Folding thermodynamics of peptides

A simplified interaction potential for protein folding studies at the atomic level is discussed and tested on a set of peptides with approximately 20 residues each. The test set contains both alpha-helical (Trp cage, F(s)) and beta-sheet (GB1p, GB1m2, GB1m3, Betanova, LLM) peptides. The model, which is entirely sequence-based, is able to fold these different peptides for one and the same choice of model parameters. Furthermore, the melting behavior of the peptides is in good quantitative agreement with experimental data. Apparent folded populations obtained using different observables are compared, and are found to be very different for some of the peptides (e.g., Betanova). In other cases (in particular, GB1m2 and GB1m3), the different estimates agree reasonably well, indicating a more two-state-like melting behavior.     

Compact and ordered collapse of randomly generated RNA sequences

As the raw material for evolution, arbitrary RNA sequences represent the baseline for RNA structure formation and a standard to which evolved structures can be compared. Here, we set out to probe, using physical and chemical methods, the structural properties of RNAs having randomly generated oligonucleotide sequences that were of sufficient length and information content to encode complex, functional folds, yet were unbiased by either genealogical or functional constraints. Typically, these unevolved, nonfunctional RNAs had sequence-specific secondary structure configurations and compact magnesium-dependent conformational states comparable to those of evolved RNA isolates. But unlike evolved sequences, arbitrary sequences were prone to having multiple competing conformations. Thus, for RNAs the size of small ribozymes, natural selection seems necessary to achieve uniquely folding sequences, but not to account for the well-ordered secondary structures and overall compactness observed in nature.     

Secretion of metastasis related gangliosides by mouse B16-melanoma in circulation in vivo and in culture media in vitro

Mouse B16LuF1 melanoma cells of lower metastatic potential to lung were treated in vitro with same concentration (50 microM) of gangliosides prepared from plasma of mice bearing lung metastasis of B16LuF5, B16LuF9 or B16LuF10 melanoma cell lines of increasing metastatic potential to lung (LuF1 < LuF5 < LuF9 < LuF10) and injected to normal mice through tail vein. The number of metastatic tumor nodules formed in lung increased gradually in mice receiving B16LuF5, B16LuF9 and B16LuF10-ganglioside-treated B16LuF1 cells compared to mice receiving B16LuF1 cells without any ganglioside treatment. Similarly, mouse B16LuF1 melanoma cells treated in vitro with 50 microM concentration of gangliosides prepared from spent culture media of B16LuF5, B16LuF9 or B16LuF10 cells cultured in vitro were injected to normal mice through tail vein. The number of metastatic tumor nodules formed in lung increased gradually in mice receiving B16LuF5, B16LuF9 and B16LuF10-ganglioside-treated B16LuF1 cells compared to mice receiving B16LuF1 cells without any ganglioside treatment. The results indicated that metastasis-associated gangliosides present in plasma and culture media of B16-melanoma of increasing metastatic potential to lung enhanced metastatic potential of B16LuF1 cells. The increasing concentration of metastasis-associated gangliosides present in plasma and in culture media of B16-melanoma of increasing metastatic potential possibly determined increase in metastatic potential of B16LuF1-melanoma cells.     

Oligomerization of amyloid Abeta16-22 peptides using hydrogen bonds and hydrophobicity forces

The 16-22 amino-acid fragment of the beta-amyloid peptide associated with the Alzheimer's disease, Abeta, is capable of forming amyloid fibrils. Here we study the aggregation mechanism of Abeta16-22 peptides by unbiased thermodynamic simulations at the atomic level for systems of one, three, and six Abeta16-22 peptides. We find that the isolated Abeta16-22 peptide is mainly a random coil in the sense that both the alpha-helix and beta-strand contents are low, whereas the three- and six-chain systems form aggregated structures with a high beta-sheet content. Furthermore, in agreement with experiments on Abeta16-22 fibrils, we find that large parallel beta-sheets are unlikely to form. For the six-chain system, the aggregated structures can have many different shapes, but certain particularly stable shapes can be identified.     

