Probing the existence of non-thermal Terahertz radiation induced changes of the protein solution structure.

During the last decades discussions were taking place on the existence of global, non-thermal structural changes in biological macromolecules induced by Terahertz (THz) radiation. Despite numerous studies, a clear experimental proof of this effect for biological particles in solution is still missing. We developed a setup combining THz-irradiation with small angle X-ray scattering (SAXS), which is a sensitive method for detecting the expected structural changes. We investigated in detail protein systems with different shape morphologies (bovine serum albumin, microtubules), which have been proposed to be susceptible to THz-radiation, under variable parameters (THz wavelength, THz power densities up to 6.8 mW/cm2, protein concentrations). None of the studied systems and conditions revealed structural changes detectable by SAXS suggesting that the expected non-thermal THz-induced effects do not lead to alterations of the overall structures, which are revealed by scattering from dissolved macromolecules. This leaves us with the conclusion that, if such effects are present, these are either local or outside of the spectrum and power range covered by the present study.

A Case Study on the Customized Nutrition Intervention for a Patient with Primary Gastrointestinal Non-Hodgkin Lymphoma Underlying Chronic Kidney Disease.

Non-Hodgkin lymphoma comprises 2.1% of the total number of cancers in South Korea. Among those, diffuse large B cell lymphoma (DLBCL) comprises the largest percentage. Nutrition interventions have been highlighted because nutritional status in non-Hodgkin's lymphoma patients has a significant impact on treatment and prognosis, but relevant studies are inadequate. Therefore, the aim of this study was to share the case of a nutrition intervention for a patient with primary gastrointestinal non-Hodgkin lymphoma underlying chronic kidney disease who was comorbid with tumor lysis syndrome, which was a complication of a specific chemotherapy. The subject is a 76-year-old patient who was diagnosed with DLBCL. He had abdominal pain, constipation, and anorexia. After chemotherapy, he experienced the tumor lysis syndrome. The patient's condition was continuously monitored, and various nutrition interventions, such as nutrition counseling and education, provision of therapeutic diet, oral nutritional supplement, change of meal plans, and parenteral nutrition support were attempted. As a result of the nutrition intervention, oral intake was increased from 27% of the energy requirement to 70% and from 23% of the protein requirement to 77%. Despite the various nutrition interventions during the hospitalization, there were no improvements in weight and nutrition-related biochemical parameters or malnutrition. However, it was meaningful in that the patient was managed to prevent worsening and the planned third chemotherapy could be performed. These results can be used as the basis for establishing guidelines for nutritional interventions customized to patients under the same conditions.

A versatile vector for mycobacterial protein production with a functional minimized acetamidase regulon.

Recombinant protein expression is a prerequisite for diverse investigations of proteins at the molecular level. For targets from Mycobacterium tuberculosis it is favorable to use M. smegmatis as an expression host, a species from the same genus. In the respective shuttle vectors, target gene expression is controlled by the complex tetra-cistronic acetamidase regulon. As a result, the size of those vectors is large, rendering them of limited use, especially when the target proteins are expressed from multi-cistronic operons. Therefore, in the current work we present a versatile new expression vector in which the acetamidase regulon has been minimized by deleting the two genes amiD and amiS. We assessed the functional properties of the resulting vector pMyCA and compared it with those of the existing vector pMyNT that contains the full-length acetamidase regulon. We analyzed the growth features and protein expression patterns of M. smegmatis cultures transformed with both vectors. In addition, we created mCherry expression constructs to spectroscopically monitor the expression properties of both vectors. Our experiments showed that the minimized vector exhibited several advantages over the pMyNT vector. First, the overall yield of expressed protein is higher due to the higher yield of bacterial mass. Second, the heterologous expression was regulated more tightly, offering an expression tool for diverse target proteins. Third, it is suitable for large multi-protein complexes that are expressed from multi-cistronic operons. Additionally, our results propose a new understanding of the regulation mechanism of the acetamidase regulon with the potential to construct more optimized vectors in the future.

