In Vitro Assembly of Tau Protein: Mapping the Regions Involved in Filament Formation

Unraveling the mechanism of self-assembly of the protein tau into paired helical filaments (PHFs) is a crucial step toward the understanding of Alzheimer's and other neuropathological diseases at the molecular level. In an effort to map the role of different regions of tau in the mechanism of self-assembly, we have studied the polymerization ability of different tau fragments using an in vitro assay. Our results indicate that the N-terminal domain interferes with tau's ability to polymerize in vitro. The effect seems to be size dependent. Particularly, an isoform of tau from the peripheral nervous system, which has a much larger N-terminal domain, was found unable to form filaments in our in vitro assay. This finding can explain why in Alzheimer's patients PHFs only accumulate in the neurons from the central nervous system. We also report that a short segment of tau located in the third microtubule binding repeat (residues 317 to 335, peptide 1/2R) is probably the minimal segment of that region able to grow into filaments in vitro and in the presence of heparin. In contrast with whole peptide 1/2R, peptides corresponding to either the N-terminal or C-terminal halves of this segment were unable to form filaments. Finally, our polymerization studies of peptides from the C-terminal domain reveal a short sequence spanning residues 391 to 407 that grows into filaments in vitro. This tau segment forms filaments regardless of whether is incubated with heparin. Moreover, such filaments differ in diameter and morphology, suggesting a different mechanism of self-assembly.

What can we learn about protein folding from Ising-like models?

Ising-like models have been remarkably successful in reproducing all the experimental data available on the equilibrium and kinetics of secondary structure formation in short peptides. Over the past two years, very similar models have been used to predict the folding of complete proteins, with encouraging results. Although Ising-like models are probably too simple to describe all aspects of protein folding, the results obtained so far indicate that they can play a critical role in the study of protein folding by bridging the gap between experiment and more detailed theoretical approaches.

Interplay between hydrophobic cluster and loop propensity in beta-hairpin formation

Autonomously folding beta-hairpins have recently emerged as powerful tools for elucidating the origins of antiparallel beta-sheet folding preferences. Analysis of such model systems has suggested four potential sources of beta-sheet stability: (1) the conformational propensity of the loop segment that connects adjacent strands; (2) favorable contacts between side-chains on adjacent strands; (3) interstrand hydrogen bonds; and (4) the intrinsic beta-sheet propensities of the strand residues. We describe the design and analysis of a series of isomeric 20 residue peptides in which factors (1)-(4) are identical. Differences in beta-hairpin formation within this series demonstrate that these four factors, individually, are not sufficient to explain beta-sheet stability. In agreement with the prediction of a simple statistical mechanical model for beta-hairpin formation, our results show that the separation between the loop segment and an interstrand cluster of hydrophobic side-chains strongly influences beta-hairpin size and stability, with a smaller separation leading to greater stability.

Experimental conditions for testing the inhibitory activity of chloroquine on the formation of beta-hematin

Some antimalarial drugs act by inhibiting the process of ferriprotoporphyrin IX polymerization which protects the parasite against the noxious effect of this product of host cell hemoglobin digestion. As the quest for new drugs with a similar mode of action continues, high-throughput screening methods are needed. We demonstrate herein that such a recently described screening technique (Basilico et al., J. Antimicrob. Chemother. 42, 55-60, 1998) is considerably disturbed by certain ions. Thus, at the assay's pH 2.6, the phosphate ions are responsible for the inhibitory activity of chloroquine phosphate, rather than chloroquine itself. Using a combination of solubility tests and Fourier transform infrared spectrometry we also show that two alternative methods using higher pH's are also prone to salt effects and demonstrate that these can be minimized by extensive washing of the product with DMSO.

Effectiveness and pitfalls of initial highly active antiretroviral therapy in HIV-infected patients in routine clinical practice

OBJECTIVE

To assess the long-term effectiveness of and factors associated with response to protease inhibitors (PIs) in a cohort of treatment-naive HIV-infected patients.

DESIGN AND SETTING

Prospective study in a tertiary care centre.

SUBJECTS

A total of 207 treatment-naive patients starting PIs from March 1996 to May 1998.

MAIN OUTCOME MEASURES

Clinical, virological and immunological outcomes, and adherence to therapy after 12 months.

RESULTS

Baseline median CD4 cell count and viral load were 160 cells/mm3 and 5 log10 copies/ml, respectively. After 48 weeks, 168 patients (81%) reached plasma HIV-RNA levels below 400 copies/ml, and the mean increase in CD4 cell count was 196 cells/mm3. Clinical events were observed in 29 patients (14%) after a median time of 100 days on therapy, yet mortality was extremely low (0.9%). By multivariate analysis, adherence over 90% [relative risk (RR), 16.66; 95% confidence interval (CI), 5.26-50; P=0.00001] and AIDS diagnosis at baseline (RR 0.35; 95% CI, 0.14-0.90; P=0.02) were the strongest predictors for virological suppression. An immunological recovery over 100 cells/mm3 was significantly associated with an initial virological response (RR 2.94; 95% CI, 1.31-6.66; P=0.009) and adherence over 90% (RR 3.44; 95% CI, 1.61-7.69; P=0.005). There were high rates of change with the first PI (40%), mostly due to adverse events (51%), but it did not compromise long-term effectiveness.

CONCLUSIONS

Initial PI treatment in the clinical setting is able to reach equally good outcomes as those found in controlled trials. Changes in therapy due to toxicity do not compromise a successful outcome, which clearly depends on an adequate adherence to therapy.

A search for natural bioactive compounds in Bolivia through a multidisciplinary approach. Part IV. Is a new haem polymerisation inhibition test pertinent for the detection of antimalarial natural products?

