Transmembrane protein structures without X-rays

Transmembrane (TM) proteins constitute 15-30% of the genome, but <1% of the structures in the Protein Data Bank. This discrepancy is disturbing, and emphasizes that structure determination of TM proteins remains challenging. The challenge is greatest for proteins from eukaryotes, the structures of which remain intractable despite tremendous advances that have been made towards structure determination of bacterial TM proteins. Notably, >50% of the membrane protein families in eukaryotes lack bacterial homologs. Therefore, it is conceivable that many more years will elapse before high-resolution structures of eukaryotic TM proteins emerge. Until then, integrated approaches that combine biochemical and computational analyses with low-resolution structures are likely to have increasingly important roles in providing frameworks for the mechanistic understanding of membrane-protein structure and function.     

Les récentes découvertes à Baerya dans le district de Bijie, au nord de la province de Guizhou (Chine)

Fauna associated with stone artifacts have recently been uncovered, in the course of a survey from a cave site named Baerya, town land of Bijie, Guizhou province. The first observations suggest a human occupation. In the absence of chrono-stratigraphic data, it is not possible to assess the age of the site. Nevertheless the presence of lower Pleistocene fauna suggests a very ancient age for this human occupation. Further field research will be necessary to determinate the age and nature of the site.     

Inhibition of monoamine oxidase by 8-benzyloxycaffeine analogues

Based on recent reports that several (E)-8-styrylcaffeinyl analogues are potent reversible inhibitors of monoamine oxidase B (MAO-B), a series of 8-benzyloxycaffeinyl analogues were synthesized and evaluated as inhibitors of baboon liver MAO-B and recombinant human MAO-A and -B. The 8-benzyloxycaffeinyl analogues were found to inhibit reversibly both MAO isoforms with enzyme–inhibitor dissociation constants (K_i values) ranging from 0.14 to 1.30 μM for the inhibition of human MAO-A, and 0.023–0.59 μM for the inhibition of human MAO-B. The most potent MAO-A inhibitor was 8-(3-methylbenzyloxy)caffeine while 8-(3-bromobenzyloxy)caffeine was the most potent MAO-B inhibitor. The analogues inhibited human and baboon MAO-B with similar potencies. A quantitative structure–activity relationship (QSAR) study indicated that the MAO-B inhibition potencies of the 8-benzyloxycaffeinyl analogues are dependent on the Hansch lipophilicity (π) and Hammett electronic (σ) constants of the substituents at C-3 of the benzyloxy ring. Electron-withdrawing substituents with a high degree of lipophilicity enhance inhibition potency. These results are discussed with reference to possible binding orientations of the inhibitors within the active site cavities of MAO-A and -B.     

pANT: a method for the pairwise assessment of nonfunctionalization times of processed pseudogenes

We present a method for pairwise Assessment of Nonfunctionalization Times (pANT) in processed pseudogenes. Contrary to existing methods for estimating nonfunctionalization times, pANT utilizes previously calculated probabilities of nucleotide substitution as explicit rate measurements, rather than assume that the substitution rates are the same for all nucleotides. Thus, the method allows a more accurate computation of the time that has elapsed since the nonfunctionalization of a pseudogene. Whereas existing methods require the sequence of an orthologous functional gene, which is not always at hand, pANT only uses the pairwise alignment of the gene/pseudogene pair, thus expanding the range of problems that can be tackled. To estimate evolutionary times in nonfunctional sequences, pANT measures the differences in the pairwise alignment of a gene and its paralogous processed pseudogene, using only the first and second codon positions. It assumes that, because of functional constraints, these positions in the sequence of the functional homolog have not changed since the time of nonfunctionalization of the pseudogene. Hence, the sequence of the gene may be used as the ancestor of the pseudogene. We show that the method's reliance on a detailed substitution matrix, which is derived separately for each species, makes it more accurate than existing methods. We applied pANT to the case of the unitary alpha-1,3-galactosyltransferase human pseudogene and found that our estimate of the nonfunctionalization time was in agreement with that obtained by taxonomic and paleontological considerations pertaining to the divergence between platyrrhines (New World monkeys) and cattarhines (Old World monkeys).     