WXG100 protein superfamily consists of three subfamilies and exhibits an α-helical C-terminal conserved residue pattern.

Members of the WXG100 protein superfamily form homo- or heterodimeric complexes. The most studied proteins among them are the secreted T-cell antigens CFP-10 (10 kDa culture filtrate protein, EsxB) and ESAT-6 (6 kDa early secreted antigen target, EsxA) from Mycobacterium tuberculosis. They are encoded on an operon within a gene cluster, named as ESX-1, that encodes for the Type VII secretion system (T7SS). WXG100 proteins are secreted in a full-length form and it is known that they adopt a four-helix bundle structure. In the current work we discuss the evolutionary relationship between the homo- and heterodimeric WXG100 proteins, the basis of the oligomeric state and the key structural features of the conserved sequence pattern of WXG100 proteins. We performed an iterative bioinformatics analysis of the WXG100 protein superfamily and correlated this with the atomic structures of the representative WXG100 proteins. We find, firstly, that the WXG100 protein superfamily consists of three subfamilies: CFP-10-, ESAT-6- and sagEsxA-like proteins (EsxA proteins similar to that of Streptococcus agalactiae). Secondly, that the heterodimeric complexes probably evolved from a homodimeric precursor. Thirdly, that the genes of hetero-dimeric WXG100 proteins are always encoded in bi-cistronic operons and finally, by combining the sequence alignments with the X-ray data we identify a conserved C-terminal sequence pattern. The side chains of these conserved residues decorate the same side of the C-terminal α-helix and therefore form a distinct surface. Our results lead to a putatively extended T7SS secretion signal which combines two reported T7SS recognition characteristics: Firstly that the T7SS secretion signal is localized at the C-terminus of T7SS substrates and secondly that the conserved residues YxxxD/E are essential for T7SS activity. Furthermore, we propose that the specific α-helical surface formed by the conserved sequence pattern including YxxxD/E motif is a key component of T7SS-substrate recognition.

Parent-reported ISAAC written questionnaire may underestimate the prevalence of asthma in children aged 10-12 years.

OBJECTIVES: The aim of the present study was to compare the validity of the International Study of Asthma and Allergies in Childhood (ISAAC) written (WQ) and audiovisual questionnaires (AVQ 3.0) in two age-groups (10-12 and 13-15 years, respectively). METHODS: The 13-15 year olds performed the self-completed the WQ and AVQ on the same day. The 10-12 year olds performed the self-completed the AVQ and the parent-completed WQ was completed by their parents. The methacholine challenge test was conducted in 10-12 year olds from one elementary school. RESULTS: In 10-12 year olds, the AVQ detected a generally higher prevalence of asthma symptoms than WQ. In 13-15 year olds, this was reversed. In 10-12 year olds, poor agreement was found between the parent-completed WQ and the self-reported AVQ. In 13-15 year olds, moderate agreement was found between the self-reported WQ and AVQ. Low sensitivity was found, in predicting bronchial hyper-responsiveness (BHR) for all questions of both WQ and AVQ in 10-12 year olds. However, the AVQ had slightly higher sensitivity than WQ, with the exception of wheeze ever, although it was not statistically significant. CONCLUSION: The ISAAC AVQ may be another effective instrument for assessing the prevalence of asthma symptoms in children aged 10-12 years, whereas the parent-reported-WQ may underestimate the prevalence of asthma symptoms in this age-group.

Polymorphisms in GSDMA and GSDMB are associated with asthma susceptibility, atopy and BHR.

