Structural signatures of enzyme binding pockets from order-independent surface alignment: a study of metalloendopeptidase and NAD binding proteins

Detecting similarities between local binding surfaces can facilitate identification of enzyme binding sites and prediction of enzyme functions, and aid in our understanding of enzyme mechanisms. Constructing a template of local surface characteristics for a specific enzyme function or binding activity is a challenging task, as the size and shape of the binding surfaces of a biochemical function often vary. Here we introduce the concept of signature binding pockets, which captures information on preserved and varied atomic positions at multiresolution levels. For proteins with complex enzyme binding and activity, multiple signatures arise naturally in our model, forming a signature basis set that characterizes this class of proteins. Both signatures and signature basis sets can be automatically constructed by a method called SOLAR (Signature Of Local Active Regions). This method is based on a sequence-order-independent alignment of computed binding surface pockets. SOLAR also provides a structure-based multiple sequence fragment alignment to facilitate the interpretation of computed signatures. By studying a family of evolutionarily related proteins, we show that for metzincin metalloendopeptidase, which has a broad spectrum of substrate binding, signature and basis set pockets can be used to discriminate metzincins from other enzymes, to predict the subclass of metzincins functions, and to identify specific binding surfaces. Studying unrelated proteins that have evolved to bind to the same NAD cofactor, we constructed signatures of NAD binding pockets and used them to predict NAD binding proteins and to locate NAD binding pockets. By measuring preservation ratio and location variation, our method can identify residues and atoms that are important for binding affinity and specificity. In both cases, we show that signatures and signature basis set reveal significant biological insight.     

Subfascial periareolar augmentation mammaplasty

Subfascial placement of implants was introduced 3 years ago. Collected data reveal very promising short-term and long-term results in comparison with subglandular and subpectoral positioned implants. The clinical experiences of 69 breast augmentations in the subfascial position are reported. The indications for this technique are proposed. The incidence of complications is described from clinical experiences and compared with that for other methods. From January of 1998 through May of 2002, 328 patients underwent periareolar augmentation mammaplasty; 105 patients had a subglandular mammaplasty, 154 patients had a subpectoral mammaplasty, and from August of 1999 through May of 2002, 69 patients had a subfascial augmentation mammaplasty. The mean postoperative follow-up time was 3.6 years in the subglandular group, 3.5 years in the subpectoral group, and 2.9 years in the subfascial group. In comparing the results of the subglandular augmentation group with those of the subpectoral and subfascial augmentation groups, the total rate of complications diminished significantly. The long-term complications of severe capsular contracture, rippling, and nipple sensation and numbness in subglandular augmentation mammaplasty could be significantly reduced (p < 0.05). The subfascial augmentation mammaplasty unites all the advantages of the subpectoral augmentation mammaplasty but eliminates the disadvantages of increased postoperative discomfort and disturbing muscle movement of the breast.     

Validation of a gas chromatography-mass spectrometry method for the determination of pg/ml levels of 17beta-estradiol and 17beta-trenbolone in bovine serum

A method for the quantitation of pg/ml levels of 17beta-estradiol and 17beta-trenbolone in bovine serum by gas chromatography/electron-capture mass spectrometry has been developed and validated. Using the area ratios of the integrated molecular-ion peaks of the analytes to their corresponding deuterated internal standards, [2,4,16,16-2H4] 17beta-estradiol (17beta-estradiol-d(4)) and [16,16-2H2] 17beta-trenbolone (17beta-trenbolone-d(2)), and non-weighted linear regression, two calibration curves per analyte; 5-50 and 50-500 pg/ml for 17beta-estradiol in sera, and 25-250 and 250-2500 pg/ml for 17beta-trenbolone in sera, respectively, were constructed. Splitless injection of 200 fg 17beta-estradiol and 1000 fg 17beta-trenbolone could be detected and quantified. Tested batches of control bovine sera did not exhibit interference for 17beta-trenbolone, and showed expected background presence of endogenous 17beta-estradiol. Intra-day residual errors did not exceed 20%, and regression correlations were greater than 0.99. Intra-day precision data was similar to inter-day precision data. Using this method, 16 samples can be processed within one working day.     

Rust fungi causing galls, witches' brooms, and other abnormal plant growths in northwestern Argentina

Conspicuous galls and witches' brooms frequently are symptoms of rust infections on plant hosts in the ecologically diverse northwestern region of Argentina. These symptoms are caused by systemic or locally systemic spermogonial-aecial infections, although uredinial and telial infections also might be involved. Sixteen species of rust fungi are treated in this paper, most of which cause a plant response that results in enlarged growth. Ypsilospora tucumanensis J.R. Hern. & J.F. Hennen on Inga edulis is described as a species new to science. Puccinia cordiae Arthur is cited as a new record for Argentina. These rusts also are included: Chaconia ingae, Gerwasia imperialis, Kuehneola loeseneriana, Prospodium appendiculatum, Prospodium elegans, Prospodium perornatum, Puccinia bougainvilleae, Puccinia pampeana, Ravenelia argentinica, Ravenelia hieronymi, Ravenelia papillosa, Ravenelia spegazziniana, Uromyces cestri and Uropyxis rickiana. For some of the scientific names, lectotype specimens have been designated.     