The search for new antimalarial agents in plant crude extracts using traditional screening tests is time-consuming and expensive. New in vitro alternative techniques, based on specific metabolic or enzymatic process, have recently been developed to circumvent testing of antimalarial activity in parasite culture. The haem polymerisation inhibition test (HPIA) was proposed as a possible routine in vitro assay for the detection of antimalarial activity in natural products. A total of 178 plant extracts from the Pharmacopeia of the Bolivian ethnia Tacana, were screened for their ability to inhibit the polymerisation of haematin. Five extracts from Aloysia virgata (Ruíz & Pavón) A.L. Jussieu (Verbenaceae), Bixa orellana L. (Bixaceae), Caesalpinia pluviosa D.C. (Caesalpiniaceae), Mascagnia stannea (Griseb) Nied. (Malpighiaceae) and Trichilia pleenea (Adr. Jussieu) (Meliaceae) demonstrated more than 70% inhibition of haematin polymerisation at 2.5 mg/ml. The extracts were also tested for antimalarial activity in culture against F32 strain (chloroquine-sensitive) and D2 strain (chloroquine-resistant) of Plasmodium falciparum and in vivo against P. berghei. The extract from Caesalpinia pluviosa was the only one that showed activity in HPIA and in the classical test in culture. The accuracy and pertinence of HPIA, applied to natural products is discussed.

[Environmental contamination with Toxocara sp. eggs in public squares and parks from Santiago, Chile, 1999]

Most of cases of visceral larva migrans syndrome are caused by Toxocara canis larvae. Man acquires the infection by accidental ingestion of ripe eggs of the helminth. In order to find out the frequency of the presence of Toxocara sp. eggs in dog fecal specimens from public places of Santiago city in 1999 july-september a study was carried out in 84 squares and 12 parks from 32 counties. Three fecal samples were collected in each of these places, making a total of 288. Each sample was processed according to a modified Telemann method and three smears of each were microscopically examined. Toxocara sp. eggs were found in 39 (13.5%) fecal specimens. In 28/84 (33.3%) squares and in 8/12 (66.7%) parks these eggs were detected. These results make necessary the control of dogs and cats populations with the aim of reduce the presence of animals without responsible owners. It should be advisable to prevent dogs and cats defecation in public areas grounds, trying to exclude these animals from recreation areas.

A search for natural bioactive compounds in Bolivia through a multidisciplinary approach. Part III. Evaluation Of the antimalarial activity of plants used by Alteños Indians

A total of 40 plant extracts traditionally used by the Alteños Indians, a native community living between the Andean block and the tropical valleys of Bolivia, were screened for antimalarial activity in vitro on Plasmodium falciparum chloroquine resistant (Indo) strain, and in vivo on rodent malaria Plasmodium vinckei petteri. Eleven extracts displayed good or moderate activity in vivo, and ten extracts good or very good antimalarial activity in vitro. Results of the screening are discussed here, in relation with the traditional use of plants.

Phenotypic testing predicts virological response in successive protease inhibitor-based regimens

OBJECTIVE

To evaluate the importance of the number of active drugs, as determined by phenotypic resistance testing, in achieving virological response in successive salvage regimens.

DESIGN

Phenotypic study of 57 plasma samples corresponding to 24 patients who had sequentially received three protease inhibitor-containing regimens. Phenotypic susceptibility to a drug (active drug) was defined as less than a four-fold-increase in the IC50 in comparison with the wild type.

MAIN OUTCOME MEASURE

Virological response according to the number of active drugs (three versus two or fewer), HIV load, length of antiretroviral exposure, and line of protease inhibitor-based therapy (first, second and third regimen).

RESULTS

Before the first protease inhibitor-based therapy, the median time on antiretroviral treatment was 42 months, and before the second and third protease inhibitor-salvage regimens it was 10 and 8 months, respectively. The number of patients receiving three active drugs simultaneously was 24, 35 and 31% in each line of therapy. At week 12, a close correlation was found between the presence of three active drugs in the antiretroviral regimen and the rate of virological response, in comparison with those patients receiving two or fewer active drugs [76 versus 45%, relative risk (RR), 1.7; 95% confidence interval (CI) 1.1-2.6; P = 0.028]. In a multivariate analysis, the use of two or fewer active drugs was an independent predictor of lack of response, regardless of HIV load, length of previous antiretroviral exposure and line of salvage therapy (RR, 4.5; 95%CI, 1.1-18.3; P = 0.03). Of note, a higher rate of response was observed in patients receiving the first protease inhibitor-containing regimen in comparison with those in subsequent protease inhibitor-based salvage regimens (83 versus 50 versus 28%, P < 0.01), even when only those patients receiving three active drugs were included (100 versus 71 versus 60%).

CONCLUSIONS

This data confirm the usefulness of phenotypic testing in guiding antiretroviral therapy in heavily pretreated patients. The number of active drugs and the line of salvage therapy are independent predictors of virological response, regardless of HIV load and the length of antiretroviral exposure.

Medicinal plants uses of the Tacana, an Amazonian Bolivian ethnic group

We present the results of an ethnopharmacological investigation of a Bolivian lowland ethnic group, the Tacana. The Tacana have a long tradition of exchange with highland communities. Though facing rapid acculturation, highlighted by the loss of the Tacana language among the younger generations, the knowledge and uses of medicinal plants are still alive. Of the approximately 450 different plant species collected during this survey, 33% had medicinal uses. We present an overview of the traditional Tacana ethnomedicine and pharmacopoeia.

Aminothiol multidentate chelators against Chagas disease

Three compounds of an aminothiol family of iron chelators were examined for activity against trypomastigote (human) and epimastigote (vector) forms of Trypanosoma cruzi: tetraethyl and tetramethyl derivatives of ethane-1,2-bis (N-1-amino-3-ethyl butyl-3-thiol) (BAT-TE and BAT-TM) and N',N',N'-tris-(2-methyl-2-mercaptopriopyl)- 1,4,7-triazacyclonane (TAT). BAT-TE at 270 microM completely arrested the growth of trypomastigote forms in mouse blood stored at 4 degrees C for 24 h (IC(50) 67.7+/-7 microM), while BAT-TM arrested growth at 630 microM (IC(50) 158+/-17 microM) and TAT at concentrations >800 microM (IC(50) 415+/-55 microM). In T. cruzi-infected mice, BAT-TE and BAT-TM had no anti-trypanosomal activity in doses up to 200 mg/kg, whether the route of administration was intraperitoneal or oral, and TAT was not tested due to insufficient quantity. TAT had an IC(50) of 52+/-7 microM against the epimastigote forms while BAT-TM and BAT-TE were inhibitory only at concentrations >250 microM. The trypanocidal activity of BAT derivatives in blood stored at 4 degrees C makes these compounds potential candidates for the purpose of clearing donated blood of trypomastigotes.