The gasdermin A (GSDMA) and gasdermin B (GSDMB) genes are located at 17q21.2. The GSDM family genes have been studied in the gastrointestinal tract but recent reports suggest that GSDMB is associated with childhood asthma in several populations. We investigated the association of the GSDMA and GSDMB variants with asthma in Korean children, and to assess the effect of these variants on intermediate phenotypes of asthma. Asthmatic (n = 778) and normal (n = 522) children were enrolled and genotypes were determined using PCR-RFLP. Asthma susceptibility was associated with GG of the GSDMA (rs7212938) and TT of GSDMB (rs7216389). And a combination of risk alleles of two polymorphisms was associated with asthma susceptibility and a frequency of those was higher in asthmatic children with increased levels of total IgE (aOR 1.77, 95% CI 1.15-2.72) and BHR (aOR 1.54, 95% CI 0.99-2.40) compared to normal. Also, we observed a significant association between haplotype of two polymorphisms and asthma susceptibility. The region including the GSDMA and GSDMB polymorphisms may be associated with asthma susceptibility and intermediate phenotypes of asthma, such as elevated IgE and BHR, in Korean children with asthma. These results strongly support an important role for the GSDMA and GSDMB in the development of childhood asthma.

Changes in the prevalence of childhood asthma in seoul from 1995 to 2008 and its risk factors.

PURPOSE: To investigate the prevalence of asthma and determine its risk factors in elementary school students in Seoul. METHODS: A modified International Study of Asthma and Allergies in Childhood (ISAAC) questionnaire was used to survey 4,731 elementary school students from five areas in Seoul between April and October, 2008. RESULTS: In elementary school children, the lifetime and recent 12-month prevalence of wheezing were 11.7% and 5.6%, respectively. The lifetime prevalence of asthma diagnosis was 7.9%, and the recent 12-month prevalence of asthma treatment was 2.7%. Male sex (adjusted odds ratio [aOR], 1.90; 95% confidence interval [CI], 1.36-2.66), history of atopic dermatitis (AD) (aOR, 2.76; 95% CI, 1.98-3.84), history of allergic rhinitis (AR) (aOR, 3.71; 95% CI, 2.61-5.26), history of bronchiolitis before 2 years of age (aOR, 2.06; 95% CI, 1.39-3.07), use of antibiotics during infancy for >3 days (aOR, 1.88; 95% CI, 1.35-2.62), parental history of asthma (aOR, 2.83; 95% CI, 1.52-5.27), exposure to household molds during infancy (aOR, 1.84; 95% CI, 1.18-2.89), and the development or aggravation of asthma symptoms within 6 months after moving to a new house (aOR, 11.76; 95% CI, 5.35-25.86) were the independent risk factors for wheezing within 12 months. CONCLUSIONS: The prevalence of wheezing and asthma in elementary school students in 2008 was similar to that in the past decade. Male sex, history of AD, history of AR, history of bronchiolitis before 2 years of age, parental asthma, use of antibiotics during infancy, exposure to molds in the house during infancy, and development or aggravation of asthma symptoms within 6 months after moving to a new house, could be risk factors for wheezing within 12 months.

Bronchiectasis in children: 10-year experience at a single institution.

PURPOSE: Bronchiectasis in children is still one of the most common causes of childhood mortality in developing countries. The aim of this study was to investigate the epidemiological characteristics, clinical features, underlying etiologic factors, and distinct change in the management of patients with bronchiectasis at Asan Medical Center Children's Hospital of Seoul. METHODS: A retrospective study of children diagnosed with bronchiectasis was conducted between January 1999 and December 2008. All patients underwent a comprehensive examination to identify etiologic factors. Data analysis in terms of age at onset, initial presenting symptoms, underlying etiology, distinct change in treatment, distribution of pulmonary involvement on computed tomography (CT), and causative microbiological flora triggering secondary infections was performed. RESULTS: The median age at the time of the diagnosis of bronchiectasis was 7.6 years (range, 2 months to 18 years). Persistent coughing was the most common symptom. The underlying etiologies identified in 79 patients (85.8%) included bronchiolitis obliterans (32.6%), childhood respiratory infection (20.6%), interstitial lung disease (17.3%), immunodeficiency (8.6%), and primary ciliary dyskinesia (4.3%). In 53 children (67%), the identified cause led to a distinct and individualized change in management. The distribution of CT abnormalities had no correlation with the underlying cause of bronchiectasis. CONCLUSIONS: Selected Korean children with bronchiectasis were reviewed to identify diverse underlying etiologies. All children with bronchiectasis should be comprehensively investigated because identifying underlying causes may have a major impact on their management and prognosis.