Binding of estrogen and progesterone-BSA conjugates to glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the effects of the free steroids on GAPDH enzyme activity: physiological implications

In this study rat brain solubilized plasmalemma-microsomal fractions (B-P3) or cytosolic fractions were applied to P-3-BSA (progesterone linked to BSA at C-3 position) and E-6-BSA (17beta-estradiol linked to BSA at C-6 position) affinity columns. It is interesting that a 37 kDa protein was retained by both columns which was identified as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) by N-terminal sequencing. The 37 kDa protein (GAPDH) was not retained by either a control BSA conjugated affinity column or a corticosterone-BSA affinity column. E-6-BSA bound to GAPDH with higher binding affinity than P-3-BSA or T-3-BSA (testosterone linked to BSA at C-3 position) affinity columns. In addition, the binding of 17beta-E-6-BSA to GAPDH was impeded by free estrogen (17beta-estradiol) completely. Binding studies of E-6-BSA and P-3-BSA to commercial GAPDH from rabbit skeletal muscle using radiolabeled ligand binding assays revealed that P-3-BSA had 10x lower GAPDH binding affinity than E-6-BSA. Next, the effects of estrogen and progesterone on GAPDH activity were studied. Rapid and significant increases in V(max) and changes in K(m) were observed by the addition of 10 nM estradiol, whereas 100 nM progesterone decreased only V(max) significantly. Testosterone, corticosterone, 17alpha-estradiol, and diethylstilbestrol did not affect the enzyme activity. The results indicate that GAPDH is a target site for 17beta-estradiol and progesterone and suggest possible roles in the regulation of cellular metabolism and synaptic remodeling in which GAPDH has been reported to be involved.     

Diabetes-Related Changes in Rat Cerebral Occludin and Zonula Occludens-1 (ZO-1) Expression

The endothelial or epithelial tight junctions create a barrier to diffusion of solutes. Since experimental diabetes mellitus is associated with considerable alterations in the blood-brain barrier (BBB), it is possible that specific tight junction proteins may be altered in diabetes. To test this hypothesis, Western and Northern blot analysis were carried out to measure the steady-state level of occludin and zonula occludens-one (ZO-1) proteins and mRNA levels in cerebral tissue of streptozotocin-induced diabetic rats and the results were compared to insulin treated diabetic rats and vehicle injected control rats. The cerebral occludin content in diabetic rats (115.4 ± 18.6 arbitrary units) was significantly reduced compared to insulin-treated diabetic rats (649.1 ± 141.2) or control rats (552.9 ± 82.9), p < 0.001. The ZO-1 content of cerebral tissue from diabetic rats (1240.6 ± 199.7 arbitrary units) was not significantly altered compared to controls (1310.8 ± 256.9). The cerebral occludin mRNA content relative to G3PDH mRNA was 1.35 ± 0.07 and 1.34 ± 0.19 in control and diabetic rats respectively. The cerebral ZO-1 mRNA content relative to G₃PDH mRNA in diabetic and control rats was 1.135 ± 0.123 and 0.956 ± 0.038 respectively. These differences did not achieve statistical significance. It is concluded that diabetes alters the molecular anatomy of the tight junctions in cerebral tissue by altering the content of select structural proteins.     

Purification and characterization of protein tyrosine phosphatase PTP-MEG2

PTP-MEG2 is an intracellular protein tyrosine phosphatase with a putative lipid-binding domain at the N-terminus. The present study reports expression, purification, and characterization of the full-length form of the enzyme plus a truncated form containing the catalytic domain alone. Full-length PTP-MEG2 was expressed with an adenovirus system and purified from cytosolic extracts of human 293 cells infected with the recombinant adenovirus. The purification scheme included chromatographic separation of cytosolic extracts on fast flow Q-Sepharose, heparin-agarose, l-histidyldiazobenzylphosphonic acid agarose, and hydroxylapatite. The enrichment of PTP-MEG2 from the cytosol was about 120-fold. The truncated form of PTP-MEG2 was expressed in E. coli cells as a non-fusion protein and purified by using a chromatographic procedure similar to that used for the full-length enzyme. The purified full-length and truncated enzymes showed single polypeptide bands on SDS-polyacrylamide gel electrophoresis under reducing conditions and behaved as monomers on gel exclusion chromatography. With para-nitrophenylphosphate and phosphotyrosine as substrates, both forms of the enzyme exhibited classical Michaelis-Menten kinetics. Their responses to pH, ionic strength, metal ions, and protein phosphatase inhibitors are similar to those observed with other characterized tyrosine phosphatases. Compared with full-length PTP-MEG2, the truncated DeltaPTP-MEG2 displayed significantly higher V(max) and lower K(m) values, suggesting that the N-terminal putative lipid-binding domain may have an inhibitory role. The full-length and truncated forms of PTP-MEG2 were also expressed as GST fusion proteins in E. coli cells and purified to near homogeneity through affinity columns. However, the specific phosphatase activities of the GST fusion proteins were 10-25-fold below those obtained with the correspondent non-fusion proteins.