A germacranolide from cyathocline lutea

While Cyathocline lyrata only afforded known compounds, the aerial parts of C. lutea gave a new sesquiterpene lactone, 5β-hydroxy-4,9-oxidogermacr-11-en-6,12-olide.     

How cooperative are protein folding and unfolding transitions?

A thermodynamically and kinetically simple picture of protein folding envisages only two states, native (N) and unfolded (U), separated by a single activation free energy barrier, and interconverting by cooperative two‐state transitions. The folding/unfolding transitions of many proteins occur, however, in multiple discrete steps associated with the formation of intermediates, which is indicative of reduced cooperativity. Furthermore, much advancement in experimental and computational approaches has demonstrated entirely non‐cooperative (gradual) transitions via a continuum of states and a multitude of small energetic barriers between the N and U states of some proteins. These findings have been instrumental towards providing a structural rationale for cooperative versus noncooperative transitions, based on the coupling between interaction networks in proteins. The cooperativity inherent in a folding/unfolding reaction appears to be context dependent, and can be tuned via experimental conditions which change the stabilities of N and U. The evolution of cooperativity in protein folding transitions is linked closely to the evolution of function as well as the aggregation propensity of the protein. A large activation energy barrier in a fully cooperative transition can provide the kinetic control required to prevent the accumulation of partially unfolded forms, which may promote aggregation. Nevertheless, increasing evidence for barrier‐less “downhill” folding, as well as for continuous “uphill” unfolding transitions, indicate that gradual non‐cooperative processes may be ubiquitous features on the free energy landscape of protein folding.     

Charge-mediated Fab-Fc interactions in an IgG1 antibody induce reversible self-association,cluster formation,and elevated viscosity

Concentration-dependent reversible self-association (RSA) of monoclonal antibodies (mAbs) poses a challenge to their pharmaceutical development as viable candidates for subcutaneous delivery. While the role of the antigen-binding fragment (Fab) in initiating RSA is well-established, little evidence supports the involvement of the crystallizable fragment (Fc). In this report, a variety of biophysical tools, including hydrogen exchange mass spectrometry, are used to elucidate the protein interface of such non-covalent protein-protein interactions. Using dynamic and static light scattering combined with viscosity measurements, we find that an IgG1 mAb (mAb-J) undergoes RSA primarily through electrostatic interactions and forms a monomer-dimer-tetramer equilibrium. We provide the first direct experimental mapping of the interface formed between the Fab and Fc domains of an antibody at high protein concentrations. Charge distribution heterogeneity between the positively charged interface spanning complementarity-determining regions CDR3H and CDR2L in the Fab and a negatively charged region in C_H3/Fc domain mediates the RSA of mAb-J. When arginine and NaCl are added, they disrupt RSA of mAb-J and decrease the solution viscosity. Fab-Fc domain interactions between mAb monomers may promote the formation of large transient antibody complexes that ultimately cause increases in solution viscosity. Our findings illustrate how limited specific arrangements of amino-acid residues can cause mAbs to undergo RSA at high protein concentrations and how conserved regions in the Fc portion of the antibody can also play an important role in initiating weak and transient protein-protein interactions.     

SecB-Mediated Protein Export Need Not Occur via Kinetic Partitioning

In Escherichia coli, the cytosolic chaperone SecB is responsible for the selective entry of a subset of precursor proteins into the Sec pathway. In vitro, SecB binds to a variety of unfolded substrates without apparent sequence specificity, but not native proteins. Selectivity has therefore been suggested to occur by kinetic partitioning of substrates between protein folding and SecB association. Evidence for kinetic partitioning is based on earlier observations that SecB blocks the refolding of the precursor form of maltose-binding protein (preMBP)⁵ and slow-folding maltose-binding protein (MBP) mutants, but not faster-folding mature wild-type MBP. In order to quantitatively validate the kinetic partitioning model, we have independently measured each of the rate constants involved in the interaction of SecB with refolding preMBP (a physiological substrate of SecB) and mature MBP. The measured rate constants correctly predict substrate folding kinetics over a wide range of SecB, MBP, and preMBP concentrations. Analysis of the data reveals that, for many substrates, kinetic partitioning is unlikely to be responsible for SecB-mediated protein export. Instead, the ability of SecB-bound substrates to continue folding while bound to SecB and their ability to interact with other components of the secretory machinery such as SecA may be key opposing determinants that inhibit and promote protein export, respectively.     

