The disulfide bridge pattern of snake venom disintegrins, flavoridin and echistatin.

Flavoridin and echistatin, isolated from the venom of Trimeresurus flavoviridis and Echis carinatus, respectively, belong to the disintegrin family of integrin beta 1 and beta 3 inhibitors of low molecular weight RGD-containing, cysteine-rich peptides. Since disulfide bonds are critical for expression of biological activity, we sought to determine their location in these two proteins. In flavoridin, direct evidence for the existence of linkage between Cys4-Cys19 and between Cys45 and Cys64 was obtained by analysis of proteolytic products, and indirect evidence suggests links between Cys6-Cys14 and Cys13-Cys36. In echistatin, links between Cys8-Cys37 and Cys20-Cys39 were identified by direct chemical analysis.     

Quantitation of model digestive mixtures by 13C NMR.

13C nuclear magnetic resonance (NMR) spectra were obtained at 50.3 and 100.5 MHz for methanolic and aqueous mixtures of sodium taurocholate, 1-monocapryloyl-rac-glycerol, and caprylic acid. Distortionless Enhancement by Polarization Transfer (DEPT) was used to improve spectral sensitivity and resolution, and to generate calibration curves for quantitative determinations of each lipid in methanol. Alternatively, the heights for nonoverlapping peaks in a 13C NMR spectrum acquired with inverse-gated decoupling provide reliable quantitative estimates for each component of the mixture, particularly when the data are obtained in methanol. These experiments also demonstrate the feasibility of detailed NMR structural investigations in model systems for glyceride digestion.     

Triterpenoid saponins from Clinopodium polycephalum.

A new triterpenoid saponin, clinopodiside A, has been isolated from Clinopodium polycephalum. Its structure was established by spectroscopic methods and X-ray diffraction analysis as 3-O-beta-D-glucopyranosyl(1----6)-[ beta-D-glucopyranosyl (1----4)]-beta-D-glucopyranosyl-olean-11,13(18)-diene-3 beta,16 beta, 23,28-tetrol.     

The dilemma of negative analysis of variance estimators of intraclass correlation

Summary At least two common practices exist when a negative variance component estimate is obtained, either setting it to zero or not reporting the estimate. The consequences of these practices are investigated in the context of the intraclass correlation estimation in terms of bias, variance and mean squared error (MSE). For the one-way analysis of variance random effects model and its extension to the common correlation model, we compare five estimators: analysis of variance (ANOVA), concentrated ANOVA, truncated ANOVA and two maximum likelihood-like (ML) estimators. For the balanced case, the exact bias and MSE are calculated via numerical integration of the exact sample distributions, while a Monte Carlo simulation study is conducted for the unbalanced case. The results indicate that the ANOVA estimator performs well except for designs with family size n = 2. The two ML estimators are generally poor, and the concentrated and truncated ANOVA estimators have some advantages over the ANOVA in terms of MSE. However, the large biases may make the concentrated and truncated ANOVA estimators objectionable when intraclass correlation () is small. Bias should be a concern when a pooled estimate is obtained from the literature since <0.05 in many genetic studies.     

A fluorometric study with 1-anilinonaphthalene-8-sulfonic acid (ANS) of the interactions of ATP and ADP with rubisco activase

The interactions of ATP and ADP with rubisco activase purified from spinach were investigated by measuring enhanced fluorescence due to ANS-binding to the protein. Evidence of conformational changes was observed from the differences in the interaction of ANS with rubisco activase in the presence of excess ATP and ADP. Fluorescent changes associated with the titration of a rubisco activase-ANS mixture with ATP and ADP indicated that the binding of ADP to rubisco activase was much tighter than that of ATP. The concentration of Mg2+ and pH had significant effects on the affinities of rubisco activase for ATP and ADP, with higher pH and Mg2+ concentration facilitating the binding of ATP to rubisco activase in the presence of ADP. The physiological implications of the binding characteristics of ATP and ADP with rubisco activase on the light-dark regulation of rubisco are discussed.     

