Exclusively NOESY-based automated NMR assignment and structure determination of proteins

A fully automated method is presented for determining NMR solution structures of proteins using exclusively NOESY spectra as input, obviating the need to measure any spectra only for obtaining resonance assignments but devoid of structural information. Applied to two small proteins, the approach yielded structures that coincided closely with conventionally determined structures.

Non-invasive ventilation in severe asthma attack, its possibilities and problems

Asthma attack is characterized by episodic attacks of cough, dyspnea and wheeze occurring due to bronchoconstriction, airway hyperresponsiveness and mucous hypersecretion. Although nationwide clinical guidelines have been published to establish the standard care of asthma, choices in the treatment of fatal asthma attacks remain of clinical significance. Especially, in a severe asthma attack, despite the application of conventional medical treatment, respiratory management is critical. Even though non-invasive ventilation (NIV) has been shown to be effective in a wide variety of clinical settings, reports of NIV in asthmatic patients are scarce. According to a few prospective clinical trials reporting promising results in favour of the use of NIV in a severe asthma attack, a trial of NIV prior to invasive mechanical ventilation seems acceptable and may benefit patients by decreasing the need for intubation and by supporting pharmaceutical treatments. Although selecting the appropriate patients for NIV use is a key factor in successful NIV application, how to distinguish such patients is quite controversial. Larger high quality clinical trails are urgently required to confirm the benefits of NIV to patients with severe asthma attack. In this article, we focus on the body of evidence supporting the use of NIV in asthma attacks and discuss its advantages as well its problems.

Long-term changes in airway-wall thickness on computed tomography in asthmatic patients

BACKGROUND

Effects of long-term treatment with inhaled corticosteroids (ICSs) on airway-wall thickness in patients with asthma remain unknown.

OBJECTIVES

To determine whether airway-wall thickness consistently decreases after long-term ICS treatment, and to analyze factors contributing to long-term airway-wall changes in asthmatics.

METHODS

A retrospective analysis of long-term changes in airway-wall thickness using computed tomography was performed in 14 patients with asthma. Wall area corrected by body surface area (WA/BSA) was examined at baseline, 12 weeks after the commencement of ICSs (second measurement), and at least 2 years (mean +/- SEM. 4.2 +/- 0.5) after the second measurement (third measurement). Mean +/- SEM changes in WA/BSA from the second to the third measurements were analyzed.

RESULTS

The mean change in WA/BSA was not significant between the second and the third measurements (-0.27 +/- 0.59 mm2/m2/y). Overall, the changes were significantly associated with disease duration but not with other clinical indices. When the 14 patients were divided into 2 groups using a cutoff value of 0.32 mm2/m2/y for the mean change in WA/BSA, for the 5 patients whose WA/BSA exceeded this cutoff, daily ICS doses were not reduced and both forced expiratory volume in the first second (FEV1) and forced vital capacity decreased significantly. For the remaining 9 patients, daily ICS doses were reduced and long-term FEV1 values did not change.

CONCLUSIONS

Despite long-term treatment with ICSs, airway-wall thickness did not consistently decrease. One possible mechanism underlying poor response to long-term treatment may be long-standing asthma.

A mechanism for single-stranded DNA-binding protein (SSB) displacement from single-stranded DNA upon SSB-RecO interaction

Displacement of single-stranded DNA (ssDNA)-binding protein (SSB) from ssDNA is necessary for filament formation of RecA on ssDNA to initiate homologous recombination. The interaction between RecO and SSB is considered to be important for SSB displacement; however, the interaction has not been characterized at the atomic level. In this study, to clarify the mechanism underlying SSB displacement from ssDNA upon RecO binding, we examined the interaction between Thermus thermophilus RecO and cognate SSB by NMR analysis. We found that SSB interacts with the C-terminal positively charged region of RecO. Based on this result, we constructed some RecO mutants. The R127A mutant had considerably decreased binding affinity for SSB and could not anneal SSB-coated ssDNAs. Further, the mutant in the RecOR complex prevented the recovery of ssDNA-dependent ATPase activity of RecA from inhibition by SSB. These results indicated that the region surrounding Arg-127 is the binding site of SSB. We also performed NMR analysis using the C-terminal peptide of SSB and found that the acidic region of SSB is involved in the interaction with RecO, as seen in other protein-SSB interactions. Taken together with the findings of previous studies, we propose a model for SSB displacement from ssDNA where the acidic C-terminal region of SSB weakens the ssDNA binding affinity of SSB when the dynamics of the C-terminal region are suppressed by interactions with other proteins, including RecO.

CD24 gene exon 2 dimorphism does not affect disease susceptibility in Japanese sarcoidosis patients

BACKGROUND

CD24 proteins are expressed on several inflammatory cells, and play an important role for the T-cell activation.

OBJECTIVES

The aim of this study is to investigate the relationship of a CD24 gene polymorphism to disease susceptibility or clinical findings including bronchoalveolar lavage (BAL) cell profiles in Japanese sarcoidosis patients.

