Synergy between simulation and experiment in describing the energy landscape of protein folding

Experimental data from protein engineering studies and NMR spectroscopy have been used by theoreticians to develop algorithms for helix propensity and to benchmark computer simulations of folding pathways and energy landscapes. Molecular dynamic simulations of the unfolding of chymotrypsin inhibitor 2 (CI2) have provided detailed structural models of the transition state ensemble for unfolding/folding of the protein. We now have used the simulated transition state structures to design faster folding mutants of CI2. The models pinpoint a number of unfavorable local interactions at the carboxyl terminus of the single alpha-helix and in the protease-binding loop region of CI2. By removing these interactions or replacing them with stabilizing ones, we have increased the rate of folding of the protein up to 40-fold (tau = 0.4 ms). This correspondence, and other examples of agreement between experiment and theory in general, Phi-values and molecular dynamics simulations, in particular, suggest that significant progress has been made toward describing complete folding pathways at atomic resolution by combining experiment and simulation.     

Lipoprotein changes and reduction in the incidence of major coronary heart disease events in the Scandinavian Simvastatin Survival Study (4S)

BACKGROUND: The Scandinavian Simvastatin Survival Study (4S) randomized 4444 patients with coronary heart disease (CHD) and serum cholesterol 5.5 to 8.0 mmol/L (213 to 310 mg/dL) with triglycerides < or =2.5 mmol/L (220 mg/dL) to simvastatin 20 to 40 mg or placebo once daily. Over the median follow-up period of 5.4 years, one or more major coronary events (MCEs) occurred in 622 (28%) of the 2223 patients in the placebo group and 431 (19%) of the 2221 patients in the simvastatin group (34% risk reduction, P<.00001). Simvastatin produced substantial changes in several lipoprotein components, which we have attempted to relate to the beneficial effects observed. METHODS AND RESULTS: The Cox proportional hazards model was used to assess the relationship between lipid values (baseline, year 1, and percent change from baseline at year 1) and MCEs. The reduction in MCEs within the simvastatin group was highly correlated with on-treatment levels and changes from baseline in total and LDL cholesterol, apolipoprotein B, and less so with HDL cholesterol, but there was no clear relationship with triglycerides. We estimate that each additional 1% reduction in LDL cholesterol reduces MCE risk by 1.7% (95% CI, 1.0% to 2.4%; P<.00001). CONCLUSIONS: These analyses suggest that the beneficial effect of simvastatin in individual patients in 4S was determined mainly by the magnitude of the change in LDL cholesterol, and they are consistent with current guidelines that emphasize aggressive reduction of this lipid in CHD patients.     

Congenital cystic diseases of liver and extrahepatic bile ducts

The paper presents 30-year experience in treating 158 patients with congenital cystic diseases of the liver and bile ducts. Depending on the pattern of hepatobiliary lesions, the diagnostic value of techniques, such as ultrasound, computerized tomography, scintigraphy of the liver duodenoscopy with THCG was defined. Analyzing the late outcomes provided recommendations for the most optimal surgical management: cystic fenestration and tunneling in hepatic polycystosis, pericystectomy in solitary cysts of the liver, different varieties of bile draining operations in choledochal cysts and Caroli's disease.     

Thyroid hormone induces protein secretion and morphological changes in astroglial cells with an increase in expression of glial fibrillary acidic protein

Degradation and utilization of protein by Prevotella ruminicola B1(4), a proteolytic bacterium that is prominent in the rumen, was examined. In preliminary experiments, proteinaceous N sources produced faster growth rates than did NH4Cl, based on changes in optical density over time. However, ammonium chloride produced a greater maximum cell density than did proteinaceous N sources. Of the proteinaceous N sources, an enzymatic hydrolysate of soybean protein with a relative peptide size of 3 AA residues produced a greater growth rate and maximum cell density compared with the other proteinaceous N sources. Further experiments revealed that P. ruminicola B1(4) grew faster and to a greater final dry weight with soybean protein than with casein. Degradation of both proteins was low as was indicated by the slow disappearance of soluble protein, low concentrations of free AA and peptides, and the decrease in ammonia concentrations over time. Patterns of degradation did differ between the two proteins, however. Accumulation of peptides and free AA from soybean protein peaked 2 h earlier than those from casein, and concentrations of free AA and peptides from soybean protein were lower on average than those from casein. Prevotella ruminicola B1(4) preferentially utilized Asp, Ile, Leu, Lys, and Arg from soybean protein compared with casein. The relative size of peptides that accumulated from both proteins, as determined by the ratio of ninhydrin reaction after HCl hydrolysis to ninhydrin reaction before HCl hydrolysis, suggested that part of the proteolytic activity of P. ruminicola B1(4) is a dipeptidase. Our findings suggest that P. ruminicola may have a greater impact on peptide degradation than on protein degradation in the rumen.     