The search for natural bioactive compounds through a multidisciplinary approach in Bolivia. Part II. Antimalarial activity of some plants used by Mosetene indians

Forty-six different species collected in the Mosetene ethnia, dwelling in the Andean Piedmont of Bolivia, were screened for antimalarial properties. Thirty-three extracts were screened for antimalarial activity in vitro on Plasmodium falciparum chloroquine resistant strain (Indo), and forty-seven extracts were evaluated in vivo on the rodent malaria P. vinckei petteri 279BY. Only two plants are specifically used in combination by the Mosetene against malaria attack (Hymenachne donacifolia and Tesseria integrifolia), but they did not display any activity in vivo at 1000 mg/kg. The in vivo most active extracts were Swietenia macrophylla bark, Trema micrantha bark and Triplaris americana bark, not all of them were used for antimalarial purposes by the Mosetene. The following extracts were moderately active: Jacaratia digitata inner bark and Momordica charantia aerial part (both traditionally used as febrifuge), Kalanchoe pinnate aerial part (used in inflammatory processes), Lunania parviflora twigs and leaves, Phyllanthus acuminatus (used as piscicide), Tynanthus schumannianus fruit (used against diarrhoea), Triumfetta semitrilobata (used as febrifuge, to alleviate kidney and gynecological pain) and finally Solanum mammosum fruit (used against scabies). We present here the results of this screening, emphazing on the in vivo antimalarial activity of the selected plants. The antimalarial in vivo activity of the selected species, in relation with their traditional Mosetene use is then discussed.

A search for natural bioactive compounds in Bolivia through a multidisciplinary approach. Part I. Evaluation of the antimalarial activity of plants used by the Chacobo Indians

Thirty extracts of plants traditionally used by the Chacobos, a native community living in the Amazonian part of Bolivia, were screened in vitro and/or in vivo for antimalarial activity. Two of the four species designated as antimalarial, Geissospermum laeve and Maquira coriacea, displayed rather good activity, corroborating their traditional uses. However, they did show a rather high toxicity in vivo. Among twelve species used to cure symptoms relevant to malaria, five showed good activity: Apuleia leiocarpa, Bauhinia guianensis, Nectandra cuspidata, Sparattanthelium amazonum, Tanaecium jaroba. Two species, Qualea paraensis and Sclerolobium aff. guianense, used to treat scabies, showed interesting antimalarial activity in vivo; three other species (Iryanthera laevis, Prunus amplifolia, Pterocarpus aff. amazonum) used for various medicinal purposes, apparently not related with a Plasmodium infection, also showed antimalarial activity. Finally, one species (Derris amazonica) used as a piscicide displayed good in vitro activity, in the same way as one Annonaceae, Guatteria aff. schomburgkiana, used for construction purposes.

Fast kinetics and mechanisms in protein folding

This review describes how kinetic experiments using techniques with dramatically improved time resolution have contributed to understanding mechanisms in protein folding. Optical triggering with nanosecond laser pulses has made it possible to study the fastest-folding proteins as well as fundamental processes in folding for the first time. These include formation of alpha-helices, beta-sheets, and contacts between residues distant in sequence, as well as overall collapse of the polypeptide chain. Improvements in the time resolution of mixing experiments and the use of dynamic nuclear magnetic resonance methods have also allowed kinetic studies of proteins that fold too fast (greater than approximately 10(3) s-1) to be observed by conventional methods. Simple statistical mechanical models have been extremely useful in interpreting the experimental results. One of the surprises is that models originally developed for explaining the fast kinetics of secondary structure formation in isolated peptides are also successful in calculating folding rates of single domain proteins from their native three-dimensional structure.

Organ doses, detriment and genetic risk from interventional vascular procedures in Málaga (Spain)

Nowadays, the radiological risk from simple X-ray procedures is well known. The purpose of this work has been to estimate the population risk from digital angiographic and interventional procedures and to compare it with the one from simple procedures in the same population. The population risk has been estimated according to the following quantities: genetically significant dose, somatic significant dose, collective effective dose, annual per caput effective dose and detriment. These have been estimated from dose area product and organ dose. Organ dose values were estimated with the Eff-Dose software. A population of 605410 people were included in the study. In 1996, 1312 patients were to digital interventional vascular procedures in Malaga, and 159 of them were selected in this research project to obtain the dose area product and organ dose. The results obtained for the quantities evaluated are: genetically significant dose, 4.1 microGy; somatic significant dose, 0.9 mSv; collective effective dose, 11.65 person-Sv: annual per caput effective dose, 0.02 mSv and detriment, 0.65 radiogenic cancers per year. These procedures supply a high radiation dose, so they should have a greater contribution to population dose and risk than simple examinations. However, our results indicate just the opposite.

Acute cholestatic hepatitis by cytomegalovirus in an immunocompetent patient resolved with ganciclovir

We report a case of acute cholestatic hepatitis in an immunocompetent young male with cytomegalovirus (CMV) primoinfection episode. The severity of the clinical symptoms led to a high-dose treatment with parenteral ganciclovir, with an immediate response and total resolution of symptoms. Therapeutic options are discussed, particularly the use of ganciclovir, even in immunocompetent patients when the severity of the symptoms could demand it.