Proteome-wide identification of mycobacterial pupylation targets.

Mycobacteria use a unique system for covalently modifying proteins based on the conjugation of a small protein, referred to as prokaryotic ubiquitin-like protein (PUP). In this study, we report a proteome-wide analysis of endogenous pupylation targets in the model organism Mycobacterium smegmatis. On affinity capture, a total of 243 candidate pupylation targets were identified by two complementary proteomics approaches. For 41 of these protein targets, direct evidence for a total of 48 lysine-mediated pupylation acceptor sites was obtained by collision-induced dissociation spectra. For the majority of these pupylation targets (38 of 41), orthologous genes are found in the M. tuberculosis genome. Interestingly, approximately half of these proteins are involved in intermediary metabolism and respiration pathways. A considerable fraction of the remaining targets are involved in lipid metabolism, information pathways, and virulence, detoxification and adaptation. Approximately one-third of the genes encoding these targets are located in seven gene clusters, indicating functional linkages of mycobacterial pupylation targets. A comparison of the pupylome under different cell culture conditions indicates that substrate targeting for pupylation is rather dynamic.

The Effects of Lactobacillus rhamnosus on the Prevention of Asthma in a Murine Model.

PURPOSE: Lactobacilli are probiotic bacteria that are effective in the management of allergic diseases or gastroenteritis. It is hypothesized that such probiotics have immunoregulatory properties and promote mucosal tolerance. Our goal was to investigate whether Lactobacillus casei rhamnosus Lcr35 could inhibit airway inflammation in an ovalbumin (OVA)-induced murine model of asthma. METHODS: BALB/c mice aged 6 weeks were used in the present study. Lactobacillus casei rhamnosus Lcr35 was administered daily, starting 1 week prior to the first OVA sensitization (group 1) and 2 days before the first 1% OVA airway challenge (group 2). Mice that received only saline at both sensitization and airway challenge time points were used as negative controls (group 3), and those that had OVA-induced asthma were used as positive controls (group 4). Airway responsiveness to methacholine was assessed, and bronchoalveolar lavage (BAL) was performed. At the endpoint of the study, total IgE as well as OVA-specific IgE, IgG(1) and IgG(2a) in serum was measured by enzyme-linked immunosorbent assay. Lung pathology was also evaluated. RESULTS: Airway hyperresponsiveness, total cell counts and the proportion of eosinophils in BAL fluid were significantly decreased in group 1 compared with group 4 (P<0.05). Total serum IgE levels were also significantly decreased in group 1 compared with group 4. Serum levels of OVA-specific IgE, IgG(1) and IgG(2a) were not significantly influenced by treatment with Lcr35. There was significantly less peribronchial and perivascular infiltration of inflammatory cells in group 1 compared with group 4; however, there were no significant differences in methacholine challenge, BAL, serology or histology between groups 2 and 4. CONCLUSIONS: Oral treatment with Lcr35 prior to sensitization can attenuate airway inflammation and hyperreactivity in a mouse model of allergic airway inflammation. These results suggest that Lcr35 may have potential for preventing asthma.

The peroxisomal receptor Pex19p forms a helical mPTS recognition domain.

The protein Pex19p functions as a receptor and chaperone of peroxisomal membrane proteins (PMPs). The crystal structure of the folded C-terminal part of the receptor reveals a globular domain that displays a bundle of three long helices in an antiparallel arrangement. Complementary functional experiments, using a range of truncated Pex19p constructs, show that the structured alpha-helical domain binds PMP-targeting signal (mPTS) sequences with about 10 muM affinity. Removal of a conserved N-terminal helical segment from the mPTS recognition domain impairs the ability for mPTS binding, indicating that it forms part of the mPTS-binding site. Pex19p variants with mutations in the same sequence segment abolish correct cargo import. Our data indicate a divided N-terminal and C-terminal structural arrangement in Pex19p, which is reminiscent of a similar division in the Pex5p receptor, to allow separation of cargo-targeting signal recognition and additional functions.