Comparative computational analysis of prion proteins reveals two fragments with unusual structural properties and a pattern of increase in hydrophobicity associated with disease-promoting mutations

Prion diseases are a group of neurodegenerative disorders associated with conversion of a normal prion protein, PrPC, into a pathogenic conformation, PrPSc. The PrPSc is thought to promote the conversion of PrPC. The structure and stability of PrPC are well characterized, whereas little is known about the structure of PrPSc, what parts of PrPC undergo conformational transition, or how mutations facilitate this transition. We use a computational knowledge-based approach to analyze the intrinsic structural propensities of the C-terminal domain of PrP and gain insights into possible mechanisms of structural conversion. We compare the properties of PrP sequences to those of a PrP paralog, Doppel, and to the distributions of structural propensities observed in known protein structures from the Protein Data Bank. We show that the prion protein contains at least two sequence fragments with highly unusual intrinsic propensities, PrP(114-125) and helix B. No segments with unusual properties were found in Doppel protein, which is topologically identical to PrP but does not undergo structural rearrangements. Known disease-promoting PrP mutations form a statistically significant cluster in the region comprising helices B and C. Due to their unusual properties, PrP(114-125) and the C terminus of helix B may be considered as primary candidates for sites involved in conformational transition from PrPC to PrPSc. The results of our study also show that most PrP mutations associated with neurodegenerative disorders increase local hydrophobicity. We suggest that the observed increase in hydrophobicity may facilitate PrP-to-PrP or/and PrP-to-cofactor interactions, and thus promote structural conversion.     

HIV-1 Tat-mediated apoptosis in human brain microvascular endothelial cells

The integrity of the blood-brain barrier (BBB) is critical for normal brain function. Neuropathological abnormalities in AIDS patients have been associated with perivascular HIV-infected macrophages, gliosis, and abnormalities in the permeability of the BBB. The processes by which HIV causes these pathological conditions are not well understood. To characterize the mechanism by which HIV-1 Tat protein modulates human brain microvascular endothelial cell (HBMEC) functions, we studied the effects of HIV-1 Tat in modulating HBMEC apoptosis and permeability. Treatment of HBMEC with HIV-1 Tat led to Flk-1/KDR and Flt-4 receptor activation and the release of NO. The protein levels of endothelial NO synthase (NOS) and inducible NOS were increased by HIV-1 Tat stimulation. Importantly, HIV-1 Tat caused apoptosis of HBMEC, as evidenced by changes in the cleavage of poly(A)DP-ribose polymerase, DNA laddering, and incorporation of fluorescein into the nicked chromosomal DNA (TUNEL assay). HIV-1 Tat-mediated apoptosis in HBMEC was significantly inhibited in the presence of N-nitro-L-arginine methyl ester (an inhibitor of NOS) and wortmannin (a phosphoinositol 3-kinase inhibitor). Furthermore, HIV-1 Tat treatment significantly increased HBMEC permeability, and pretreatment with both N-nitro-L-arginine methyl ester and wortmannin inhibited the Tat-induced permeability. Taken together, these results indicate that dysregulated production of NO by HIV-1 Tat plays a pivotal role in brain endothelial injury, resulting in the irreversible loss of BBB integrity, which may lead to enhanced infiltration of virus-carrying cells across the BBB.     

