Is there a unifying mechanism for protein folding?

Proteins appear to fold by diverse pathways, but variations of a simple mechanism - nucleation-condensation - describe the overall features of folding of most domains. In general, secondary structure is inherently unstable and its stability is enhanced by tertiary interactions. Consequently, an extensive interplay of secondary and tertiary interactions determines the transition-state for folding, which is structurally similar to the native state, being formed in a general collapse (condensation) around a diffuse nucleus. As the propensity for stable secondary structure increases, folding becomes more hierarchical and eventually follows a framework mechanism where the transition state is assembled from pre-formed secondary structural elements.     

Is glucokinase responsible for the anomeric specificity of glycolysis in pancreatic islets?

At a low concentration of D-glucose (3.3 mM), the phosphorylation rate of this hexose in rat pancreatic islet homogenates incubated at 8 degrees C is higher with the beta- than with the alpha-anomer, as expected from the anomeric specificity of hexokinase. In the presence of a high concentration of glucose 6-phosphate (3.0 mM), which inhibits hexokinase but not glucokinase, the phosphorylation rates of the two anomers are not significantly different from one another. Nevertheless, in intact islets exposed at 8 degrees C to the same low concentration of D-glucose, the alpha-anomer augments, more than the beta-anomer, the production of lactic acid and net uptake of 45Ca. At the same concentration (3.3 mM), the alpha-anomer is also more potent than the beta-anomer in enhancing insulin release from perfused pancreases stimulated at 37 degrees C by L-leucine or by the combination of Ba2+ and theophylline. It is concluded that the participation of glucokinase is not essential for the anomeric specificity of glycolysis and insulin release in rat pancreatic islets.     

Is the endogenous antipyretic neuropeptide alpha-MSH responsible for reduced fever in aged rabbits?

The reduced febrile response in aged man has been noted since the beginning of clinical thermometry. Our previous research on aged rabbits and squirrel monkeys disclosed a similar reduced fever, presumably due to a decrease in central receptors for endogenous pyrogen. However, because central alpha-melanocyte stimulating hormone (MSH) appears to have a potent role in physiological control of fever, it may be that increased release of the peptide is responsible for the reduced febrile response in aged animals. To test this idea, antiserum specific to MSH was administered intracerebroventricularly to rabbits of known age. The antiserum given according to three schedules of treatment augmented fever caused by IV injections of interleukin-1 (IL-1) in young (less than 2 years) male and female rabbits. Aged female rabbits (3-5+ years) and females aged 2-3 years showed significant augmentation of fever only after pretreatment plus acute injection of antiserum. A single ICV injection of MSH (200 ng) reduced fever in all groups with the greatest antipyretic effect in the aged females. The results indicate that while aged rabbits have an increased antipyretic response to central MSH, binding of the endogenous peptide does not result in marked increases in fever in these animals. Thus, whereas a change in central MSH sensitivity may contribute to reduced fever in aged homeotherms, a reduction in central pyrogen receptors appears to be the most parsimonious explanation.     

How do RNA folding algorithms work?

Programs such as MFOLD and ViennaRNA are widely used to predict RNA secondary structures. How do these algorithms work? Why can't they predict RNA pseudoknots? How accurate are they, and will they get better?     

Is topmouth gudgeon Pseudorasbora parva responsible for the decline in sunbleak Leucaspius delineatus populations?

In England, a severe decline of introduced sunbleak Leucaspius delineatus populations has been attributed to the introduction of the invasive topmouth gudgeon Pseudorasbora parva . In France, however, after 4 years of P. parva colonization in a large natural lake, no demonstrated impacts on the native L. delineatus populations have been observed. This suggests that the original impacts observed in England, such as spawning inhibition and high mortality, were the result of an emerging pathogen, the rosette-like agent, hosted by L. delineatus rather than P. parva .     

Is there an en route folding intermediate for cold shock proteins?

Cold shock proteins (Csps) play an important role in cold shock response of a diverse number of organisms ranging from bacteria to humans. Numerous studies of the Csp from various species showed that a two-state folding mechanism is conserved and the transition state (TS) appears to be very compact. However, the atomic details of the folding mechanism of Csp remain unclear. This study presents the folding mechanism of Csp in atomic detail using an all-atom Go model-based simulations. Our simulations predict that there may exist an en route intermediate, in which β strands 1-2-3 are well ordered and the contacts between β1 and β4 are almost developed. Such an intermediate might be too unstable to be detected in the previous fluorescence energy transfer experiments. The transition state ensemble has been determined from the P(fold) analysis and the TS appears even more compact than the intermediate state.     

Catalytic amyloids: Is misfolding folding?