A simple model for calculating the kinetics of protein folding from three-dimensional structures

An elementary statistical mechanical model was used to calculate the folding rates for 22 proteins from their known three-dimensional structures. In this model, residues come into contact only after all of the intervening chain is in the native conformation. An additional simplifying assumption is that native structure grows from localized regions that then fuse to form the complete native molecule. The free energy function for this model contains just two contributions-conformational entropy of the backbone and the energy of the inter-residue contacts. The matrix of inter-residue interactions is obtained from the atomic coordinates of the three-dimensional structure. For the 18 proteins that exhibit two-state equilibrium and kinetic behavior, profiles of the free energy versus the number of native peptide bonds show two deep minima, corresponding to the native and denatured states. For four proteins known to exhibit intermediates in folding, the free energy profiles show additional deep minima. The calculated rates of folding the two-state proteins, obtained by solving a diffusion equation for motion on the free energy profiles, reproduce the experimentally determined values surprisingly well. The success of these calculations suggests that folding speed is largely determined by the distribution and strength of contacts in the native structure. We also calculated the effect of mutations on the folding kinetics of chymotrypsin inhibitor 2, the most intensively studied two-state protein, with some success.

Antimalarial activity and cytotoxicity of (-)-roemrefidine isolated from the stem bark of Sparattanthelium amazonum

(-)-Roemrefidine, an aporphine alkaloid isolated from Sparattanthelium amazonum Martius (Hernandiaceae) a vine from Bolivia, has been found to be active against both resistant and sensitive strains of Plasmodium falciparum in vitro and against P. berghei in mice. The compound demonstrated no cytotoxic activity against three cell lines (KB, HEp-2 and HeLa).

[Cytomegalovirus granulomatous hepatitis in an immunocompetent patient]

A case of granulomatous hepatitis induced by cytomegalovirus in a 34-year-old immunocompetent male with no other history of interest is presented. The clinical severity of the picture with progressive cholestasis, evening fever peaks and the development of echographic signs of portal hypertension led to treatment with high doses of intravenous ganciclovir. Rapid clinical improvement was observed with normalization of the analytical parameters after 15 days of treatment. The pathologic, clinical and therapeutic aspects of the liver infection by cytomegalovirus in an immunocompetent patient are discussed.

Antiprotozoal activity of aporphine alkaloids isolated from Unonopsis buchtienii (Annonaceae)

On a preliminary screening, substantial leishmanicidal activity was observed for the petroleum ether and alkaloidal extracts of the stem bark of Unonopsis buchtienii, the alkaloids and sterols isolated from these were studied. Of the alkaloids, liriodenine exhibited the highest activity against Leishmania major and L donovani (IC100 = 3.12 micrograms/mL). On the other hand, O-methylmoschatoline and the petroleum ether extract without alkaloids showed an interesting in vitro activity against Trypanosoma brucei with an IC100 of 6.25 micrograms/mL. The highest cytotoxic activities were found with the petroleum ether extracts without alkaloids and with all alkaloids isolated (IC50 < 9 micrograms/mL for Vero cell line).

A novel antiprotozoal aminosteroid from Saracha punctata

A new aminosteroid, 3beta-amino-22,26-epiminocholest-5-ene named sarachine (1), and two known flavonoids, eriodictyol (2) and 7-O-beta-D-glucopyranosyl-eriodictyol (3), were isolated from the leaves of Saracha punctata. The alkaloid was found to inhibit the growth of Leishmania braziliensis promastigotes (100% at 25 microM) and of Trypanosoma cruzi epimastigotes in culture (50% at 25 microM) and showed a strong in vitro antiplasmodial activity with an IC50 of 25 nM.

A statistical mechanical model for beta-hairpin kinetics

Understanding the mechanism of protein secondary structure formation is an essential part of the protein-folding puzzle. Here, we describe a simple statistical mechanical model for the formation of a beta-hairpin, the minimal structural element of the antiparallel beta-pleated sheet. The model accurately describes the thermodynamic and kinetic behavior of a 16-residue, beta-hairpin-forming peptide, successfully explaining its two-state behavior and apparent negative activation energy for folding. The model classifies structures according to their backbone conformation, defined by 15 pairs of dihedral angles, and is further simplified by considering only the 120 structures with contiguous stretches of native pairs of backbone dihedral angles. This single sequence approximation is tested by comparison with a more complete model that includes the 2(15) possible conformations and 15 x 2(15) possible kinetic transitions. Finally, we use the model to predict the equilibrium unfolding curves and kinetics for several variants of the beta-hairpin peptide.

Position dependence of non-polar amino acid intrinsic helical propensities

Until now and based on the success of the helix/coil transition theory it has been assumed that the alpha-helical propensities of the amino acids are position independent. This has been critical to derive the set of theoretical parameters for the 20 natural amino acids. Here, we have analyzed the behavior of several non-polar residues, Val, Ile, Leu, Met and Gly at the N-cap, at each position of the first helical turn and at a central helical position of a 16-residue peptide model system that starts with eight consecutive alanine residues. We have interpreted the results from these experiments with the model of the helix/coil transition (AGADIR), that indicates that the intrinsic helical propensity is position dependent. Gly, Val and Ile are more favorable at the first turn than in the middle of the alpha-helix, while for Leu and Met we observe the opposite behavior. The differences between the observed helical propensities are as large as 1.0 kcal/mol in some cases. Molecular modeling calculations using the ECEPP/2 force-field equipped with a hydration potential show that this effect can be explained by the combination of three factors: (a) the side-chains in the first helix turn are more solvent-exposed; (b) they have fewer intramolecular van der Waals' contacts; and (c) they posses higher configurational entropy than that in the central position of an alpha-helix. The position-dependent results of the calculations are in reasonable agreement with the experimental estimates and with the intrinsic propensities of the amino acids derived from the statistical analysis of the protein structure database.