Cytomorphologic spectrum of carcinoma ex pleomorphic adenoma

OBJECTIVE: To delineate the cytomorphologic features of carcinoma ex pleomorphic adenoma (CPA) and identify the diagnostic pitfalls. STUDY DESIGN: Smears of 14 cases suspected as CPA on fine needle aspiration over a period of 15 years were reviewed. Cytohistologic correlation was done in 10 cases. RESULTS: All cases had a salivary gland mass of 1-16 years' duration, with a rapid increase in size in 10 cases. Epithelial cells predominated over stroma in 11 of 14 cases. Group I showed unequivocal malignant cells admixed with benign epithelial and stromal components of pleomorphic adenoma (PA), which were considered diagnostic of CPA on review. The cytologic differential diagnosis in these cases included mucoepidermoid carcinoma, carcinosarcoma and metastatic adenocarcinoma. Group II comprised 7 cases suspected to be cellular PA with atypia or CPA. These showed mild to moderate degrees of pleomorphism, absence of unequivocal malignant cells, and a variable proportion of benign epithelial and stromal components. Four of them were histologically confirmed as CPA. CONCLUSION: Sampling error is an important cause of diagnostic pitfalls. Correlation with clinical data is essential in diagnosis of CPA on cytology. In a proper clinical setting, extensive fine needle aspiration sampling should be done initially. Any degree of nuclear atypia in PA should be documented, alerting the clinician and histopathologist to the possibility of CPA.     

Utility of repeat fine needle aspiration in acute suppurative lesions. Follow-up of 263 cases

OBJECTIVE: To determine the clinical value of repeat fine needle aspiration (FNA) as a follow-up strategy in the management of patients in India, clinically suspected of having tuberculosis (TB) but showing a cytologic picture of acute suppuration. STUDY DESIGN: Repeat aspirates from 263 patients presenting with lymph node or soft tissue masses were analyzed. The previous FNA of these cases had shown acute inflammatory exudate but no epithelioid granuloma or acid-fast bacilli (AFB). RESULTS: The repeat FNA helped to detect 55% additional cases of TB within a period of 8 weeks; 67% of them were diagnosed in the second and third weeks. Diagnostic yield rose to 59% after the third FNA. AFB were detected in 34 (13.3%) cases that showed a low bacterial load. In addition, nontubercular lesions, such as epidermal inclusion cyst (4), cysticercosis (3), sialadenitis (2) and metastatic carcinoma (8), were diagnosed. CONCLUSION: All cases showing acute suppuration without granulomas or AFB on the first FNA should be reevaluated by follow-up FNA and staining for AFB. This will enhance the diagnostic yield of tuberculosis in developing countries, where molecular diagnostics are too costly or unavailable. This procedure is cost effective as compared to biopsy and culture. In addition to tuberculosis, many unexpected nontubercular lesions may also be unmasked. Repeat FNA reduces sampling and screening errors, improves sensitivity and helps to study the evolution of epithelioid granulomas.     

Morphologic spectrum of papillary carcinoma of the thyroid: role of cytology in identifying the variants

OBJECTIVE: To evaluate the efficacy of fine needle aspiration cytology (FNAC) in the diagnosis of morphologic variants of papillary carcinoma of the thyroid (PCT) and to determine the reasons for misdiagnosis in discrepant cases on cytology. STUDY DESIGN: Fine needle aspiration smears from 158 histologically proven cases of PCT were blindly reviewed and an attempt made to subclassify them into different variants on the basis of various architectural and morphologic features. Cytohistologic correlation was performed to assess the efficacy of cytology in correctly identifying these variants. RESULTS: In cases with satisfactory aspirates, the diagnosis of papillary carcinoma was correctly made in 112 of 139 (80.5%) histologically proven cases of PCT. Subclassification was correct in 87 of 96 (90.6%) cases of classic papillary carcinoma and in 25 of 43 (58.1%) of the other variants of PCT with adequate aspirates. Cytohistologic agreement was 100% in columnar cell variant (CCV) and high grade variant (HGV). Although there was overlap in the morphologic features of tall cell variant (TCV) and Hürthle cell variant, cytology correctly identified 60% and 76.4% of these cases, respectively. The accuracy of cytology was limited in diagnosing follicular variant as only 50% of these cases could be correctly typed on cytology. Nodular fascitis-like stroma and diffuse sclerosis variants could not be diagnosed on cytology. CONCLUSION: Though FNAC is of limited value in typing the variants of PCT due to overlapping morphologic features, it can provide clues to the diagnosis in certain aggressive variants such as TCV, CCV and HGV. Early diagnosis in these cases can assist clinicians with management.     

In silico modeling and hydrogen peroxide binding study of rice catalase

Homology modeling of the catalase, CatC cloned and sequenced from rice (Oryza sativa L., cv Ratna an Indica cultivar) has been performed based on the crystal structure of the catalase CatF (PDB code 1m7s) by using the software MODELLER. With the aid of molecular mechanics and molecular dynamics methods, the final model is obtained and is further assessed by PROCHECK and VERIFY - 3D graph, which show that the final refined model is reliable. With this model, a flexible docking study with the hydrogen peroxide, the substrate for catalase, is performed and the results indicate that Arg310, Asp343 and Arg346 in catalase are three important determinant residues in binding as they have strong hydrogen bonding contacts with the substrate. These hydrogen-bonding interactions play an important role for the stability of the complex. Our results may be helpful for further experimental investigations.