Originally regarded as a disease symptom, amyloids have shown a rich diversity of functions, including biologically beneficial ones. As such, the traditional view of polypeptide aggregation into amyloid-like structures being ‘misfolding’ should rather be viewed as ‘alternative folding.’ Various amyloid folds have been recently used to create highly efficient catalysts with specific catalytic efficiencies rivaling those of enzymes. Here we summarize recent developments and applications of catalytic amyloids, derived from both de novo and bioinspired designs, and discuss how progress in the last 2 years reflects on the field as a whole.     

Is protein folding hierarchic? I. Local structure and peptide folding

The folding reactions of some small proteins show clear evidence of a hierarchic process, whereas others, lacking detectable intermediates, do not. Nevertheless, we argue that both classes fold hierarchically and that folding begins locally. If this is the case, then the secondary structure of a protein is determined largely by local sequence information. Experimental data and theoretical considerations support this argument. Part I of this article reviews the relationship between secondary structures in proteins and their counterparts in peptides.     

Protein folding: could hydrophobic collapse be coupled with hydrogen-bond formation?

A judicious examination of an exhaustive PDB sample of soluble globular proteins of moderate size (N<102) reveals a commensurable relationship between hydrophobic surface burial and number of backbone hydrogen bonds. An analysis of 50,000 conformations along the longest all-atom MD trajectory allows us to infer that not only the hydrophobic collapse is concurrent with the formation of backbone amide-carbonyl hydrogen bonds, they are also dynamically coupled processes. In statistical terms, hydrophobic clustering of the side chains is inevitably conducive to backbone burial and the latter process becomes thermodynamically too costly and kinetically unfeasible without amide-carbonyl hydrogen-bond formation. Furthermore, the desolvation of most hydrogen bonds is exhaustive along the pathway, implying that such bonds guide the collapse process.     

Are the same or different amino acid residues responsible for correct and incorrect protein folding?

It has been shown for 20 proteins that amino acid residues included into the protein folding nucleus, determined experimentally, are often involved in the theoretically determined amyloidogenic fragments. For 18 proteins, Φ-values indicative of the extent of residue involvement into the folding nucleus are on average higher for amino acid residues within amyloidogenic regions. Amyloidogenic fragments were predicted for 20 proteins by two methods chosen from four on the basis of comparison of prediction of amyloidogenic regions known from experimental data. Since theoretical folding nuclei are detected by the protein three-dimensional structure and amyloidogenic regions by the protein chain primary structure, the detected regularity makes possible predictions of folding nucleation sites on the basis of amino acid sequence.     

Prolyl isomerization: How significant for in vivo protein folding?

Suggestive but not decisive evidence indicates that in vivo peptide chain folding is completed in a time not much longer than that required for covalent peptide synthesis. Extrapolation of model peptide rates of the cis–trans prolyl isomerization leads to the prediction tht protein folding should be much slower than the apparent in vivo rates. On the assumption that rapid protein folding in vivo is the rule, three routes are suggested by which a protein undergoing biosynthesis can avoid a strongly slowed folding rate: (1) by a peptide chain-elongation process that adds only trans peptide bonds, follwed by a rapid folding process that incorporates them into a three-dimensional structure, raising the energy barrier to isomerization; (2) by folding to produce three dimensional structures that position prolyl residues largely in chain turns on the protein surface, where the residue may be either cis or trans without large effects on the protein structure and function; (3) prolyl cis–trans isomerization may be speeded by the formation of peptide loops.     

Interleukin 8 production in whole blood assays: Is interleukin 10 responsible for the downregulation observed in sepsis?

Reduced cytokine production in ex vivo cultures has been regularly reported in patients suffering from sepsis syndrome. Using whole blood assays, we have now demonstrated that in sepsis patients, normal production of IL-8 was achieved with the higher concentration of lipopolysaccharide (LPS; 1 microg/ml) and with heat-killed streptococci, whereas the IL-8 production induced by lower LPS concentration (0.1 microg/ml) was significantly reduced as compared to healthy controls. In contrast, in patients undergoing cardiac surgery associated with cardio-pulmonary bypass, a group of patients with inflammation in the absence of infectious insult, none of the studied IL-8 productions were affected. Among the various anti-inflammatory cytokines known to regulate IL-8 production which we tested (i.e. IL-4, IL-10, IL-13, TGF-beta), IL-10 was the most active inhibitory cytokine in whole blood assays performed with blood samples from healthy subjects. However, its activity was not influenced by the amounts of LPS used. In addition, IL-10 also inhibited the heat-killed streptococci-induced IL-8 production and was the only cytokine to inhibit the release of IL-8 when TNF was added to LPS. It is worth noting that IL-13 which also inhibited the heat-killed streptococci-induced IL-8 production, failed to do so when the TNF production was analysed. Together, these data suggest that while circulating IL-10 in septic patients may be responsible for the hyporeactivity of circulating leukocytes, its presence is not sufficient to explain the observed dysregulation which occurs in septic patients.     

Is disturbed clearance of apoptotic keratinocytes responsible for UVB-induced inflammatory skin lesions in systemic lupus erythematosus?

