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.     

Activity of two lignin biosynthesis enzymes during development of a maize internode

To ascertain the temporal relationships of phcnylpropanoid and lignin pathway enzymes, phenylalanine ammonia-lyase (PAL) and cinnamyl alcohol- NADPH dehydrogenase(CAD), with lignin concentration, PAL and CAD activities and lignin concentrations were assessed during progressive development of the 10th internode in maize (Zea mays L). Enzyme activities were quantified and lignin concentrations were determined by the detergent system of fiber fractiona- tion from lower, middle, and upper sections of the elongating internode harvested 3, 5, 7, 9, 11, 13, and 15 days after the internode had reached 10 mm in length. Over 15 days, a coordinated, sequential, and basipetal pattern of enzyme activities and lignin accumulation evolved through the internode, spanning the stages of rapid elongation, cellular differentiation, and secondary cell wall formation. PAL activity was initiated first, rising to peak activity in elongating tissue, and falling basipetally in tissues as they matured. CAD activity rose in fully elongated, maturing internode tissue where PAL activity was waning following its peak activity. Lignin accumulated in tissues with high CAD activity. CAD activity and lignin deposition patterns were similar: simultaneously increasing in activity and deposition over time while activity and deposition also shifting basipetally through the internode, keeping pace with secondary cell wall formation. Lignin concentration correlated significantly with CAD, but not with PAL.     

Testing the validity of the spherical DEM model in simulating real granular screening processes

We investigate the flow of a granular material over a vibrated horizontal screen. We perform a direct quantitative comparison, across a range of operating conditions, between laboratory scale experiments and simulations using the discrete element method (DEM). We test the extent to which the commonly employed DEM approximation of particles being spherical affects the ability of the model to realistically reproduce the behaviour of industrial screening systems where the particles are generally non-spherical in shape.The simulation geometry and input particle size distribution are set up to exactly match the experimental system, which consists of a horizontal screen with a wire mesh cloth onto which quarry rock is fed at a series of input flow rates. The screen is vibrated, causing the granular bed to flow over the deck and vertically stratify with finer material passing through the screen, where it is collected in a series of bins located along the length of the screen. The size distribution of the material flowing through each section of the screen is found by analyzing the contents of each collection bin.The best agreement is found for very low flow rates, where the vast majority of the below aperture size material is rapidly captured just after it enters the screen in both the simulation and experiment. At higher flow rates, significant quantitative errors are found with the over-prediction of the flow rate through the screen for near grate sized particles. This is attributed to the higher rate of percolation through the bed and the easier capture by the screen surface of the spherical shaped material. The near aperture sized spherical particles also show a very strong tendency to peg the screen, becoming trapped in the screen openings and limiting further flow through those parts the screen. The use of spherical particles in the DEM simulation of vibrating screens is therefore found to be inadequate for modelling realistic flow and separation of particles that are not actually spherical.     

Enhancement of Surfactants in Nanoparticles Produced by an Electrospray Aerosol Generator

Electrospray aerosol generators (EAGs) disperse conducting solutions into air, promptly neutralize the particles to remove the excess charge, and evaporate the residual solvent with a dry air flow. For solutions containing multiple solutes, the particles may become enhanced in the more surface-active solutes. The extent of the enhancement was estimated for nanoparticles electrosprayed from a solution containing NaCl and surfactant sodium dodecyl sulfate (SDS) mixed in a 9:1 weight ratio. A tandem particle mobility analyzer was used to quantify the hygroscopic growth factor (GF). The relative fractions of NaCl and SDS in the particles were estimated from the measured GFs assuming that NaCl and SDS take up water independently of each other. The nanoparticles were considerably enhanced in SDS relative to the starting solution, with the NaCl:SDS weight ratio increasing with the distance from the EAG electrified capillary tip to the neutralizer, and reaching ～1:1 at the longest distances probed. The enhancement in SDS likely occurred during particle fission events as particles traveled from the capillary to the neutralizer. This study has practical ramifications for aerosol nanotechnology and aerosol-assisted drug delivery, which rely on EAG as an instrument of choice for nanoparticle generation.

Copyright 2012 American Association for Aerosol Research     

Microstructures and mechanical properties of welded Fe-12Cr-20Mn austenitic stainless steel

The effects of welding on the tensile and fatigue properties of fully annealed and cold-worked Fe-12Cr-20Mn austenitic stainless steel were evaluated. Room temperature and 500 °C tensile tests and room temperature cantilever beam fatigue tests were accomplished on specimens that contained autogenous bead-on-plate welds. The tensile and fatigue properties of the fully annealed material were not significantly influenced by welding. The tensile properties of the welded cold-worked material were also not significantly affected by the presence of a weldment. However, welding caused a large reduction of the fatigue life of the cold-worked material. Fatigue cracks preferentially initiated at large Mn-Si inclusions that formed in the fusion zones of the weldments.     

Melanin Distribution in Human Skin: Influence of Cytoskeletal,Polarity, and Centrosome-Related Machinery of Stratum basale Keratinocytes

Melanin granules cluster within supra-nuclear caps in basal keratinocytes (KCs) of the human epidermis, where they protect KC genomic DNA against ultraviolet radiation (UVR) damage. While much is known about melanogenesis in melanocytes (MCs) and a moderate amount about melanin transfer from MC to KC, we know little about the fate of melanin once inside KCs. We recently reported that melanin fate in progenitor KCs is regulated by rare asymmetric organelle movement during mitosis. Here, we explore the role of actin, microtubules, and centrosome-associated machinery in distributing melanin within KCs. Short-term cultures of human skin explants were treated with cytochalasin-B and nocodazole to target actin filaments and microtubules, respectively. Treatment effects on melanin distribution were assessed by the Warthin–Starry stain, on centrosome-associated proteins by immunofluorescence microscopy, and on co-localisation with melanin granules by brightfield microscopy. Cytochalasin-B treatment disassembled supra-nuclear melanin caps, while nocodazole treatment moved melanin from the apical to basal KC domain. Centrosome and centriolar satellite-associated proteins showed a high degree of co-localisation with melanin. Thus, once melanin granules are transferred to KCs, their preferred apical distribution appears to be facilitated by coordinated movement of centrosomes and centriolar satellites. This mechanism may control melanin’s strategic position within UVR-exposed KCs.