Development of the Structural Core and of Conformational Heterogeneity during the Conversion of Oligomers of the Mouse Prion Protein to Worm-like Amyloid Fibrils

Understanding how structure develops during the course of amyloid fibril formation by the prion protein is important for understanding prion diseases. Determining how conformational heterogeneity manifests itself in the fibrillar and pre-fibrillar amyloid aggregates is critical for understanding prion strain phenotypes. In this study, the formation of worm-like amyloid fibrils by the mouse prion protein has been characterized structurally by hydrogen-deuterium exchange coupled to mass spectrometry. The structural cores of these fibrils and of the oligomer on the direct pathway of amyloid fibril formation have been defined, showing how structure develops during fibril formation. The structural core of the oligomer not on the direct pathway has also been defined, allowing the delineation of the structural features that make this off-pathway oligomer incompetent to directly form fibrils. Sequence segments that exhibit multiple local conformations in the three amyloid aggregates have been identified, and the development of structural heterogeneity during fibril formation has been characterized. It is shown that conformational heterogeneity is not restricted to only the C-terminal domain region, which forms the structural core of the aggregates; it manifests itself in the N-terminal domain of the protein as well. Importantly, all three amyloid aggregates are shown to be capable of disrupting lipid membrane structure, pointing to a mechanism by which they may be toxic.     

Deinococcus mumbaiensis sp. nov., a radiation-resistant pleomorphic bacterium isolated from Mumbai, India

A radiation-resistant, Gram-negative and pleomorphic bacterium (CON-1) was isolated from a contaminated tryptone glucose yeast extract agar plate in the laboratory. It was red pigmented, nonmotile, nonsporulating, and aerobic, and contained MK-8 as respiratory quinone. The cell wall of this bacterium contained ornithine. The major fatty acids were C16:0, C16:1, C17:0, C18:1 and iso C18:0. The DNA of CON-1 had a G+C content of 70 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that CON-1 exhibited a maximum similarity (94.72%) with Deinococcus grandis. Based on the genotypic, phenotypic and chemotaxonomic characteristics, the bacterium CON-1 was identified as a new species of the genus Deinococcus, for which the name Deinococcus mumbaiensis sp. nov. is proposed. The type strain of D. mumbaiensis is CON-1 (MTCC 7297(T)=DSM 17424(T)).     

Effect of salt stress on cucumber: Na+–K+ ratio, osmolyte concentration, phenols and chlorophyll content

A pot experiment with 17 diverse genotypes of cucumber with four levels of salt stress viz., 0, 2, 4 and 6 dS m^?1 was carried out during 2006. ANOVA revealed significant differences amongst genotypes and genotype × salt stress interaction indicating the genetic variability and differential response of the genotypes to different salt stress levels. The salt stress adversely affected the biochemical parameters; effects were severe under 4 dS m^?1. No genotype could survive at 6 dS m^?1. Sodium content, Na⁺–K⁺ ratio, proline, reducing sugars, phenol and yield reduction (%) increased significantly as the salt stress increased. Potassium, chlorophyll, membrane stability index and fruit yield decreased significantly under salt stress in all genotypes. However, the genotypes CRC-8, CHC-2 and G-338 showed lower accumulation of sodium, lesser depletion of potassium, lower Na⁺–K⁺ ratio and higher accumulation of proline, reducing sugars, phenols, better membrane stability and lower yield reduction (%) under salt stress, while CH-20 and DC-1 were sensitive to salt stress. Thus, a combination of traits such as higher membrane stability, lower Na⁺–K⁺ ratio, higher osmotic concentration and selective uptake of useful ions and prevention of over accumulation of toxic ions contribute to salt stress tolerance in cucumber. These traits would be useful selection criteria during salt stress breeding in cucumber.     

Effect of Long-term Fluoride Exposure on Growth, Nutrient Utilization and Fluoride Kinetics of Calves Fed Graded Levels of Dietary Protein

In order to assess the influence of dietary protein levels on the fluoride (F) bioavailability, 30 crossbred calves (6-8 months; approximately 104 kg BW) initially exposed to different dietary protein levels were allotted into six groups in a 3?×?2 factorial design. The factors included three different levels of protein viz. normal (100%; NP), low (75%; LP), and high (125%; HP) as per Kearl recommendations besides two levels of supplemental fluorine (as sodium fluoride) at 0 or 200 mg/kg diet. The animals were fed on the respective concentrate mixture and wheat straw for 210 days. A metabolism trial was conducted at 200 days post-feeding to study digestibility, plane of nutrition, and nutrient balances. The final body weight at the end of 210 days was lower (p?<?0.01) in animals fed 200 mg/kg F (164.2?±?8.92 kg) compared to those fed no F (200.7?±?8.05 kg). Calves on LP diets attained lower (p?<?0.05) average daily gain in comparison to NP or HP fed calves. The F-supplemented calves exhibited lower (p?<?0.01) voluntary feed intake than their non-supplemented control. The digestibility of proximate nutrients other than ether extract exhibited higher (p?<?0.01) values in F-fed calves attributable chiefly to reduced consumption of dry matter. The calves fed extra F retained lower mean daily nitrogen; calcium, and phosphorus compared to the calves fed no F. The mean daily intake, excretion, and retention of F were higher (p?<?0.01) in the F-supplemented calves. A significant (p?<?0.01) interaction between protein levels and F was evident in the urinary excretion of F; calves on LP diet exhibiting lower urinary excretion. Consequently, the bioavailability of F tended to be higher on LP than NP or HP diets. From the results, it is concluded that protein levels in the diet do not impart significant influence on susceptibility to fluorosis in crossbred calves. However, the bioavailability of F tended to increase on diets low in protein.