Strategies for reducing solvent toxicity in extractive fermentations

The toxicity of an Alamine 336/oleyl-alcohol extraction system on Lactobacillus delbrueckii was investigated. It was shown that the solvent affected the cells through the water-soluble portion and the immiscible portion of the solvent. While immobilization significantly protected the cells from the immiscible solvent phase, the water-soluble part of the solvent still caused toxicity to the microorganisms due to diffusion of the solvent into the matrix. Adding soybean oil to the kappa-carrageenan matrix could trap the diffusing solvent molecules, and therefore reduce the toxic effect from the water soluble portion of the solvent. The protective ability of soybean oil was quantified through mathematical modeling and experimentation.     

Binding of the antitumor drug nogalamycin and its derivatives to DNA: structural comparison

The three-dimensional molecular structures of the complexes between a novel antitumor drug nogalamycin and its derivative U-58872 with a modified DNA hexamer d[m5CGT(pS)Am5CG] have been determined at 1.7- and 1.8-A resolution, respectively, by X-ray diffraction analyses. Both structures (in space group P6(1)) have been refined with constrained refinement procedure to final R factors of 0.208 (3386 reflections) and 0.196 (2143 reflections). In both complexes, two nogalamycins bind to the DNA hexamer double helix in a 2:1 ratio with the elongated aglycon chromophore intercalated between the CpG steps at both ends of the helix. The aglycon chromophore spans across the GC Watson-Crick base pairs with its nogalose lying in the minor groove and the aminoglucose lying in the major groove of the distorted B-DNA double helix. Most of the sugars remain in the C2'-endo pucker family, except three deoxycytidine residues (terminal C1, C7, and internal C5). All nucleotides are in the anti conformation. Specific hydrogen bonds are found in the complex between the drug and guanine-cytosine bases in both grooves of the helix. One hydroxyl group of the aminoglucose donates a hydrogen bond to the N7 of guanine, while the other receives a hydrogen bond from the N4 amino group of cytosine. The orientation of these two hydrogen bonds suggests that nogalamycin prefers a GC base pair with its aglycon chromophore intercalating at the 5'-side of a guanine (between NpG), or at the 3'-side of a cytosine (between CpN) with the sugars pointing toward the GC base pair. The binding of nogalamycin to DNA requires that the base pairs in DNA open up transiently to allow the bulky sugars to go through, suggesting that nogalamycin prefers GC sequences embedded in a stretch of AT sequences.     

Differential scanning calorimetry study of mixed-chain phosphatidylcholines with a common molecular weight identical with diheptadecanoylphosphatidylcholine

To examine the thermotropic phase behavior of various mixed-chain phosphatidylcholines in excess water and to compare it with the known behavior of identical-chain phosphatidylcholines, we have carried out high-resolution differential scanning calorimetric (DSC) studies on aqueous dispersions of 10 different mixed-chain phosphatidylcholines. These lipids, C(16):C(18)PC, C(18):C(16)PC, C(15):C(19)PC, C(19):C(15)PC, C(14):C(20)PC, C(20):C(14)PC, C(13):C(21)PC, C(21):C(13)PC, C(12):C(22)PC, and C(22):C(12)PC, have a common molecular weight which is the same as that of C(17):C(17)PC, an identical-chain phosphatidylcholine with a molecular weight of 762.2. When the values of any of the thermodynamic parameters (Tm, delta H, and delta S) of the mixed-chain phosphatidylcholines and C(17):C(17)PC are plotted against the normalized chain-length difference (delta C/CL), a linear function with negative slope is obtained provided that the value of delta C/CL is within the range of 0.09-0.4. The linear relationship suggests that these mixed-chain phospholipids are packed in the gel-state bilayer similar to the bilayer structure of C(17):C(17)PC at T less than Tm; however, the negative slope suggests that the conformational statistics of the hydrocarbon chain and the lateral lipid-lipid interactions of these phosphatidylcholines in the gel-state bilayer are perturbed proportionally by a progressive increase in the chain-length inequivalence between the two acyl chains within each lipid molecule. When the value of delta C/CL for mixed-chain phosphatidylcholines reaches the range of 0.44-0.55, the thermotropic phase behavior deviates markedly from that of less asymmetric phosphatidylcholines, suggesting that these highly asymmetric lipids are packed into mixed interdigitated bilayers at T less than Tm. The heating and cooling pathways of aqueous dispersions prepared from the 10 mixed-chain phospholipids are also discussed.