METHODS

A previously reported functional single nucleotide polymorphism (SNP) of CD24 gene exon 2 was examined in 186 Japanese sarcoidosis patients and 146 sex and age-matched healthy controls using restriction fragment length polymorphism method. The distribution of genotypes was compared between the two groups. The association between genotypes or alleles and clinical features or BAL cell profiles was also examined.

RESULTS

There were no significant differences in the distribution of genotypes or allele frequencies between sarcoidosis and controls. There were also no significant differences in clinical features or BAL cell profiles among patients with different genotypes of CD24.

CONCLUSIONS

There was no relationship between a CD24 exon 2 SNP and disease susceptibility or clinical findings in Japanese sarcoidosis patients.

Significance of plasma NT-proBNP levels as a biomarker in the assessment of cardiac involvement and pulmonary hypertension in patients with sarcoidosis

BACKGROUND

Cardiac involvement and pulmonary hypertension (PH) are life-threatening complications in sarcoidosis.

OBJECTIVE

This study aimed to investigate the utility of plasma NT-proBNP in the assessment of these conditions in sarcoidosis patients.

STUDY DESIGN AND METHODS

A prospective, observational study was performed on 150 consecutive Japanese sarcoidosis patients. Doppler echocardiography was performed in all subjects, and those who were successfully evaluated for PH status were included in the analysis. Cardiac sarcoidosis was diagnosed based on Japanese guidelines, and PH was defined as estimated systolic pulmonary artery pressure (sPAP) > or = 35 mmHg. The diagnostic accuracy of NT-proBNP according to the presence of cardiac sarcoidosis and PH was assessed based on receiver-operator characteristic (ROC) curves.

RESULTS

130 subjects were successfully evaluated for PH status. Of these, 29 met the diagnostic criteria of cardiac sarcoidosis, and 21 were diagnosed with PH. Plasma NT-proBNP levels were significantly higher in patients with cardiac sarcoidosis (p < 0.0001). Stepwise regression analysis showed that presence of cardiac sarcoidosis, decreased ejection fraction and increased sPAP were all independently associated with higher plasma NT-proBNP levels. Plasma NT-proBNP showed good accuracy in identifying patients with cardiac sarcoidosis (area under the ROC curve; AURC = 0.913). However, even when patients with cardiac sarcoidosis were excluded, plasma NT-proBNP levels could not be used reliably to identify patients with PH (AURC = 0.681).

CONCLUSION

In patients with sarcoidosis, plasma NT-proBNP levels are a useful biomarker to identify cardiac involvement, but not to identify PH.

NMR protein structure determination in living E. coli cells using nonlinear sampling

The cell is a crowded environment in which proteins interact specifically with other proteins, nucleic acids, cofactors and ligands. Atomic resolution structural explanation of proteins functioning in this environment is a main goal of biochemical research. Recent improvements to nuclear magnetic resonance (NMR) hardware and methodology allow the measurement of high-resolution heteronuclear multidimensional NMR spectra of macromolecules in living cells (in-cell NMR). In this study, we describe a protocol for the stable isotope ((13)C, (15)N and (2)H) labeling and structure determination of proteins overexpressed in Escherichia coli cells exclusively on the basis of information obtained in living cells. The protocol combines the preparation of the protein in E. coli cells, the rapid measurement of the three-dimensional (3D) NMR spectra by nonlinear sampling of the indirectly acquired dimensions, structure calculation and structure refinement. Under favorable circumstances, this in-cell NMR approach can provide high-resolution 3D structures of proteins in living environments. The protocol has been used to solve the first 3D structure of a protein in living cells for the putative heavy metal-binding protein TTHA1718 from Thermus thermophilus HB8 overexpressed in E. coli cells. As no protein purification is necessary, a sample for in-cell NMR measurements can be obtained within 2-3 d. With the nonlinear sampling scheme, the duration of each 3D experiment can be reduced to 2-3 h. Once chemical shift assignments and NOESY peak lists have been prepared, structure calculation with the program CYANA and energy refinement can be completed in less than 1 h on a powerful computer system.

Electrostatic interaction between oxysterol-binding protein and VAMP-associated protein A revealed by NMR and mutagenesis studies

Oxysterol-binding protein (OSBP), a cytosolic receptor of cholesterol and oxysterols, is recruited to the endoplasmic reticulum by binding to the cytoplasmic major sperm protein (MSP) domain of integral endoplasmic reticulum protein VAMP-associated protein-A (VAP-A), a process essential for the stimulation of sphingomyelin synthesis by 25-hydroxycholesterol. To delineate the interaction mechanism between VAP-A and OSBP, we determined the complex structure between the VAP-A MSP domain (VAP-A(MSP)) and the OSBP fragment containing a VAP-A binding motif FFAT (OSBP(F)) by NMR. This solution structure explained that five of six conserved residues in the FFAT motif are required for the stable complex formation, and three of five, including three critical intermolecular electrostatic interactions, were not explained before. By combining NMR relaxation and titration, isothermal titration calorimetry, and mutagenesis experiments with structural information, we further elucidated the detailed roles of the FFAT motif and underlying motions of VAP-A(MSP), OSBP(F), and the complex. Our results show that OSBP(F) is disordered in the free state, and VAP-A(MSP) and OSBP(F) form a final complex by means of intermediates, where electrostatic interactions through acidic residues, including an acid patch preceding the FFAT motif, probably play a collective role. Additionally, we report that the mutation that causes the familial motor neuron disease decreases the stability of the MSP domain.