Molecular basis of the head-to-tail assembly of giant muscle proteins obscurin-like 1 and titin.

Large filament proteins in muscle sarcomeres comprise many immunoglobulin-like domains that provide a molecular platform for self-assembly and interactions with heterologous protein partners. We have unravelled the molecular basis for the head-to-tail interaction of the carboxyl terminus of titin and the amino-terminus of obscurin-like-1 by X-ray crystallography. The binary complex is formed by a parallel intermolecular beta-sheet that presents a novel immunoglobulin-like domain-mediated assembly mechanism in muscle filament proteins. Complementary binding data show that the assembly is entropy-driven rather than dominated data by specific polar interactions. The assembly observed leads to a V-shaped zipper-like arrangement of the two filament proteins.

Difference in TB10.4 T-cell epitope recognition following immunization with recombinant TB10.4, BCG or infection with Mycobacterium tuberculosis.

Most novel vaccines against infectious diseases are based on recombinant Ag; however, only few studies have compared Ag-specific immune responses induced by natural infection with that induced by the same Ag in a recombinant form. Here, we studied the epitope recognition pattern of the tuberculosis vaccine Ag, TB10.4, in a recombinant form, or when expressed by the pathogen Mycobacterium tuberculosis (M.tb), or by the current anti-tuberculosis vaccine, Mycobacterium bovis BCG. We showed that BCG and M.tb induced a similar CD4+ T-cell specific TB10.4 epitope-pattern, which differed completely from that induced by recombinant TB10.4. This difference was not due to post-translational modifications of TB10.4 or because TB10.4 is secreted from BCG and M.tb as a complex with Rv0287. In addition, BCG and TB10.4/CAF01 were both taken up by DC and macrophages in vivo, and in vitro uptake experiments revealed that both TB10.4 and BCG were transported to Lamp+-compartments. BCG and TB10.4 however, were directed to different types of Lamp+-compartments in the same APC, which may lead to different epitope recognition patterns. In conclusion, we show that different vectors can induce completely different recognition of the same protein.

Stoichiometric protein complex formation and over-expression using the prokaryotic native operon structure.

In prokaryotes, operon encoded proteins often form protein-protein complexes. Here, we show that the native structure of operons can be used to efficiently overexpress protein complexes. This study focuses on operons from mycobacteria and the use of Mycobacterium smegmatis as an expression host. We demonstrate robust and correct stoichiometric expression of dimers to higher oligomers. The expression efficacy was found to be largely independent of the intergenic distances. The strategy was successfully extended to express mycobacterial protein complexes in Escherichia coli, showing that the operon structure of gram-positive bacteria is also functional in gram-negative bacteria. The presented strategy could become a general tool for the expression of large quantities of pure prokaryotic protein complexes for biochemical and structural studies.

Structure-based prediction of the Saccharomyces cerevisiae SH3-ligand interactions.

A great challenge in the proteomics and structural genomics era is to discover protein structure and function, including the identification of biological partners. Experimental investigation is costly and time-consuming, making computational methods very attractive for predicting protein function. In this work, we used the existing structural information in the SH3 family to first extract all SH3 structural features important for binding and then used this information to select the right templates to homology model most of the Saccharomyces cerevisiae SH3 domains. Second, we classified, based on ligand orientation with respect to the SH3 domain, all SH3 peptide ligands into 29 conformations, of which 18 correspond to variants of canonical type I and type II conformations and 11 correspond to non-canonical conformations. Available SH3 templates were expanded by chimera construction to cover some sequence variability and loop conformations. Using the 29 ligand conformations and the homology models, we modelled all possible complexes. Using these complexes and in silico mutagenesis scanning, we constructed position-specific ligand binding matrices. Using these matrices, we determined which sequences will be favorable for every SH3 domain and then validated them with available experimental data. Our work also allowed us to identify key residues that determine loop conformation in SH3 domains, which could be used to model human SH3 domains and do target prediction. The success of this methodology opens the way for sequence-based, genome-wide prediction of protein-protein interactions given enough structural coverage.

Bimolecular fluorescence complementation in structural biology.

