Denaturation studies reveal significant differences between GFP and blue fluorescent protein

Green fluorescent protein (GFP) is an unusually stable fluorescent protein that belongs to a family of related auto-fluorescent proteins (AFPs). These AFPs have been generated from jellyfish GFP by mutating the amino acids in the chromophore or its vicinity. Variants that emit light in the blue region (Blue Fluorescent Protein, BFP), red region, or yellow region are readily available and are widely used in diverse applications. Previously, we had used fluorescence spectroscopy to study the effect of pH on the denaturation of GFP with SDS, urea, and heat. Surprisingly, we found that SDS, urea or heat, did not have any significant effect on the fluorescence of GFP at pH 7.5 or 8.5, however, at pH 6.5, the protein lost all fluorescence within a very short period of time. These results suggested that GFP undergoes a structural/stability shift between pH 6.5 and 7.5, with the GFP structure at pH 6.5 being very sensitive to denaturation by SDS, urea, and heat. In the present study, we wanted to explore whether the stability or structure of the closely related BFP is also pH dependent. As expected, we found heat-induced denaturation and renaturation of BFP to be pH dependent, very much like GFP. However, when exposed to other denaturants like urea/heat or SDS we found BFP to behave very differently than GFP. Unlike GFP, which at pH 8.5 and 7.5 is very resistant to SDS-induced denaturation, BFP readily lost about 20% of its fluorescence at pH 8.5 and about 60% fluorescence at pH 7.5. Also, our denaturation and renaturation studies show that under certain conditions, BFP is more stable than GFP, such that under conditions where GFP is completely denatured, BFP still retained significant fluorescence. Taken together, our preliminary results show that despite being very similar in both amino acid sequences and overall structures, there may be subtle and important structural/conformational differences between BFP and GFP.     

Structure–function relationships in A and B granules from wheat starches of similar amylose content

Five wheat (Triticum aestivum L.) starches, from the varieties Sunco, Sunsoft, SM1118, and SM1028, with similar amylose content, and a waxy wheat were separated into large (A) and small (B) granules. The unfractionated starches, and isolated A and B granules, were characterized structurally and evaluated for their functional properties. The amylopectin chain length distribution revealed that A granules had a lower proportion of short chains with degree of polymerization (DP) 6-12 and a higher proportion of chains with DP 25-36 than B granules. X-ray diffraction (XRD) patterns showed predominantly A-type crystallinity for all of the starches. No differences in the crystallinity were found between unfractionated, A and B granules. Small-angle X-ray scattering (SAXS) patterns of the starches at 55% hydration showed that the lamellar repeat distance in A granules was larger than that of B granules for all the starches examined. However, the lamellar distances of both A and B granules from the waxy wheat were smaller than those of Sunco, Sunsoft, SM1118 and SM1028 starches. The swelling power of the B granules was greater than that of A granules from all five starches. The kinetics of digestion of A and B granules with α-amylase in vitro were complex, with B granules initially digested to a greater extent than A granules. After 4 h of incubation, A granules showed greater digestibility than B granules, except in the case of waxy starch where unfractionated and fractionated granules had similar in vitro digestibility. Correlations between structural and functional parameters were more significant for the isolated A and B granules than for the unfractionated starches. This study demonstrates that A and B granules differ in structure and functionality, and that some correlations between these properties could be masked in unfractionated starches with bimodal granule size distribution.     

Structural characterization of wheat starch granules differing in amylose content and functional characteristics

Small-angle X-ray scattering (SAXS) together with several complementary techniques, such as differential scanning calorimetry and X-ray diffraction, have been employed to investigate the structural features that give diverse functional properties to wheat starches (Triticum aestivum L.) within a narrow range of enriched amylose content (36–43%). For these starches, which come from a heterogeneous genetic background, SAXS analysis of duplicate samples enabled structural information to be obtained about their lamellar architecture where differences in lamellar spacing among samples were only several tenths of nanometer. The SAXS analysis of these wheat starches with increased amylose content has shown that amylose accumulates in both crystalline and amorphous parts of the lamella. Using waxy starch as a distinctive comparison with the other samples confirmed a general trend of increasing amylose content being linked with the accumulation of defects within crystalline lamellae. We conclude that amylose content directly influences the architecture of semi-crystalline lamellae, whereas thermodynamic and functional properties are brought about by the interplay of amylose content and amylopectin architecture.     

