Open interface and large quaternary structure movements in 3D domain swapped proteins: insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease A

Bovine pancreatic ribonuclease (RNase A) forms two three-dimensional (3D) domain swapped dimers. Crystallographic investigations have revealed that these dimers display completely different quaternary structures: one dimer (N-dimer), which presents the swapping of the N-terminal helix, is characterized by a compact structure, whereas the other (C-dimer), which is stabilized by the exchange of the C-terminal end, shows a rather loose assembly of the two subunits. The dynamic properties of monomeric RNase A and of the N-dimer have been extensively characterized. Here, we report a molecular dynamics investigation carried out on the C-dimer. This computational experiment indicates that the quaternary structure of the C-dimer undergoes large fluctuations. These motions do not perturb the proper folding of the two subunits, which retain the dynamic properties of RNase A and the N-dimer. Indeed, the individual subunits of the C-dimer display the breathing motion of the beta-sheet structure, which is important for the enzymatic activity of pancreatic-like ribonucleases. In contrast to what has been observed for the N-dimer, the breathing motion of the two subunits of the C-dimer is not coupled. This finding suggests that the intersubunit communications in a 3D domain swapped dimer strongly rely on the extent of the interchain interface. Furthermore, the observation that the C-dimer is endowed with a high intrinsic flexibility holds interesting implications for the specific properties of 3D domain swapped dimers. Indeed, a survey of the quaternary structures of the other 3D domain swapped dimers shows that large variations are often observed when the structural determinations are conducted in different experimental conditions. The 3D domain swapping phenomenon coupled with the high flexibility of the quaternary structure may be relevant for protein-protein recognition, and in particular for the pathological aggregations.     

5-Alkyl-2-alkylamino-6-(2,6-difluorophenylalkyl)-3,4-dihydropyrimidin-4(3H)-ones, a new series of potent, broad-spectrum non-nucleoside reverse transcriptase inhibitors belonging to the DABO family

2-Alkylamino-6-[1-(2,6-difluorophenyl)alkyl]-3,4-dihydro-5-alkylpyrimidin-4(3H)-ones (F(2)-NH-DABOs) 4, 5 belonging to the dihydro-alkoxy-benzyl-oxopyrimidine (DABO) family and bearing different alkyl- and arylamino side chains at the C(2)-position of the pyrimidine ring were designed as active against wild type (wt) human immunodeficiency virus type 1 (HIV-1) and some relevant HIV-1 mutants. Biological evaluation indicated the importance of the further anchor point of compounds 4, 5 into the non-nucleoside binding site (NNBS): newly synthesized compounds were highly active against both wild type and the Y181C HIV-1 strains. In anti-wt HIV-1 assay the potency of amino derivatives did not depend on the size or shape of the C(2)-amino side chain, but it associated with the presence of one or two methyl groups (one at the pyrimidine C(5)-position and the other at the benzylic carbon), being thymine, alpha-methyluracil or alpha-methylthymine derivatives almost equally active in reducing wt HIV-1-induced cytopathogenicity in MT-4 cells. Against the Y181C mutant strain, 2,6-difluorobenzyl-alpha-methylthymine derivatives 4d, 5h'-n' showed the highest potency and selectivity among tested compounds, both a properly sized C(2)-NH side chain and the presence of two methyl groups (at C(5) and benzylic positions) being crucial for high antiviral action.     

A retrospective analysis of human cystic echinococcosis in Sardinia (Italy), an endemic Mediterranean region,from 2001 to 2005

To assess the current impact of human CE in Sardinia (Italy) and to monitor the changes over time, a survey has been carried out for the period 2001–2005 using hospital inpatient discharge reports (HDR) as information source, supplementing data wherever possible with additional information retrieved directly from medical records. The total of 726 admissions with “Echinococcosis” as primary diagnosis (annual rate of 8.9 per 100,000 inhabitants) concerned 540 CE cases with an annual mean incidence rate of 6.62 per 100,000 inhabitants. Male-to-female ratio was 1.36, suggesting a marked risk associated with traditional male occupations. Age-specific incidence showed increasing rates of clinical CE with age for both genders. The liver was found to be the most common localization, affecting 72% of patients, while pulmonary CE was more frequent in males than in females. CE risk was unevenly distributed in the island. The more pastoral areas had the highest probability of humans becoming infected, with an incidence rate of clinical cases of ~ 14.0 per 100,000 for areas with sheep/inhabitants index of > 6. Compared to the past, incidence rates appear to be decreasing both for pulmonary and hepatic localizations, while there is a reversal of the CE “urbanization” trend resulting in “ruralization”, accompanied by a greater degree of parasite ecological “isolation” and focus-points of infection risk. In spite of this decrease, the cost of hospital care alone (~4 million euros) suggests that the monetary plus non-monetary costs of CE are still very high but not fully recognised.     

Pneumococcal pili are composed of protofilaments exposing adhesive clusters of Rrg A

Pili have been identified on the cell surface of Streptococcus pneumoniae, a major cause of morbidity and mortality worldwide. In contrast to Gram-negative bacteria, little is known about the structure of native pili in Gram-positive species and their role in pathogenicity. Triple immunoelectron microscopy of the elongated structure showed that purified pili contained RrgB as the major compound, followed by clustered RrgA and individual RrgC molecules on the pilus surface. The arrangement of gold particles displayed a uniform distribution of anti-RrgB antibodies along the whole pilus, forming a backbone structure. Antibodies against RrgA were found along the filament as particulate aggregates of 2-3 units, often co-localised with single RrgC subunits. Structural analysis using cryo electron microscopy and data obtained from freeze drying/metal shadowing technique showed that pili are oligomeric appendages formed by at least two protofilaments arranged in a coiled-coil, compact superstructure of various diameters. Using extracellular matrix proteins in an enzyme-linked immunosorbent assay, ancillary RrgA was identified as the major adhesin of the pilus. Combining the structural and functional data, a model emerges where the pilus RrgB backbone serves as a carrier for surface located adhesive clusters of RrgA that facilitates the interaction with the host.     

Gastrointestinal stromal tumor. A study of 158 cases: clinicopathological features and prognostic factors

OBJECTIVE: To increase knowledge on the behavior of gastrointestinal stromal tumors (GISTs) and factors influencing therapy. STUDY DESIGN: The clinicomorphological features of 158 GISTs were analyzed. Survival analysis was performed on the whole series, as well as on a selected group of patients with high risk GIST who did not receive imatinib mesylate. The impact of imatinib mesylate on the prognosis was investigated. RESULTS: Most of the GISTs had a benign behavior. The risk class was a powerful prognostic factor but was unable to predict the outcome in a single case; even patients in the high risk class not receiving imatinib mesylate had a low mortality rate. In this group, it was the mitotic activity that better correlated with prognosis, and a cut point of 10 mitoses per 50 high-power field can be fixed to discriminate cases with favorable or unfavorable outcome. Patients with GISTs presenting as aggressive disease received great benefit from imatinib mesylate therapy. CONCLUSION: Mitotic activity is important in predicting the outcome of patients with high risk GIST who present at diagnosis without dissemination. This finding can have therapeutic implications.