Analysis of dynamics and mechanism of ligand binding to Artocarpus integrifolia agglutinin. A 13C and 19F NMR study

Binding of 13C-labeled N-acetylgalactosamine (13C-GalNAc) and N-trifluoroacetylgalactosamine (19F-GalNAc) to Artocarpus integrifolia agglutinin has been studied using 13C and 19F nuclear magnetic resonance spectroscopy, respectively. Binding of these saccharides resulted in broadening of the resonances, and no change in chemical shift was observed, suggesting that the alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc experience a magnetically equivalent environment in the lectin combining site. The alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc were found to be in slow exchange between free and protein bound states. Binding of 13C-GalNAc was studied as a function of temperature. From the temperature dependence of the line broadening, the thermodynamic and kinetic parameters were evaluated. The association rate constants obtained for the alpha-anomers of 13C-GalNAc and 19F-GalNAc (k+1 = 1.01 x 10(5) M-1.s-1 and 0.698 x 10(5) M-1.s-1, respectively) are in close agreement with those obtained for the corresponding beta-anomers (k+1 = 0.95 x 10(5) M-1.s-1 and 0.65 x 10(5) M-1.s-1, respectively), suggesting that the two anomers bind to the lectin by a similar mechanism. In addition these values are several orders of magnitude slower than those obtained for diffusion controlled processes. The dissociation rate constants obtained are 49.9, 56.9, 42, and 43 s-1, respectively, for the alpha- and beta-anomers of 13C-GalNAc and 19F-GalNAc. A two-step mechanism has been proposed for the interaction of 13C-GalNAc and 19F-GalNAc with A. integrifolia lectin in view of the slow association rates and high activation entropies. The thermodynamic parameters obtained for the association and dissociation reactions suggest that the binding process is entropically favored and that there is a small enthalpic contribution.     

Verapamil counteracts depression but not long-lasting potentiation of the hippocampal population spike

In transversely sectioned rat hippocampal slices, population spikes and population "EPSPs" were recorded from CA1 neurones in response to the stimulation of Schaffer collateral and commissural inputs. High frequency tetanic stimulation (400 Hz, 200 pulses) of an input induced LLP of the homosynaptic response without significantly changing the heterosynaptic response. This LLP was not interrupted by either a 400 Hz tetanus given to the heterosynaptic input or by verapamil (0.33 microM) which blocks Ca++ channels, but not transmitter release. A low frequency tetanus (20 Hz, 200 pulses) given to an input induces co-occurring homosynaptic and heterosynaptic depressions of about 20 min duration. This tetanus could also mask an established LLP in homosynaptic or heterosynaptic pathway. Verapamil counteracts homo- and heterosynaptic depressions. The population spike as well as the population "EPSP" were depressed following iontophoretic application of Ca++ (2-100 nA) at the CA1 cell body area. These results indicate that homosynaptic and heterosynaptic depressions are at least partly due to an accumulation of Ca++ into CA1 neurones. An established LLP is not interrupted by LLP of another input. Homo- and heterosynaptic depressions mask, but not reverse, LLP.     

Proton binding sites and conformational analysis of H+K(+)-ATPase

It is proposed that the hydronium ion, H3O+, binds to the E1 conformation of the alpha-subunit of gastric proton pump. The H3O+ binding cavities are characterized parametrically based on valence, sequence, geometry, and size considerations from comparative modeling. The cavities have scope for accommodating monovalent cations of different ionic radii. The H3O+ transport is proposed to be aided by arenes which are arranged regularly along the pump starting from N-domain through the transmembrane region. Step-by-step structural changes accompanying H3O+ occlusion are studied in detail. The observations corroborate well with earlier experimental studies.     

Vermiculite as an economic support for immobilization of neutral protease

A new and cheap support, vermiculite was successfully used to immobilize neutral protease by adsorption and hexamethylene diamine mediated coupling using glutaraldehyde as a bifunctional agent. Neutral protease immobilized on vermiculite by adsorption showed maximum retained activity than HMD mediated coupling. The optimum temperature for both free and immobilized neutral protease was found to be 45°C. However, the pH and thermal stabilities of immobilized neutral protease was observed to be better than that of the free enzyme. The storage stability of the immobilized enzyme was also studied.     

Reversible inhibitors of beta-glucosidase

A variety of reversible inhibitors of sweet almond beta-glucosidase were examined. These included simple sugars and sugar derivatives, amines and phenols. With respect to the sugar inhibitors and, indeed, the various glycoside substrates, the enzyme has what can be considered a "relaxed specificity". No single substituent on glucose, for example, is essential for binding. Replacement of a hydroxyl group with an anionic substituent reduces the affinity while substitution with a cationic (amine) substituent enhances the affinity. Amines, in general, are good inhibitors, binding more tightly than the corresponding alcohols: pKiRNH3+ = 0.645pKiROH + 1.77 (n = 9, r = 0.97). The affinity of a series of 10 primary amines was found to be strongly influenced by substituent hydrophobicity: pKi = 0.52 pi + 1.32 (r = 0.95). The major binding determinant of the glycoside substrates is the aglycon moiety. Thus, the Ki values of phenols are similar in magnitude to the Ks values of the corresponding aryl beta-glucoside. The pH dependence for the inhibition by various phenols indicates that it is the un-ionized phenol which binds to the enzyme when an enzymic group of pKa = 6.8 (+/- 0.1) is protonated. The affinity of the phenol inhibitor is dependent on its basicity with a Br?nsted coefficient for binding of beta = -0.26 (n = 14, r = 0.98). The pH dependence of the binding of two particularly potent beta-glucosidase inhibitors was also examined. 1-Deoxynojirimycin (1,5-dideoxy-1,5-imino-D-glucitol) has a pH-corrected Ki = 6.5 microM, and D-glucono-1,5-lactam has a pH-corrected Ki = 29 microM.(ABSTRACT TRUNCATED AT 250 WORDS)     