Reduction of triceps muscle force after shortening of the distal humerus: a computational model

A retrospective case reference study examining the use of alcohol and tobacco in 303 women aged 40 or over suffering from oral or oropharyngeal cancer was conducted in the south-west Netherlands. Both alcohol and tobacco consumption are important in the development of oral and oropharyngeal cancer with increased consumption of both markedly increasing the risks of cancer, but alcohol having the greater effect.     

Prediction of the biologically active sites in eclosion hormone from the silkworm, Bombyx mori

The structure-activity relationship of eclosion hormone from the silkworm, Bombyx mori, was analyzed. First, the probable active residues in silkworm eclosion hormone and also tobacco hornworm eclosion hormone were predicted by the average distance map method. To examine the contributions of those residues to the activity of silkworm eclosion hormone, Gly-substituted mutants for those predicted residues were produced by site-directed mutagenesis and their activities were evaluated by a bioassay. Finally, Glu12, Met24 and Phe25 were estimated to be the crucial residues for the eclosion hormone activity. The possibility of the development of a blocker of an eclosion hormone receptor on the basis of the present work is also discussed.      

Morphological aspects of particle uptake by lung phagocytes

Macrophages residing on the inner epithelial surfaces of airways and alveoli are the only lung phagocytes exposed directly to the environment. Their phagocytic and microbicidal activities are essential for maintaining this organ in a clean and sterile state. The morphology of these phagocytes can be investigated in situ only after implementing special techniques, which involve intravascular triple-perfusion of aqueous fixatives or instillation of nonpolar ones. Such studies have revealed the engulfment of particles by these cells to be rapid, the process being essentially complete within a day. Particles are entrapped within phagosomes and the host cells eventually transported out of the lungs by mucociliary action, macrophages with higher loads being more rapidly eliminated than those with lower ones. Very small particles or those persisting on the epithelial surfaces may be taken up by the eponymous cells. Translocation of particles into the underlying connective tissue and their subsequent phagocytosis by interstitial macrophages prolongs their retention time in the lungs. The still poorly studied pleural macrophages might be involved in cell-mediated immune responses within the pleural space. Intravascular pulmonary macrophages figure largely in the phagocytosis of circulating particles. The role played by dendritic cells in particle uptake by the lungs is not well understood. Airway and alveolar macrophages are the primary phagocytes of the lung. In nonoverload situations and for particles >1 microm, a small proportion of those recruited suffices to remove material from the epithelial surface before other phagocytes, with an apparently greater immunological potential, gain access to it.     

Perturbations Involving nu1 of NCCN

From high-resolution infrared spectra of 14N12C12C14N, 14N13C13C14N, and 15N12C12C15N, we find that the levels 1000(0)0(0), 1000(0)1(1), 1000(0)2(0,2), and 1000(0)3(1,3) have very pronounced perturbations. Our analysis shows that these perturbations are due to a vibrational resonance among the levels 1000(0)0(0), 0102(0)2(0), and 0102(0)2(2) in the one case, and equivalent levels with one or more additional quanta of nu5 in the other three cases. The resonance constant for the perturbation involving nu1 is 0.25 cm-1. It has the dependence on v5 and l5 that is expected for the sextic potential constant, K124455, although it seems too large for such a high-order constant. The Deltal (or Deltak) = 2 interaction between, for instance, 1000(0)0(0) and 0102(0)2(2e) is shown to be primarily due to the l-type resonance mixing of the 0102(0)2(0) and 0102(0)2(2e) states. The resonance is nearly "turned off" for the 1000(0)2(0,2) and 1000(0)3(1,3) states of 14N13C13C14N because there are no level crossings between the interacting states and the band centers are too far away to have an obvious effect, although careful analysis shows that the perturbation can be seen in their effective centrifugal distortion constants. The spectrum of 15N12C12C15N shows level crossings only in the case of the 1000(0)1(1), 1000(0)2(0,2), and 1000(0)3(1,3) states. Copyright 1999 Academic Press.     

Anterior rhinomanometry in nasal allergen challenges

Even simple and relatively safe provocation procedures like nasal allergen challenges, should aim to allow detection of positivity with the less possible discomfort to the patient. The objective of this work was to evaluate if the use of rhinomanometric measurements during nasal provocation procedures could allow a decrease in the total administered allergen dose, causing less symptoms to the patients but without increasing the number of false-negatives, comparatively to clinical scores or nasal peak-flow measurements. Our results showed that performing rhinomanometric measurements during nasal HDM challenge procedures can lead in many patients to a reduction in the total dose of allergen administered during the challenge, without loss of sensitivity or specificity. This allergen dose reduction translates in less time consumed during the provocation and less patients' discomfort.     

Design of constructions for the expression of proteolytic antibody light chain

A new system for the expression of a catalytic light chain antibody to the vasoactive intestinal peptide is described. The system made possible the isolation the large amounts of a homogeneous protein without any additional peptide domains. The preparation obtained can be used in further experiments on light chain crystallization and in X-ray-structural analysis of its catalytic center.