Outcome of patients with toxic epidermal necrolysis syndrome revisited

Toxic epidermal necrolysis syndrome is an uncommon, acute, life-threatening, medication-induced disorder with a reported mortality rate of 20 to 60 percent. Different variables have been identified as risk factors. The extent to which these variables, when combined, affect the mortality and outcome in toxic epidermal necrolysis syndrome patients has not yet been reliably defined. Because of the high mortality rate, the logistic analysis of studied variables was performed to see whether a prognostic algorithm could be developed to aid the management of these patients. Thus, a retrospective review of 56 consecutive toxic epidermal necrolysis syndrome patients treated over a period of 13 years was undertaken in the authors' burn center. The demographics included age, sex, race, and total body surface area involved. The other variables studied were comorbidities, sepsis, steroid administration, and the interval between onset of rash and burn center admission. Data were subjected to Fisher's exact test and logistic analysis. Thirty-six patients (64.3 percent) were alive and 20 (35.7 percent) died. Univariate analysis indicated that the male/female ratio was 12:24 for survivors and 9:11 for nonsurvivors (p = 0.4). The white/nonwhite ratio was 80 percent for survivors and 54 percent for nonsurvivors (p = 0.58). The median age was 48.4 +/- 22.8 years (survivors, 41.7 +/- 22.0; nonsurvivors, 60.5 +/- 19.5; p = 0.002). Total body surface area involvement for survivors was 56.9 +/- 32 and 77.7 +/- 21 for nonsurvivors (p = 0.005). The presence of one or more comorbidities between the two groups differed (53 percent survivors and 90 percent nonsurvivors, p = 0.007), indicating eight times higher odds of dying in their presence. The average time between the onset of symptoms and admission to the burn unit was 5.25 +/- 3.4 days for survivors and 7.15 +/- 4.5 days for nonsurvivors (p = 0.08). The presence of sepsis (19.4 percent survivors, 95 percent nonsurvivors, p < 0.001) decreased odds for survival by a factor of 79. Steroids given as a single dose or multiple doses before the patient's transfer to the burn unit were not significantly associated with death (44 percent survivors, 65 percent nonsurvivors, p = 0.14). A multivariate logistic regression model yielded odds ratios of 1.11 (95 percent confidence interval, 1.03 to 1.19) for age in years, 304 (95 percent confidence interval, 8.83 to 10,400) for the presence of sepsis, and 1.03 (95 percent confidence interval, 0.99 to 1.08) for body surface area in percent. All those entering the burn unit with sepsis died. Equivalently, no survivors had sepsis before admission to the burn unit, whereas 55 percent of nonsurvivors had sepsis before admission and 40 percent developed sepsis after admission. When investigating the effect of age and sepsis, no patients over age 60 ever having sepsis survived, whereas all those who were under 60 and without sepsis survived. Likewise, all patients whose age was over 60 and whose total body surface area involved was over 60 percent died. The main factors contributing to the mortality from toxic epidermal necrolysis syndrome, when considering covariates separately, are the presence of sepsis at any time (odds ratio, 79), the presence of comorbidities (odds ratio, 8.05), age, and total body surface area, whereas multivariate models suggested age (odds ratio per year of additional age, 1.11), total body surface area (odds ratio per additional percent of body surface area, 1.03), and the presence of sepsis (odds ratio, 304). By using the actual coefficients in the logistic model, the log odds that the patient will die as the result of his or her condition can be summarized in the following formula: -11.5 + (10 percent of the patient's age + 3 percent of total body surface area + 5.75 if sepsis is present). The awareness of the importance of these covariates, and their early recognition as risk factors, should offer a focused approach to the patients' management and improve their outcome.     

Increasing progesterone secretion and 3β-hydroxysteroid dehydrogenase activity of human cumulus cells and granulosa-lutein cells concurrent with successful fertilization of the corresponding oocyte

In many studies it has been documented that the induction of multiple follicular growth in humans results in an asynchrony between the degree of cumulus mucification, oocyte meiotic maturation, fertilizability, and follicular cell progesterone (P₄) secretion. The present study was carried out on oocytes enclosed in fully mucified cumulus. Thus, oocyte fertilizability was correlated to human cumulus cell (hCC) and human granulosa-lutein (G-L) cell competence for P₄ secretion in culture. In the G-L cells, P₄ secretion and percentage of cells manifesting 3β-hydroxysteroid dehydrogenase (3β-HSD) activity increased concurrently with the period of culture. In the hCC, however, P₄ secretion decreased concurrently with elongation of the culture period, whereas the percentage of 3β-HSD-positive cells increased. In hCC corresponding to the fertilized oocytes, P₄ accumulation in culture medium was 1.9-fold (P < 0.001) and 1.6-fold (P < 0.02) higher on days 0–3 and 3–5 of culture, respectively, as compared to P₄ accumulation in hCC of unfertilized oocytes. Also, in hCC corresponding to the fertilized oocytes, the degree of 3β-HSD activity was found to be significantly higher shortly after aspiration and after either 3 or 5 days, compared to hCC of unfertilized oocytes. In the G-L cells pooled from all follicles yielding mature cumulus-oocyte complexes, P₄ accumulation and percentage of 3β-HSD-positive cells increased concurrently with the increase in percentage of fertilized eggs of each individual woman. These results indicate that in stimulated cycles, follicles yielding mature cumulus-oocyte complex, oocyte fertilizability, and G-L cell or hCC competence for P₄ secretion are correlated and synchronous.