Aromatic-Aromatic Interactions Database, A(2)ID: an analysis of aromatic π-networks in proteins

The geometrical arrangement of the aromatic rings of phenylalanine, tyrosine, tryptophan and histidine has been analyzed at a database level using the X-ray crystal structure of proteins from PDB in order to find out the aromatic-aromatic (π-π) networks in proteins and to understand how these aromatic rings are connected with each-other in a specific π-π network. A stringent examination of the 7848 proteins indicates that close to 89% of the proteins have occurrence of at least a network of 2π or a higher π-π network. The occurrence of π-π networks in various protein superfamilies based on SCOP, CATH and EC classifiers has also been probed in the present work. In general, we find that multidomain and membrane proteins as well as lyases show a more number of these networks. Analysis of the distribution of angle between planes of two proximal aromatic rings (?) distribution indicates that at a larger cutoff distance (between centroid of two aromatic rings), above 5?, C-H?π interactions (T-shaped orientation) are more prevalent, while π-π interactions (stacked orientation) are more prevalent at a smaller cutoff distance. The connectivity patterns of π-π networks propose strong propensity of finding arrangement of aromatic residues as clusters rather than linear arrangement. We have also made a public domain database Aromatic-Aromatic Interactions Database (A(2)ID) comprising of all types of π-π networks and their connectivity pattern present in proteins. It can be accessed by url http://203.199.182.73/gnsmmg/databases/aidb/aidb.html.     

The question of relative biological effectiveness and quality factor for auger emitters incorporated into proliferating mammalian cells

The problem of determining RBE values for Auger emitters incorporated into proliferating mammalian cells is examined. In general, the reference radiation plays a key role in obtaining experimental RBE values. Using survival of cultured Chinese hamster V79 cells as the experimental model, new data are provided regarding selection of a reference radiation for internal Auger emitters. These data show that gamma rays delivered acutely (137Cs) are more than twice as lethal as gamma rays delivered chronically with an exponentially decreasing dose rate (99mTc). The results confirm that the reference radiation should be delivered chronically in a manner consistent with the extended exposure received by the cells in the case of incorporated radionuclides. Through a direct comparison of the radiotoxicity of Auger emitters and alpha emitters, the high RBE values reported for DNA-bound Auger emitters are confirmed. These studies reveal that the DNA binding compound [125I]iododeoxyuridine (125IdU) is about 1.6 times more effective in killing V79 cells than 5.3 MeV alpha particles from intracellularly localized 210Po-citrate. In addition, toxicity studies with the radiochemicals 125IdU and [125]-iododeoxycytidine (125IdC) establish the equivalence of the radiosensitivity of thymine and cytosine base sites in the DNA. In view of these results, and information already available, the question of establishing quality factors for Auger emitters is considered. Finally, a method for calculation of the dose equivalent for internal Auger emitters is advanced.     

Digestive enzymes of three teleost fishes.

The activity of amylase, sucrase, protease and lipase has been examined in Wallago attu, Clarias batrachus and Labeo rohita. The optimum pH value for carbohydrases ranges from 5.0 to 7.0 and that for trypsin between pH 6.8 and 7.8. Lipase is active at a slightly more alkaline medium. The optimum pH for a given enzyme varies in different sections of the alimentary canal of the same fish and also from species to species. Variations are also found in the optimum substrate concentration for a given enzyme in the different sections of the alimentary canal. The activity of carbohydrases is higher in the herbivorous fish Labeo, than in the carnivorous fish Wallago, and the omnivorous fish Clarias. As for protease, maximum activity is found in Wallago. The difference is not so well marked for the activity of lipase. There is a correlation between the normal diet of the fishes and the relative activity of the digestive enzymes.     

A specific effect of copper on methylene blue sensitized photodegradation of nucleic acid derivatives

Among several metal ions tested, Cu²⁺ was unique in slowing down methylene blue sensitized photodynamic breakdown of some nucleic acid bases and nucleosides. The t_1/2 values were increased in the case of xanthine and uric acid by Cu²⁺, but without any alteration in the nature or amounts of photoproducts formed. Xanthine was degraded quantitatively to allantoin and urea. The breakdown of the sugar moiety of nucleosides was more drastically retarded than that of the purine ring. The decomposition rate and its magnitude was dependent on the concentration of Cu²⁺ as well as the nucleoside. The most profound increase in t_1/2 values was found with xanthosine—7 min for the purine ring and 65 min for the ribose moiety, at 0.6 mM Cu²⁺ Hg²⁺ in the case of xanthine, and some paramagnetic metal ions in the case of the nucleosides, slowed down the photobreakdown to a small extent; however, differential effects were not observed unlike with Cu²⁺. None of the other metal ions tested significantly influenced the process.