Bimolecular fluorescence complementation is a method of probing protein-ligand interactions under physiological conditions. It provides a state-of-the-art tool to examine interactions observed in 3D structures of multi-component protein complexes, either to validate new experimental structures or to assess the correctness of homology models. Applications of the method range from homo- and hetero-oligomeric assemblies, including non-protein-ligands. Proof-of-principle experiments have also shown the potential of bimolecular fluorescence complementation to monitor protein complexes in a conformation-dependent manner. Here, recent highlights of structure-based applications of the method are outlined and assessed in terms of project-specific findings. These examples demonstrate the power of bimolecular fluorescence complementation to become a leading analysis tool in structural biology, to independently evaluate and characterize higher-order protein complexes.

High-resolution structural analysis of mammalian profilin 2a complex formation with two physiological ligands: the formin homology 1 domain of mDia1 and the proline-rich domain of VASP.

Profilins are small proteins capable of binding actin, poly-l-proline and other proline-rich sequences, and phosphatidylinositol (4,5)-bisphosphate. A number of proline-rich ligands for profilin have been characterised, including proteins of the Ena/VASP and formin families. We have determined the high-resolution crystal structures of mouse profilin 2a in complex with peptides from two functionally important ligands from different families, VASP and mDia1. The structures show that the binding mode of the peptide ligand is strongly affected by the non-proline residues in the sequence, and the peptides from VASP and mDia1 bind to profilin 2a in distinct modes. The high resolution of the crystallographic data allowed us to detect conserved CH-pi hydrogen bonds between the peptide and profilin in both complexes. Furthermore, both peptides, which are shown to have micromolar affinity, induced the dimerisation of profilin, potentially leading to functionally different ligand-profilin-actin complexes. The peptides did not significantly affect actin polymerisation kinetics in the presence or in the absence of profilin 2a. Mutant profilins were tested for binding to poly-L-proline and the VASP and mDia1 peptides, and the F139A mutant bound proline-rich ligands with near-native affinity. Peptide blotting using a series of designed peptides with profilins 1 and 2a indicates differences between the two profilins towards proline-rich peptides from mDia1 and VASP. Our data provide structural insights into the mechanisms of mDia1 and VASP regulated actin polymerisation.

Palindromic assembly of the giant muscle protein titin in the sarcomeric Z-disk.

The Z-disk of striated and cardiac muscle sarcomeres is one of the most densely packed cellular structures in eukaryotic cells. It provides the architectural framework for assembling and anchoring the largest known muscle filament systems by an extensive network of protein-protein interactions, requiring an extraordinary level of mechanical stability. Here we show, using X-ray crystallography, how the amino terminus of the longest filament component, the giant muscle protein titin, is assembled into an antiparallel (2:1) sandwich complex by the Z-disk ligand telethonin. The pseudosymmetric structure of telethonin mediates a unique palindromic arrangement of two titin filaments, a type of molecular assembly previously found only in protein-DNA complexes. We have confirmed its unique architecture in vivo by protein complementation assays, and in vitro by experiments using fluorescence resonance energy transfer. The model proposed may provide a molecular paradigm of how major sarcomeric filaments are crosslinked, anchored and aligned within complex cytoskeletal networks.

Human alpha-defensins neutralize anthrax lethal toxin and protect against its fatal consequences.

Anthrax caused by Bacillus anthracis represents a major bioterroristic threat. B. anthracis produces lethal toxin (LeTx), a combination of lethal factor (LF) and protective antigen that plays a major role in anthrax pathogenesis. We demonstrate that human neutrophil alpha-defensins are potent inhibitors of LF. The inhibition of LF by human neutrophil protein (HNP-1) was noncompetitive. HNP-1 inhibited cleavage of a mitogen-activated protein kinase kinase and restored impaired mitogen-activated protein kinase signaling in LeTx-treated macrophages. HNP-1 rescued murine macrophages from B. anthracis-induced cytotoxicity, and in vivo treatment with HNP-1-3 protected mice against the fatal consequences of LeTx.