Beta-secretase (BACE-1) inhibitors: accounting for 10s loop flexibility using rigid active sites

BACE-1 is a flexible enzyme with experimentally determined motion in the flap region, the catalytic aspartates, and the 10s loop. Four in-house crystallographically determined complexes of tertiary carbinamine inhibitors revealed 10s loop motion in the S(3) pocket. These X-ray structures were used to correlate K(i) values, which span over five orders of magnitude, with the calculated interaction energy, using the Merck Molecular Force Field for a series of 19 tertiary carbinamine inhibitors.     

Mitochondrial DNA sequence and gene order of the Sri Lankan Schistosoma nasale is affiliated to the African/Indian group

A 1.9 kb nucleotide sequence of part of the mitochondrial (mt) genome covering the cox1-trnT-rrnL-trnC-rrnS region, and the order of the remaining mitochondrial protein-coding genes for S. nasale of Sri Lankan origin, has been determined for analysis of the possible placement of this species in the genus Schistosoma. The gene order of this species is similar to that of the African and Indian Schistosoma species, but strikingly different from the East Asian species. Analysis of an alignment of the 1.9 kb sequence with available sequences from other schistosomes indicated affinities with S. spindale (found in Sri Lanka) and African species (in particular S. intercalatum and S. haematobium). Phylogenetic trees inferred from the alignment including 1 kb of RNA (transfer RNA and ribosomal RNA) sequence for 8 other Schistosoma spp. and Fasciola hepatica as an out-group revealed that S. nasale is placed proximally to S. spindale, S. intercalatum, S. haematobium and S. mansoni in the African sub-group while the East Asian species are more distant. S. incognitum lies basal to the combined African/Indian clade. The mtDNA analysis strongly supports the hypothesis that S. nasale is closely affiliated with the African/Indian schistosome group rather than the East Asian Schistosoma species.     

Predicting peptides binding to MHC class II molecules using multi-objective evolutionary algorithms

Background  

Peptides binding to Major Histocompatibility Complex (MHC) class II molecules are crucial for initiation and regulation of immune responses. Predicting peptides that bind to a specific MHC molecule plays an important role in determining potential candidates for vaccines. The binding groove in class II MHC is open at both ends, allowing peptides longer than 9-mer to bind. Finding the consensus motif facilitating the binding of peptides to a MHC class II molecule is difficult because of different lengths of binding peptides and varying location of 9-mer binding core. The level of difficulty increases when the molecule is promiscuous and binds to a large number of low affinity peptides.     

Opposing and uncoupling effects of mTOR and S6K1 in the regulation of endothelial tissue factor expression

Rapamycin has been reported to enhance tissue factor (TF) expression. The present study investigated roles of mammalian target of rapamycin (mTOR) and its downstream S6K1 in this process. We showed here that, consistent with rapamycin, knocking-down mTOR enhanced thrombin-induced TF mRNA and protein levels, whereas silencing S6K1 mitigated up-regulation of TF protein but not TF mRNA level. The enhanced TF protein level upon mTOR-silencing was further augmented by over-expression of a constitutively active S6K1 mutant and reduced by blocking RhoA, p38^mapk or NF-κB. The results reveal an opposing and uncoupling effect of mTOR and S6K1 in regulating TF expression.     

Production of soluble Neprilysin by endothelial cells

A non-membrane bound form of Neprilysin (NEP) with catalytic activity has the potential to cleave substrates throughout the circulation, thus leading to systemic effects of NEP. We used the endothelial cell line Ea.hy926 to identify the possible role of exosomes and A Disintegrin and Metalloprotease 17 (ADAM-17) in the production of non-membrane bound NEP. Using a bradykinin based quenched fluorescent substrate (40 μM) assay, we determined the activity of recombinant human NEP (rhNEP; 12 ng), and NEP in the media of endothelial cells (10% v/v; after 24 h incubation with cells) to be 9.35 ± 0.70 and 6.54 ± 0.41 μmols of substrate cleaved over 3 h, respectively. The presence of NEP in the media was also confirmed by Western blotting. At present there are no commercially available inhibitors specific for ADAM-17. We therefore synthesised two inhibitors TPI2155-14 and TPI2155-17, specific for ADAM-17 with IC₅₀ values of 5.36 and 4.32 μM, respectively. Treatment of cells with TPI2155-14 (15 μM) and TPI2155-17 (4.3 μM) resulted in a significant decrease in NEP activity in media (62.37 ± 1.43 and 38.30 ± 4.70, respectively as a % of control; P < 0.0001), implicating a possible role for ADAM-17 in NEP release. However, centrifuging media (100,000g for 1 h at 4 °C) removed all NEP activity from the supernatant indicating the likely role of exosomes in the release of NEP. Our data therefore indicated for the first time that NEP is released from endothelial cells via exosomes, and that this process is dependent on ADAM-17.     