Mycobacterial liver abscess in a patient with AIDS

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Folding dynamics and mechanism of beta-hairpin formation

Protein chains coil into alpha-helices and beta-sheet structures. Knowing the timescales and mechanism of formation of these basic structural elements is essential for understanding how proteins fold. For the past 40 years, alpha-helix formation has been extensively investigated in synthetic and natural peptides, including by nanosecond kinetic studies. In contrast, the mechanism of formation of beta structures has not been studied experimentally. The minimal beta-structure element is the beta-hairpin, which is also the basic component of antiparallel beta-sheets. Here we use a nanosecond laser temperature-jump apparatus to study the kinetics of folding a beta-hairpin consisting of 16 amino-acid residues. Folding of the hairpin occurs in 6 micros at room temperature, which is about 30 times slower than the rate of alpha-helix formation. We have developed a simple statistical mechanical model that provides a structural explanation for this result. Our analysis also shows that folding of a beta-hairpin captures much of the basic physics of protein folding, including stabilization by hydrogen bonding and hydrophobic interactions, two-state behaviour, and a funnel-like, partially rugged energy landscape.

A study of the chemical composition of Erythroxylum coca var. coca leaves collected in two ecological regions of Bolivia

Coca-Erythroxylum coca Lamarck var. coca-remains one of the most common plants of the folk medicine of Bolivia used as a general stimulant. Aymara and Quechua natives prefer to chew the sweeter coca leaves from the Yungas (tropical mountain forests of the eastern slopes of the Andes) rather than those from the Chapare lowlands. The contents in cocaine and minor constituents of leaf samples cultivated in these regions does not rationalize this choice.

Development of the multiple sequence approximation within the AGADIR model of alpha-helix formation: comparison with Zimm-Bragg and Lifson-Roig formalisms

In this work we present the development of the multiple sequence approximation (AGADIRms) and the standard one-sequence approximation (AGADIRls) within the framework of AGADIR's alpha-helix formation model. The extensive comparison between these new formulations and the original one [AGADIR; V. Muñoz and L. Serrano (1994). Nat. Struct. Biol., Vol. 1, pp. 399-409] indicates that the standard one-sequence approximation is virtually identical to the multiple sequence approximation, while the previously used residue partition function approximation [Muñoz and Serrano (1994); (1995), J. Mol. Biol., Vol. 245, pp. 275-296] is less precise. The calculations of the average helical content performed with AGADIR are precise for peptides of less than 30 residues and progressively diverge from the multiple sequence formulation for longer peptides. The helicity distribution of heteropolypeptides with less than 50% average helical content is also well described, while those of quasi-homopolymers with high helical content tend to be-flattened. These inaccuracies lead to an underestimation of 0.017 kcal/mol for the mean-residue enthalpic contribution in AGADIR, as compared to AGADIRms and AGADIRls. The other energy contributions to alpha-helix stability are not affected by the original statistical approximation. We also discuss the particularities of the model for alpha-helix formation utilized in AGADIR and compare it with the classical Zimm-Bragg and Lifson-Roig theories. Moreover, we develop the mathematical relationships between the basic AGADIR energy contributions and helix nucleation and elongation, which permit the quantitative comparison between formalisms. Remarkably, the comparison between AGADIRms and the Lifson-Roig formalism shows that, despite the differences on treating helix/coil cooperativity, both theories give virtually identical results when an equivalent set of parameters is used. This indicates that the helix/coil transition is a solid theory independent of the particularities of the model for alpha-helix formation.

Folding kinetics of Che Y mutants with enhanced native alpha-helix propensities

In this work we study the folding kinetics of Che Y mutants in which the helical propensity of each of its five alpha-helices has been greatly enhanced by local interactions (between residues close in sequence). This constitutes an experimental test on the role of local interactions in protein folding, as well as providing new information on the details of the folding pathway of the protein Che Y. With respect to the first issue, our results show that the enhancement of helical propensities by native-like local interactions in Che Y has the following general effects: (1) the energetics of the whole Che Y folding energy landscape (folded state, intermediate, denatured state and main transition state) are affected by the enhancement of helical propensities, thus, native-like local interactions appear to have a low specificity for the native conformation; (2) our results support the idea, proposed from thermodynamic analysis of the mutants, that the denatured state under native conditions becomes more compact upon enhancement of helical propensities; (3) the rate of folding in aqueous solution decreases in all the mutants, suggesting that the optimization of the folding rate in this protein requires low secondary structure propensities. Regarding the description of the folding pathway of Che Y, we find evidence that the folding transition state of Che Y is constituted by two sub-domains with different degree of helical structure. The first includes helices 1 and 2 which are rather structured, while the second encompasses the last three helices, which are very unstructured. On the other hand, the same analysis for the folding intermediate indicates that all the five alpha-helices are, on average, rather structured. Thus, suggesting that a large structural reorganization of the last three alpha-helices must take place before folding can be completed. This conclusion indicates that the folding intermediate of Che Y is a misfolded species.

Submillisecond kinetics of protein folding

New experimental methods permit observation of protein folding and unfolding on the previously inaccessible nanosecond-microsecond timescale. These studies are beginning to establish times for the elementary motions in protein folding - secondary structure and loop formation, local hydrophobic collapse, and global collapse to the compact denatured state. They permit an estimate of about one microsecond for the shortest time in which a protein can possibly fold.

Characterisation of the isolated Che Y C-terminal fragment (79-129)--Exploring the structure/stability/folding relationship of the alpha/beta parallel protein Che Y