The anti-apoptotic activity of albumin for endothelium is inhibited by advanced glycation end products restricting intramolecular movement

Human serum albumin (HSA) inhibits endothelial apoptosis in a highly specific manner. CNBr fragmentation greatly increases the effectiveness of this activity, suggesting that this type of protection is mediated by a partially cryptic albumin domain which is transiently exposed by intramolecular movement. Advanced glycation end-product (AGE) formation in HSA greatly reduces its intra-molecular movement. This study aimed to determine if this inhibits the anti-apoptotic activity of HSA, and if such inactivation could be reversed by CNBr fragmentation. HSA-AGE was prepared by incubating HSA with glucose, and assessed using the fructosamine assay, mass spectrometry, SDS-PAGE and fluorometry. Low levels of AGE in the HSA had little effect upon its anti-apoptotic activity, but when the levels of AGE were high and the intra-molecular movement was reduced, endothelial cell survival was also found to be reduced to levels equivalent to those in cultures without HSA or serum (p > 0.001). Survival was restored by the inclusion of native HSA, despite the presence of HSA with high levels of AGE. Also, CNBr fragmentation of otherwise inactive HSA-AGE restored the anti-apoptotic activity for endothelium. Apoptosis was confirmed by DNA gel electrophoresis, transmission electron microscopy and fluorescence-activated cell sorting analysis, and there was no evidence for direct toxicity in the HSA-AGE preparations. The results are consistent with the proposed role of intra-molecular movement in exposing the anti-apoptotic domain in HSA for endothelium. The levels of AGE formation required to inhibit the anti-apoptotic activity of HSA exceeded those reported for diabetes. Nonetheless, the data from this study seems to be the first example of reduced protein function due to AGE-restricted intra-molecular movement.     

Synthesis, antimycobacterial and antitumor activities of new (1,1-dioxido-3-oxo-1,2-benzisothiazol-2(3H)-yl)methyl N,N-disubstituted dithiocarbamate/O-alkyldithiocarbonate derivatives

Reaction of 2-chloromethylsaccharin with substituted potassium dithiocarbamates and substituted potassium dithiocarbonates furnished (1,1-dioxido-3-oxo-1,2-benzisothiazol-2(3H)-yl)methyl N,N-disubstituted dithiocarbamates (4-15) and (1,1-dioxido-3-oxo-1,2-benzisothiazol-2(3H)-yl)methyl O-alkyldithiocarbonates (16-20). The new derivatives were evaluated for in vitro antimycobacterial activity against Mycobacterium tuberculosis H37Rv. Compounds 4-13, 15, and 16-20 described herein showed moderate to good inhibitory activity. In particular, seven analogs 4, 5, 6, 13, and 7, 8, and 12 exhibited excellent MIC values of 1.56 and 0.78 microg/mL, respectively. Compounds 4, 5, 10, 12, 13, and 16 were selected and screened for antitumor activity. Among the tested compounds, 4 and 5 were found to be cytotoxic, especially against leukemia cell lines CCRF-CEM, HL-60(TB), RPMI-8226, and SR with log10GI50 values lower than -6.69, and against non-small cell lung cancer NCI-H522 cell line with log10GI50 values lower than -6.31. Compound 10 was cytotoxic against leukemia cell line HL-60(TB), whereas 16 displayed favorable cytotoxicity against ovarian cancer cell line OVCAR-3 with log10GI50 values of -6.31 and -7.45, respectively.     

Analysis and network representation of hotspots in protein interfaces using minimum cut trees

We propose a novel approach to analyze and visualize residue contact networks of protein interfaces by graph‐based algorithms using a minimum cut tree (mincut tree). Edges in the network are weighted according to an energy function derived from knowledge‐based potentials. The mincut tree, which is constructed from the weighted residue network, simplifies and summarizes the complex structure of the contact network by an efficient and informative representation. This representation offers a comprehensible view of critical residues and facilitates the inspection of their organization. We observed, on a nonredundant data set of 38 protein complexes with experimental hotspots that the highest degree node in the mincut tree usually corresponds to an experimental hotspot. Further, hotspots are found in a few paths in the mincut tree. In addition, we examine the organization of hotspots (hot regions) using an iterative clustering algorithm on two different case studies. We find that distinct hot regions are located on specific sites of the mincut tree and some critical residues hold these clusters together. Clustering of the interface residues provides information about the relation of hot regions with each other. Our new approach is useful at the molecular level for both identification of critical paths in the protein interfaces and extraction of hot regions by clustering of the interface residues. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Dynamic stereochemistry of rutin (vitamin P) in solution: theoretical approaches and experimental validation