Collection of eggs and hatching and culturing second-stage larvae of Toxocara vitulorum in vitro.

Eggs of Toxocara vitulorum were harvested from the feces of infected buffalo calves and embryonated in vitro. Optimum conditions for hatch and culture of the second-stage larvae were determined. Maximum hatch of larvae occurred from eggs that were decoated by treatment with saturated Ca(OCl)2 for 16-24 min followed by treatment with CO2 and incubation at 37 C. Larvae could be cultured in RPMI-1640 medium for up to 3 mo but survived for only 3 wk in Eagle's minimum essential medium.     

Troponin T modulates sarcomere length-dependent recruitment of cross-bridges in cardiac muscle

The heterogenic nature of troponin T (TnT) isoforms in fast skeletal and cardiac muscle suggests important functional differences. Dynamic features of rat cardiac TnT (cTnT) and rat fast skeletal TnT (fsTnT) reconstituted cardiac muscle preparations were captured by fitting the force response of small amplitude (0.5%) muscle length changes to the recruitment-distortion model. The recruitment of force-bearing cross-bridges (XBs) by increases in muscle length was favored by cTnT. The recruitment magnitude was approximately 1.5 times greater for cTnT- than for fsTnT-reconstituted muscle fibers. The speed of length-mediated XB recruitment (b) in cTnT-reconstituted muscle fiber was 0.50-0.57 times as fast as fsTnT-reconstituted muscle fibers (3.05 vs. 5.32 s(-1) at sarcomere length, SL, of 1.9 microm and 4.16 vs. 8.36 s(-1) at SL of 2.2 microm). Due to slowing of b in cTnT-reconstituted muscle fibers, the frequency of minimum stiffness (f(min)) was shifted to lower frequencies of muscle length changes (at SL of 1.9 microm, 0.64 Hz, and 1.16 Hz for cTnT- and fsTnT-reconstituted muscle fibers, respectively; at SL of 2.2 microm, 0.79 Hz, and 1.11 Hz for cTnT- and fsTnT-reconstituted muscle fibers, respectively). Our model simulation of the data implicates TnT as a participant in the process by which SL- and XB-regulatory unit cooperative interactions activate thin filaments. Our data suggest that the amino-acid sequence differences in cTnT may confer a heart-specific regulatory role. cTnT may participate in tuning the heart muscle by decreasing the speed of XB recruitment so that the heart beats at a rate commensurate with f(min).     

Toward better understanding of protein secondary structure: extracting prediction rules

Although numerous computational techniques have been applied to predict protein secondary structure (PSS), only limited studies have dealt with discovery of logic rules underlying the prediction itself. Such rules offer interesting links between the prediction model and the underlying biology. In addition, they enhance interpretability of PSS prediction by providing a degree of transparency to the predicting model usually regarded as a black box. In this paper, we explore the generation and use of C4.5 decision trees to extract relevant rules from PSS predictions modeled with two-stage support vector machines (TS-SVM). The proposed rules were derived on the RS126 data set of 126 nonhomologous globular proteins and on the PSIPRED data set of 1,923 protein sequences. Our approach has produced sets of comprehensible, and often interpretable, rules underlying the PSS predictions. Moreover, many of the rules seem to be strongly supported by biological evidence. Further, our approach resulted in good prediction accuracy, few and usually compact rules, and rules that are generally of higher confidence levels than those generated by other rule extraction techniques.