To gain insight into how the three-dimensional structure, stability and folding of the protein Che Y are related to one another, we have performed a conformational analysis of a long fragment of this protein, encompassing its C-terminal 51 residues (79-129). This fragment consists of residues in the beta-strands 4 and 5 and alpha-helices 4 and 5 of native Che Y. The study has been performed by two-dimensional NMR and far-ultraviolet circular dichroism in aqueous solution and in 30% (by vol.) trifluoroethanol/ water at 273 K and 298 K. We observe little structure for this fragment in aqueous solution which could be due to low helical populations in the regions corresponding to helices 4 and 5. Within the limits of the residual helical structure experimentally detected, helix 4 appears to extend beyond the N-terminus observed in the native structure by over four residues belonging to the preceding loop. In 30% trifluoroethanol the helical content of both helices increase and helix 4 extends further to include the preceding beta-strand 4. None of the long-range NOEs present in native Che Y are observed under the explored experimental conditions. The conformational shifts of the H(alpha) protons within the alpha-helices of fragment 79-129 are identical to those of shorter synthetic peptides corresponding to the isolated alpha-helices. Thus, the fragment 79-129 appears to behave as an open chain with low local helical populations. The very low intrinsic ability for structure formation displayed by this region of Che Y at pH 2.5 suggests that in the folded protein this region could be mainly stabilised by interactions with the N-terminal Che Y region. This is in accordance with the contact map of Che Y, which shows that the strongest non-local contacts of C-terminal residues are with residues of the N-terminal region, while those within the C-terminal region are very weak. More importantly, the relationship appears to be possibly extended to the folding properties of the protein, since the C-terminal region is not structurally formed in the folding transition state of Che Y but in the final steps of the folding.

Transjugular intrahepatic portosystemic shunt for the management of hepatic hydrothorax in the absence of ascites

Hepatic hydrothorax in the absence of clinical ascites (HHAA) is a somewhat rare complication in decompensated cirrhosis. Patients with HHAA have a congenital defect in the tendinous portion of the diaphragm allowing rapid leakage of ascites into pleural cavity because of the cyclical negative intrathoracic pressure. Although several therapeutic approaches, including peritoneovenous shunt and chemical or surgical pleurodesis, have been attempted in these patients the results are largely unsatisfactory. A poor-risk surgical cirrhotic woman who was also considered not suitable for liver transplantation underwent transjugular intrahepatic portosystemic shunt (TIPS) for palliation of HHAA. After TIPS procedure hydrothorax completely resolved. TIPS can offer an attractive alternative to standard therapy in cirrhotic patients with HHAA.

Analysis of the effect of local interactions on protein stability

BACKGROUND

Protein stability appears to be governed by non-covalent interactions. These can be local (between residues close in sequence) or non-local (medium-range and long-range interactions). The specific role of local interactions is controversial. Statistical mechanics arguments point out that local interactions must be weak in stable folded proteins. However, site-directed mutagenesis has revealed that local interactions make a significant contribution to protein stability. Finally, computer simulations suggest that correctly folded proteins require a delicate balance between local and non-local contributions to protein stability.

RESULT

To analyze experimentally the effect of local interactions on protein stability, each of the five Che Y alpha-helices was enhanced in its helical propensity. alpha-Helix-promoting mutations have been designed, using a helix/coil transition algorithm tuned for heteropolypeptides, that do not alter the overall hydrophobicity or protein packing. The increase in helical propensity has been evaluated by far-UV CD analysis of the corresponding peptides. Thermodynamic analysis of the five Che Y mutants reveals, in all cases, an increase in half urea ([urea]1/2) and in Tm, and a decrease in the sensitivity to chemical denaturants (m). ANS binding assays indicate that the changes in m are not due to the stabilization of an intermediate, and the kinetic analysis of the mutants shows that their equilibrium unfolding transition can be considered as following a two-state model, while the change in m is found in the refolding reaction (m(k)f).

CONCLUSIONS

These results are explained by a variable two-state model in which the changes in half urea and Tm arise from the stabilization of the native state and the decrease in m from the compaction of the denatured state. Therefore, the net change in protein stability in aqueous solution produced by increasing the contribution of native-like local interactions in Che Y is the balance between these two conflicting effects. Our results support the idea that optimization of protein stability and cooperativity involve a specific ratio of local versus non-local interactions.

Local versus nonlocal interactions in protein folding and stability--an experimentalist's point of view

One of the classic important issues in protein folding and stability is the relative roles of noncovalent short-range (local) and long-range (nonlocal) interactions. Interest in this topic has been reinforced by recent developments in the analytical theory of protein folding and in lattice-based computer simulations. During the past few years, a wealth of experimental information relevant to this issue has been accumulating. In this review, we focus specifically on experimental aspects, discussing some general ideas that arise from the results obtained by many different groups using a variety of approaches. We also discuss a new experimental strategy that allows us to engineer the contribution of local interactions, and we discuss the first results obtained.

[Non-invasive intermittent mechanical ventilation: usefulness in treatment of chronic severe heart failure]

BACKGROUND

The higher respiratory work and less inspiratory muscle strength of patients with cardiac failure may contribute to decrease their functional capacity.

AIM

To assess the effects of non invasive intermittent mechanical ventilation on clinical parameters, peripheral perfusion, cardiac and inspiratory muscle function.

PATIENTS AND METHODS

Patients with chronic cardiac failure, functional capacity III-IV were subjected to 6 sessions of nasal non invasive intermittent ventilation during 4 hours or to simulated ventilation (controls).

RESULTS

Fifteen ventilated patients and six controls completed the protocol. Ventilated patients improved the Mahler transition score for dyspnea by 4 +/- 1.6 points. They also improved their aerobic capacity, increasing the exercise duration from 10.9 +/- 4 to 12.7 +/- 5 min and their maximal oxygen consumption from 14.6 +/- 4 to 16.4 +/- 5.7 ml/kg/min. These patients also decreased their O2 and CO2 ventilatory equivalents. Maximal inspiratory pressure increased from 67.9 +/- 23.6 to 80.19 +/- 21.4 cm H2O, sustained maximal inspiratory pressure increased from 101.4 +/- 48 to 133 +/- 53 cm H2O and maximal endurance increased from 132 +/- 52 to 162 +/- 58 g in ventilated patients. None of these variables was modified in control patients. No changes were observed in renal function, blood volume, arterial gases, spirometry or plasma catecholamine levels in any group.

CONCLUSIONS

Intermittent nasal ventilation or other measures to improve inspiratory muscle function may be beneficial for patients with severe cardiac failure.