Solution structure of the E. coli ribosome hibernation promoting factor HPF: Implications for the relationship between structure and function

The 70S Escherichia coli ribosome dimerizes to form an inactive 100S ribosome during stationary phase, which is called "ribosome hibernation". The hibernation promoting factor HPF plays a crucial role in 100S ribosome formation. However, YfiA, a known paralog of HPF inhibits 100S formation, although it shares high sequence similarity. Here, we report the first solution structure of HPF as determined by multi-dimensional NMR. HPF adopts betaalphabetabetabetaalpha-fold and the overall structure is similar to YfiA as expected. However, detailed structure comparison based on the determined structure in this study revealed that there are remarkable differences around the C-terminal portion of helix alpha2, which is not predicted by homology modeling. Furthermore, some acidic residues conserved only in HPF are located at the rim of the common basic patch.

Long-term complications and prognosis of chronic beryllium disease

BACKGROUND

Chronic beryllium disease (CBD) is a rare disease, and there are no previous reports that have followed CBD patients over several decades. Thus, the long-term complications and prognosis of this illness still remain unclear.

OBJECTIVE

The aim of this study was to investigate long-term complications and prognosis of CBD patients.

STUDY DESIGN AND METHODS

This was a retrospective study based on the medical records of all CBD patients diagnosed at Kyoto University Hospital between the period 1973 to the present day. Ultimately, ten patients whose diagnoses had been made during the period 1973 to 1977 were included. Long-term physiological and radiological change, complications and prognosis of these patients were investigated.

RESULTS

Three patients completely remitted, and one died of cor-pulmonale. Among the remaining six patients, four have been followed up for more than thirty years in our institute. The majority developed mixed patterns of lung function impairment, cavity lesions of the lung, pneumothorax, and respiratory infections.

CONCLUSIONS

Long-term prognosis of CBD was poor with several complications due to chronic parenchymal and airway lesions.

Protein structure determination in living cells by in-cell NMR spectroscopy

Investigating proteins 'at work' in a living environment at atomic resolution is a major goal of molecular biology, which has not been achieved even though methods for the three-dimensional (3D) structure determination of purified proteins in single crystals or in solution are widely used. Recent developments in NMR hardware and methodology have enabled the measurement of high-resolution heteronuclear multi-dimensional NMR spectra of macromolecules in living cells (in-cell NMR). Various intracellular events such as conformational changes, dynamics and binding events have been investigated by this method. However, the low sensitivity and the short lifetime of the samples have so far prevented the acquisition of sufficient structural information to determine protein structures by in-cell NMR. Here we show the first, to our knowledge, 3D protein structure calculated exclusively on the basis of information obtained in living cells. The structure of the putative heavy-metal binding protein TTHA1718 from Thermus thermophilus HB8 overexpressed in Escherichia coli cells was solved by in-cell NMR. Rapid measurement of the 3D NMR spectra by nonlinear sampling of the indirectly acquired dimensions was used to overcome problems caused by the instability and low sensitivity of living E. coli samples. Almost all of the expected backbone NMR resonances and most of the side-chain NMR resonances were observed and assigned, enabling high quality (0.96 ångström backbone root mean squared deviation) structures to be calculated that are very similar to the in vitro structure of TTHA1718 determined independently. The in-cell NMR approach can thus provide accurate high-resolution structures of proteins in living environments.

Body mass index in male patients with COPD: correlation with low attenuation areas on CT

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is characterised by the presence of airflow limitation caused by loss of lung elasticity and/or airway narrowing. The pathological hallmark of loss of lung elasticity is emphysema, and airway wall remodelling contributes to the airway narrowing. Using CT, these lesions can be assessed by measuring low attenuation areas (LAA) and airway wall thickness/luminal area, respectively. As previously reported, COPD can be divided into airway dominant, emphysema dominant and mixed phenotypes using CT. In this study, it is postulated that a patient's physique may be associated with the relative contribution of these lesions to airflow obstruction.

METHODS

CT was used to evaluate emphysema and airway dimensions in 201 patients with COPD. Emphysema was evaluated using percentage of LAA voxels (LAA%) and airway lesion was estimated by percentage wall area (WA%). Patients were divided into four phenotypes using LAA% and WA%.

RESULTS

Body mass index (BMI) was significantly lower in the higher LAA% phenotype (ie, emphysema dominant and mixed phenotypes). BMI correlated with LAA% (rho = -0.557, p<0.0001) but not with WA%. BMI was significantly lower in the emphysema dominant phenotype than in the airway dominant phenotype, while there was no difference in forced expiratory volume in 1 s %predicted between the two.

CONCLUSION

A low BMI is associated with the presence of emphysema, but not with airway wall thickening, in male smokers who have COPD. These results support the concept of different COPD phenotypes and suggest that there may be different systemic manifestations of these phenotypes.