Rutin, vitamin P, was extracted from Salvia macrosiphon and identified by ¹H, ¹³C, ¹H-¹H COSY, HMQC, and HMBC spectroscopy. In parallel, density functional theory (DFT) using B₃LYP functional and split-valance 6-311G∗∗ basis set has been used to optimize the structures and conformers of rutin. Also experimental and theoretical methods have been used to correlate the dependencies of ¹J, ²J, and ³J involving ¹H and ¹³C on the C5″-C6″ (ω), C6″-O6″ (θ), and C1?-O6″ (φ) torsion angles in the glycosidic moiety. New Karplus equations are proposed to assist in the structural interpretation of these couplings. ³J_HH depends mainly on the C-C (ω) torsion angle, as expected, and ²J_HH values depend on both C-C (ω) and C-O (θ) torsions. ¹J_CH values within hydroxymethyl fragments were also examined and found to depend on r_CH, which is modulated by specific bond orientation and stereoelectronic factors. In all calculations solvent effects were considered using a polarized continuum model (PCM).     

Expression of <Emphasis Type="Italic">rol</Emphasis> genes in transgenic soybean (<Emphasis Type="Italic">Glycine max</Emphasis> L.) leads to changes in plant phenotype,leaf morphology,and flowering time

Soybean (Glycine max L.) cultivar NARC-4 was transformed with constructs carrying rolA, rolB, or rolC genes, each under the control of the Cauliflower Mosaic Virus 70S promoter. Cotyledonary nodes of soybean seeds were infected with Agrobacterium tumefaciens strain LBA4404 carrying one of the three rol genes, along with nptII in the plasmid pLBR. The efficiency of the transformation varied slightly among the three constructs, with frequencies of 6, 7, and 5% for the rolA, rolB, and rolC genes, respectively, being observed. Southern blot analysis confirmed the integration of rol genes in the soybean genome with varying numbers of copies of the transgene. All transformed plants showed enhanced rooting, but the number of adventitious roots was higher for transformants carrying the rolB transgene. rolA and rolC transformants showed dwarf phenotypes, clustered branching, and variations in leaf morphology. Furthermore, these plants flowered within a short period of time and produced lower numbers of flowers. rolB transformants showed variations in phenotype, including dwarf to semi-dwarf and shrubby growth, abnormal stem growth, short internodes, variations in leaf morphology, and greenish to yellowish-green colored leaves. These plants also flowered early, but dwarf plants produced low numbers of flowers, while shrubby plants produced high numbers of flowers, but these were mostly infertile.     

In vitro antituberculosis activities of the constituents isolated from Haloxylon salicornicum

In vitro antituberculosis activities of fractions and pure compounds (1–20) including seven triterpenes, two alkaloids, two cycloheximide derivatives, two coumarins six sterol derivatives and a long chain alcohol, respectively, isolated from Haloxylon salicornicum were determined against Mycobecterium tuberculosis H37Rv. Actively growing cultures were tested by rapid colorimetric method while the stationary phase cultures were tested by drug exposure methods for bactericidal activity. The MIC values were found to be 50 μg/ml for compounds 15, 19 and 20 where as rest of the compounds invariably showed MIC value of 100 μg/ml against the logarithmic phase culture. These were compare to Isoniazid as a control drug. The compounds exhibited no activity against the stationary phase culture of M. tuberculosis H37Rv up to 200 μg/ml. Further studies are required to investigate the in vivo efficacies and activities of the compounds in combination with antimicrobials that are already being used for TB therapy.     

Mast cell fibroblastoid differentiation mediated by airway smooth muscle in asthma

Mast cell microlocalization to the airway smooth muscle (ASM) bundle is a key feature of asthma, but whether these mast cells have an altered phenotype is uncertain. In this paper, we report that in vivo, mast cells within the ASM bundle, in contrast to mast cells in the bronchial submucosa, commonly expressed fibroblast markers and the number of these cells was closely related to the degree of airway hyperresponsiveness. In vitro human lung mast cells and mast cell lines cultured with fibronectin or with primary human ASM cells acquired typical fibroblastic markers and morphology. This differentiation toward a fibroblastoid phenotype was mediated by ASM-derived extracellular matrix proteins, independent of cell adhesion molecule-1, and was attenuated by α5β1 blockade. Fibroblastoid mast cells demonstrated increased chymase expression and activation with exaggerated spontaneous histamine release. Together these data indicate that in asthma, ASM-derived extracellular matrix proteins mediate human mast cell transition to a fibroblastoid phenotype, suggesting that this may be pivotal in the development of airway dysfunction in asthma.