Analysis of i,i+5 and i,i+8 hydrophobic interactions in a helical model peptide bearing the hydrophobic staple motif

In this work we have analyzed by far-UV circular dichroism the contribution to alpha-helix stability of pairwise hydrophobic interactions in the hydrophobic staple motif [Muñoz et al. (1995) Nat. Struct. Biol. 2, 380-385]. For this, we have used a new series of alanine-based model peptides having a capping-box motif (Ser-X-X-Glu) and no other charged residues to facilitate the determination of the interaction energies with a helix/coil transition algorithm. Our results show that the favorable i,i+5 interaction between a hydrophobic residue (Leu, Met, Ile, Val, Phe) at position N' (before the N-cap) and a Leu at position N+4 (inside the helix) contributes up to -1.48 +/- 0.18 kcal/mol to alpha-helix stability at 278 and pH 7. More interestingly, the same hydrophobic residues at position N' interact favorably with an Ala at position N+4, although the interaction is weaker than that with Leu (up to -0.8 +/- 0.14 kcal/mol at 278 K and pH 7). To our knowledge, this is the first example in which a strong pairwise interaction with Ala is described and suggests that Ala could be less neutral in terms of side chain-side chain interactions than normally assumed. We observe a strong stereospecificity for the position N' which could be explained based on the extreme rigidity imposed by the formation in phase of the hydrophobic staple and capping-box motifs, as is seen in the protein structure database. We have also investigated the contribution to alpha-helix stability of a geometrically feasible i,i+8 hydrophobic interaction between residues N' and N+7.(ABSTRACT TRUNCATED AT 250 WORDS)

The distribution of alpha-helix propensity along the polypeptide chain is not conserved in proteins from the same family

We address the question of whether the distribution of secondary structure propensities of the residues along the polypeptide chain (denominated here as secondary structure profiles) is conserved in proteins throughout evolution, for the particular case of alpha-helices. We have analyzed by CD the conformation of peptides corresponding to the five alpha-helices of two alpha/beta parallel proteins (ComA and Ara). The large alpha-helical population of peptide ComA-4 detected by CD in aqueous solution has been confirmed by NMR. These proteins are members of the CheY and P21-ras families, respectively, which have been studied previously in the same way (Muñoz V, Jiménez MA, Rico M, Serrano L, 1995, J Mol Biol 245:275-296). Comparison of the helical content of equivalent peptides reveals that protein alpha-helix propensity profiles are not conserved. Some equivalent peptides show very different helical populations in solution and this is especially evident in very divergent proteins (ComA and CheY). However, all the peptides analyzed so far adopted an important population of helical conformations in the presence of 30% trifluoroethanol, indicating that there could be a conserved minimal requirement for helical propensity.

Helix design, prediction and stability

Recent work revealing that our knowledge is now sufficient to build a reasonable quantitative model for the helix/coil transition in heteropolypeptides represents a watershed in research into alpha-helix stability, prediction and design. The opportunity is presented to design specific alpha-helix propensity patterns that may be used both to modify thermodynamic properties of target proteins and peptides, and for de novo protein design. Despite these advances, the picture is not yet complete and further studies of still poorly characterized factors are required to obtain a more precise understanding of alpha-helix stability.

[Frequency of allergens in immediate, late, and dual allergic skin response at the National Institute of Pediatrics]

We studied 126 children with allergic illness in Instituto Nacional de Pediatria. We applied cutaneous test to determine the early, late and dual response. The results were 68% for the early response, 6% late response and 26% dual response. The allergens more frequently found in the early and late response were Dermatophagoides pteronyssinus, Dermatophagoides farinae and house dust. Approximately the third part of the children studied presented late cutaneous response (dual response more isolated late response). It is important to make the evaluation of the late response in patients with allergy disease for a good etiologic diagnosis.

The hydrophobic-staple motif and a role for loop-residues in alpha-helix stability and protein folding

A recurrent local structural motif is described at the amino terminus of alpha-helices, that consists of a specific hydrophobic interaction between a residue located before the N-cap, with a residue within the helix (i,i+5 interaction). NMR and CD analysis of designed peptides demonstrate its presence in aqueous solution, its contribution to alpha-helix stability and its role in defining the alpha-helix N terminus limit. Comparison between the N-terminal structures of the peptide and those in proteins with the same fingerprint sequence, shows striking similarities. The change in the polypeptide chain direction produced by the motif suggests an important role in protein folding for residues located in polypeptide segments between secondary structure elements.

Structural analysis of peptides encompassing all alpha-helices of three alpha/beta parallel proteins: Che-Y, flavodoxin and P21-ras: implications for alpha-helix stability and the folding of alpha/beta parallel proteins

In an attempt to delineate the early folding events of structurally related proteins with no sequence homology, peptides including all five alpha-helices of three alpha/beta parallel open-sheet proteins, Che-Y, flavodoxin and P21-ras, have been analyzed by circular dichroism (far-UV CD) and nuclear magnetic resonance (NMR) in water and 30% (v/v) trifluoroethanol (TFE). Comparison between the helical content estimations from far-UV CD and the results from the NMR analysis renders a reasonably good qualitative correlation, indicating that the same phenomenon is underlined by both methods. Helix limits, as indicated by the existence of (i,i + 3) nuclear Overhauser effect (NOE) cross-correlations and significant up-field conformational shifts of the C alpha H protons, are practically coincident with those in the folded protein. On the other hand, the conformation of the side-chains differs markedly from those in the folded protein. Observation of NOE cross-correlations between pairs of residues at positions i,i + 3 has been used to statistically quantify free energies of i,i + 3 side-chain-side-chain interactions between the different pairs of residues in an alpha-helix. This analysis indicates that interactions between hydrophobic side-chains seem to be quite favorable for helix formation. The behaviour in aqueous solution of the structural equivalent peptides for the three proteins is quite unrelated except for the peptides corresponding to helices two and five. We postulate that, in the alpha/beta parallel proteins, those helices that join two beta-strands flanking another non-consecutive beta-strand should not be stable for folding reasons.

