into the molecular mechanism of this regulation. We have revealed that the PPIase module of SlyD contains an additional C-terminal alpha-helix packed against the catalytic site of the domain; unexpectedly, our results show that the interaction of SlyD with nickel ions entails participation of the novel structural features of the PPIase domain, eliciting structural alterations of the catalytic pocket. We suggest that such conformational rearrangements upon metal binding underlie the ability of nickel ions to regulate the isomerase activity of SlyD.

An evidence-based approach to the management of the adult with nasal obstruction

BACKGROUND

Nasal obstruction is a common presenting symptom to the otolaryngology clinic. A variety of structural and mucosal abnormalities can interrupt the subjective sensation of nasal airflow.

METHODS

This review was based on a literature search last performed on 1 October 2008. Current texts and the MEDLINE, EMBASE and COCHRANE databases were searched using the subject heading nasal obstruction in combination with classification, diagnosis, therapy, drug therapy and surgery. Results were limited to include clinical trials, randomised controlled trials, meta-analyses, systematic reviews and review articles. Relevant references from selected articles were also reviewed.

CONCLUSION

We present an evidence-based approach to history-taking and clinical examination of an adult patient with nasal obstruction and provide an overview of management of the most common causative conditions.

Is nasal packing really required after septoplasty?

OBJECTIVE

Septoplasty is one of the most common operations performed by otorhinolaryngologists. Nasal packing is not an innocuous procedure. The most common problem encountered by the patients after septoplasty is the pain and discomfort during removal of the nasal packs. The objective of this study was to evaluate the results of septoplasty without postoperative nasal packing.

METHODS

Septoplasty was performed by standard technique. No nasal packing was used in these cases.

RESULTS

Seventy-eight patients were included in the study. The majority of the patients (64.1%; 50/78) on a morning list were operated. Sixty-two patients were discharged home the same day, the remaining others were discharged the next day. Our postoperative haemorrhage rate was 7.7% (6/78) and only 3.8% (3/78) patients required nasal packing. Majority (84.6%) of the patients were satisfied with the operation at the postoperative follow up 3 months later.

CONCLUSIONS

Septoplasty can be safely performed without postoperative nasal packing. Only 3.8% patients required nasal packing in this study.

An intramolecular switch regulates phosphoindependent FHA domain interactions in Mycobacterium tuberculosis

Forkhead-associated (FHA) domains have gained considerable prominence as ubiquitous phosphothreonine-dependent binding modules; however, their precise roles in serine and threonine kinase (STK) pathways and mechanisms of regulation remain unclear. From experiments with Rv1827, an FHA domain-containing protein from Mycobacterium tuberculosis, we derived a complete molecular description of an FHA-mediated STK signaling process. First, binding of the FHA domain to each of three metabolic enzyme complexes regulated their catalytic activities but did not require priming phosphorylation. However, phosphorylation of a threonine residue within a conserved amino-terminal motif of Rv1827 triggered its intramolecular association with the FHA domain of Rv1827, thus blocking its interactions with each of the three enzymes. The solution structure of this inactivated form and further mutagenic studies showed how a previously unidentified intramolecular phosphoswitch blocked the access of the target enzymes to a common FHA interaction surface and how this shared surface accommodated three functionally related, but structurally diverse, binding partners. Thus, our data reveal an unsuspected versatility in the FHA domain that allows for the transformation of multiple kinase inputs into various downstream regulatory signals.

Phosphorylation-mediated unfolding of a KH domain regulates KSRP localization via 14-3-3 binding

The AU-rich element (ARE)-mediated mRNA-degradation activity of the RNA binding K-homology splicing regulator protein (KSRP) is regulated by phosphorylation of a serine within its N-terminal KH domain (KH1). In the cell, phosphorylation promotes the interaction of KSRP and 14-3-3zeta protein and impairs the ability of KSRP to promote the degradation of its RNA targets. Here we examine the molecular details of this mechanism. We report that phosphorylation leads to the unfolding of the structurally atypical and unstable KH1, creating a site for 14-3-3zeta binding. Using this site, 14-3-3zeta discriminates between phosphorylated and unphosphorylated KH1, driving the nuclear localization of KSRP. 14-3-3zeta -KH1 interaction regulates the mRNA-decay activity of KSRP by sequestering the protein in a separate functional pool. This study demonstrates how an mRNA-degradation pathway is connected to extracellular signaling networks through the reversible unfolding of a protein domain.

NMR assignment of the N-terminal region of human La free and in complex with RNA

(1)H, (15)N and (13)C chemical shift assignments are presented for the N-terminal region of human La protein, in the apo and 5'-UUUU RNA-bound state. Secondary structure analysis shows conformational changes in the interdomain linker upon complex formation.