Apoptotic cells are thought to play an essential role in the pathogenesis of systemic lupus erythematosus (SLE). We hypothesise that delayed or altered clearance of apoptotic cells after UV irradiation will lead to inflammation in the skin of SLE patients. Fifteen SLE patients and 13 controls were irradiated with two minimal erythemal doses (MEDs) of ultraviolet B light (UVB). Subsequently, skin biopsies were analysed (immuno)histologically, over 10 days, for numbers of apoptotic cells, T cells, macrophages, and deposition of immunoglobulin and complement. Additionally, to compare results with cutaneous lesions of SLE patients, 20 biopsies of lupus erythematosus (LE) skin lesions were analysed morphologically for apoptotic cells and infiltrate. Clearance rate of apoptotic cells after irradiation did not differ between patients and controls. Influx of macrophages in dermal and epidermal layers was significantly increased in patients compared with controls. Five out of 15 patients developed a dermal infiltrate that was associated with increased epidermal influx of T cells and macrophages but not with numbers of apoptotic cells or epidermal deposition of immunoglobulins. Macrophages were ingesting multiple apoptotic bodies. Inflammatory lesions in these patients were localised near accumulations of apoptotic keratinocytes similar as was seen in the majority of LE skin lesions. In vivo clearance rate of apoptotic cells is comparable between SLE patients and controls. However, the presence of inflammatory lesions in the vicinity of apoptotic cells, as observed both in UVB-induced and in LE skin lesions in SLE patients, suggests that these lesions result from an inflammatory clearance of apoptotic cells.     

Is creatine kinase responsible for fatigue? Studies of isolated skeletal muscle deficient in creatine kinase.

Creatine kinase (CK) is a key enzyme for maintaining a constant ATP/ADP ratio during rapid energy turnover. To investigate the role of CK in skeletal muscle fatigue, we used isolated whole muscles and intact single fibers from CK-deficient mice (CK(-/-)). With high-intensity electrical stimulation, single fibers from CK(-/-) mice displayed a transient decrease in both tetanic free myoplasmic [Ca(2+)] ([Ca(2+)](i), measured with the fluorescent dye indo-1) and force that was not observed in wild-type fibers. With less intense, repeated tetanic stimulation single fibers and EDL muscles, both of which are fast-twitch, fatigued more slowly in CK(-/-) than in wild-type mice; on the other hand, the slow-twitch soleus muscle fatigued more rapidly in CK(-/-) mice. In single wild-type fibers, tetanic force decreased and [Ca(2+)](i) increased during the first 10 fatiguing tetani, but this was not observed in CK(-/-) fibers. Fatigue was not accompanied by phosphocreatine breakdown and accumulation of inorganic phosphate in CK(-/-) muscles. In conclusion, CK is important for avoiding fatigue at the onset of high-intensity stimulation. However, during more prolonged stimulation, CK may contribute to the fatigue process by increasing the myoplasmic concentration of inorganic phosphate.     

Is disturbed clearance of apoptotic keratinocytes responsible for UVB-induced inflammatory skin lesions in systemic lupus erythematosus?

Apoptotic cells are thought to play an essential role in the pathogenesis of systemic lupus erythematosus (SLE). We hypothesise that delayed or altered clearance of apoptotic cells after UV irradiation will lead to inflammation in the skin of SLE patients. Fifteen SLE patients and 13 controls were irradiated with two minimal erythemal doses (MEDs) of ultraviolet B light (UVB). Subsequently, skin biopsies were analysed (immuno)histologically, over 10 days, for numbers of apoptotic cells, T cells, macrophages, and deposition of immunoglobulin and complement. Additionally, to compare results with cutaneous lesions of SLE patients, 20 biopsies of lupus erythematosus (LE) skin lesions were analysed morphologically for apoptotic cells and infiltrate. Clearance rate of apoptotic cells after irradiation did not differ between patients and controls. Influx of macrophages in dermal and epidermal layers was significantly increased in patients compared with controls. Five out of 15 patients developed a dermal infiltrate that was associated with increased epidermal influx of T cells and macrophages but not with numbers of apoptotic cells or epidermal deposition of immunoglobulins. Macrophages were ingesting multiple apoptotic bodies. Inflammatory lesions in these patients were localised near accumulations of apoptotic keratinocytes similar as was seen in the majority of LE skin lesions. In vivo clearance rate of apoptotic cells is comparable between SLE patients and controls. However, the presence of inflammatory lesions in the vicinity of apoptotic cells, as observed both in UVB-induced and in LE skin lesions in SLE patients, suggests that these lesions result from an inflammatory clearance of apoptotic cells.     

Is pathological metabolism in the parental organism responsible for defective and monstrous development of the offspring?

Ohne Zusammenfassung

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Is pathological metabolism in the parental organism responsible for defective and monstrous development of the offspring?