Elucidating the folding problem of helical peptides using empirical parameters. III. Temperature and pH dependence

Explaining the helical behaviour of amino acid sequences without tertiary interactions, in aqueous solution, could be considered one of the first steps to solve the protein folding problem in a rational way. In the accompanying paper the information about the conformational behaviour of helical peptides in solution, as well as the studies on alpha-helix stability in proteins has been utilised to derive a database of energy interactions. This database, when implemented in an algorithm based on the helix-coil transition theory (AGADIR), correctly calculates the average helical behaviour in solution of 423 peptides analysed by circular dichroism. The majority of these peptides have been studied at low temperatures (0 to 10 degrees C), and neutral pH. However, in vivo, proteins fold at higher temperatures and in some cases low or high pH values. To understand protein folding it is necessary to calculate the helical behaviour of linear peptides under very different temperature and pH experimental conditions. We have included the temperature and pH effects on the helical behaviour of peptides by means of generally accepted assumptions and simplifications. The inclusion of these terms allow us to calculate the helical behaviour of polyalanine-based peptides, as well as of complex natural sequences, under different experimental conditions.

Elucidating the folding problem of helical peptides using empirical parameters. II. Helix macrodipole effects and rational modification of the helical content of natural peptides

Explaining the helical behaviour of amino acid sequences in solution could be one of the first steps in solving the protein folding problem in a rational way. The information about the conformational behaviour of helical peptides in solution, as well as the alpha-helix stability in proteins, has been utilised to derive a database with the energy contributions for various interaction taking place in an alpha-helix: intrinsic helical propensities, side-chain to side-chain interactions, main-chain to main-chain hydrogen bonds, and capping effects. This database was implemented in a algorithm based on the helix-coil transition theory (AGADIR). Here, the effects on helix stability due to interactions between charged groups and the helix macrodipole are described, quantified and implemented in AGADIR. The algorithm correctly calculates the average helical behaviour in solution of 423 peptides analysed by circular dichroism and it describes the helicity at a residue level, as found when comparing the prediction for each amino acid residue with the data derived from nuclear magnetic resonance studies. Using AGADIR we have done a rational modification of peptides corresponding to protein secondary structure elements in order to increase their helical content. The circular dichroism analysis of the mutant peptides showed a very good agreement between the experimental and calculated helical content. Moreover, in certain specific cases in which strong tertiary contacts in folded proteins do not exist, the algorithm successfully predicts the length of mutagenised alpha-helices. It is interesting to note that the final values of the parameters used do not significantly differ in absolute terms from those extracted from mutagenesis studies in proteins. This indicates that the same physico-chemical principles stand for both systems.

Intrinsic secondary structure propensities of the amino acids, using statistical phi-psi matrices: comparison with experimental scales

Today there are several different experimental scales for the intrinsic alpha-helix as well as beta-strand propensities of the 20 amino acids obtained from the thermodynamic analysis of various model systems. These scales do not compare well with those extracted from statistical analysis of three-dimensional structure databases. Possible explanations for this could be the limited size of the databases used, the definitions of intrinsic propensities, or the theoretical approach. Here we report a statistical determination of alpha-helix and beta-strand propensities derived from the analysis of a database of 279 three-dimensional structures. Contrary to what has been generally done, we have considered a particular residue as in alpha-helix or beta-strand conformation by looking only at its dihedral angles (phi-psi matrices). Neither the identity nor the conformation of the surrounding residues in the amino acid sequence has been taken into consideration. Pseudoenergy empirical scales have been calculated from the statistical propensities. These scales agree very well with the experimental ones in relative and absolute terms. Moreover, its correlation with the average of the experimental scales for alpha-helix or beta-strand is as good as the correlations of the individual experimental scales with the average. These results show that by using a large enough database and a proper definition for the secondary structure propensities, it is possible to obtain a scale as good as any of experimental origin. Interestingly the phi-psi analysis of the Ramachandran plot suggests that the amino acids could have different beta-strand propensities in different subregions of the beta-strand area.

[Quality control of total parenteral nutrition in the 1991-1992 biennium]

OBJECTIVE

To assess the degree of compliance with standards defined for Total Parenteral Nutrition (TPN) quality control in our hospital in the two-year period 1991-1992.

MATERIAL AND METHODS

All available information was assessed concerning 52 patients (32 men and 17 women) for whom a TPN course was prescribed in relation with certain pre-set indications. These patients received a total of 1140 TPN units with the TPN lasting an average of 21.9 days (range, 1-73 days). Monitoring was done by the Nutrition and Diet Section. The degree of compliance was assessed with the standards model proposed by the Providence Medical Center, Portland (USA) (PMCP) with 24 parameters (PM): indications, initiation in the first 24 hours, nutritional assessment in the first 24 hours, period of the TPN, metabolic complications (14 PM), septic complications (3 PM), nutritional consequences (2 PM) and TPN losses. All parameters were appraised and admitted, except for urea, which was corrected to standard values of our Laboratory (< 44 mg/dl), with Transferrin evaluation instead of iron binding capacity (TIBC), taking as compliance standard a figure of > 190 mg/dl. All analytical calculations were carried out in our Central Laboratory Service.

RESULTS

Of all the parameters, the following were discarded, not being calculated on a routine basis: total CO2, serous magnesium, urinary uric nitrogen, nitrogen balance, positive hemocultures, catheters and TPN losses. Levels of compliance varied between 31.9% and 100%, with 8 parameters within the standards (Initiation, 100%; evaluation in first 24 hours, 100%; extent, 100%; creatinine, 100%; total bilirubin, 92.2%; cholesterol, 99.5%; transferrin, 35.9%). Seven parameters fell short (Na, 88.1%; K, 92.9%; Cl, 89.3%; Urea, 54.4%; Glucose, 96.4%; P, 94.1%; Triglycerides, 71.9%).

CONCLUSIONS

We infer from our study that there is a need to make use of a large part of the indicators described in the literature as indicators for quality guarantee of a TPN program, and the use of new parameters must be assessed in normal monitoring.