Characterization of the polyanion-induced molten globule-like state of cytochrome c

Cytochrome c (cyt c) undergoes a poly(vinylsulphate) (PVS)-induced transition at slightly acidic pH into a molten globule-like state that resembles the effect that negatively charged membrane surfaces have on this protein. In this work, the thermodynamic properties of the molten globule-like state of cyt c in complex with PVS are studied using differential scanning calorimetry, circular dichroism, fluorescence, and absorbance spectroscopy. The temperature-induced transition of the molten globule-like state of cyt c in the complex with PVS is characterized by a significantly lower calorimetric enthalpy than in the "typical" molten globule state of cyt c, i.e. free protein at pH 2.0 in high ionic strength. Moreover, the thermally-denatured state of cyt c in the complex at pH < 6 contains nearly 50% of the native secondary structure. The dependence of the transition temperature on the pH indicates a role for histidine residues in the destabilization of the cyt c structure in the PVS complex and in stabilization of the denatured state with the residual secondary structure. A comparison of the effects of small anions and polyanions demonstrates the importance of cooperativity among the anions in the destabilization of cyt c. Predictably, other hydrophilic flexible polyanions such as heparin, polyglutamate, and polyadenylate also have a destabilizing effect on the structure of cyt c. However, a correlation between the properties of the polyanions and their effect on the protein stability is still unclear.     

A kinetic comparison between E2P and the E2P-like state induced by a beryllium fluoride complex in the Na,K-ATPase. Interactions with Rb+

Metal-fluoride complexes have been used to induce E2P-like states with the aim of studying the events that occur during E2P hydrolysis in P-type ATPases. In the present work, we compared the E2P-like state induced by a beryllium fluoride complex (BeF_x) with the actual E2P state formed through backdoor phosphorylation of the Na,K-ATPase. Formation of E2P and E2P-like states were investigated employing the styryl dye RH421. We found that BeF_x is the only fluorinated phosphate analog that, like Pi, increases the RH421 fluorescence. The observed rate constant, k_obs, for the formation of E2P decreases with [Pi] whereas that of E2BeF_x increases with [BeF_x]. This might wrongly be taken as evidence of a mechanism where the binding of BeF_x induces a conformational transition. Here, we rather propose that, like for Pi, binding of BeF_x follows a conformational-selection mechanism, i.e. it binds to the E2 conformer forming a complex that is much more stable than E2P, as seen from its impaired capacity to return to E1 upon addition of Na⁺. Although E2P and E2BeF_x are able to form states with 2 occluded Rb⁺, both enzyme complexes differ in that the affinity for the binding and occlusion of the second Rb⁺ is much lower in E2BeF_x than in E2P. The higher rates of Rb⁺ occlusion and deocclusion observed for E2BeF_x, as compared to those observed for other E2P-like transition and product states suggest a more open access to the cation transport sites, supporting the idea that E2BeF_x mimics the E2P ground state.     

Protein structure prediction assisted with sparse NMR data in CASP13

CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and ¹⁵N-¹H residual dipolar coupling data, typical of that obtained for ¹⁵N,¹³C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CASP13 also assessed whether incorporation of sparse NMR data improves the accuracy of protein structure prediction relative to nonassisted regular methods. In most cases, incorporation of sparse, noisy NMR data results in models with higher accuracy. The best NMR-assisted models were also compared with the best regular predictions of any CASP13 group for the same target. For six of 13 targets, the most accurate model provided by any NMR-assisted prediction group was more accurate than the most accurate model provided by any regular prediction group; however, for the remaining seven targets, one or more regular prediction method provided a more accurate model than even the best NMR-assisted model. These results suggest a novel approach for protein structure determination, in which advanced prediction methods are first used to generate structural models, and sparse NMR data is then used to validate and/or refine these models.     

Human p38α mitogen-activated protein kinase in the Asp168-Phe169-Gly170-in (DFG-in) state can bind allosteric inhibitor Doramapimod

Doramapimod (BIRB-796) is widely recognized as one of the most potent and selective type II inhibitors of human p38α mitogen-activated protein kinase (MAPK); however, the understanding of its binding mechanism remains incomplete. Previous studies indicated high affinity of the ligand to a so-called allosteric pocket revealed only in the ‘out’ state of the DFG motif (i.e. Asp168-Phe169-Gly170) when Phe169 becomes fully exposed to the solvent. The possibility of alternative binding in the DFG-in state was hypothesized, but the molecular mechanism was not known. Methods of bioinformatics, docking and long-time scale classical and accelerated molecular dynamics have been applied to study the interaction of Doramapimod with the human p38α MAPK. It was shown that Doramapimod can bind to the protein even when the Phe169 is fully buried inside the allosteric pocket and the kinase activation loop is in the DFG-in state. Orientation of the inhibitor in such a complex is significantly different from that in the known crystallographic complex formed by the kinase in the DFG-out state; however, the Doramapimod’s binding is followed by the ligand-induced conformational changes, which finally improve accommodation of the inhibitor. Molecular modelling has confirmed that Doramapimod combines the features of type I and II inhibitors of p38α MAPK, i.e. can directly and indirectly compete with the ATP binding. It can be concluded that optimization of the initial binding in the DFG-in state and the final accommodation in the DFG-out state should be both considered at designing novel efficient type II inhibitors of MAPK and homologous proteins.

Communicated by Ramaswamy H. Sarma     

Acaricidal properties of essential oils from agro‐industrial waste products from citric fruit against Tetranychus urticae

Tetranychus urticae is a major agricultural pest with worldwide distribution that has caused considerable damage to vegetable crops in north‐eastern Brazil. The aim of the present study was to investigate the chemical and lethal/sublethal effects of essential oils from the peels of the lime (Citrus aurantiifolia), lemon (C. limon), mandarin orange (C. reticulata) and (C. reticulata × C. sinensis) as well as selected constituents (linalool, α‐terpineol, α‐pinene, β‐pinene, terpinolene and limonene) against T. urticae. The greatest yield was achieved with the mandarin and tangerine peel oils. The chemical analysis (gas chromatography‐mass spectrometry) of the essential oils from the Citrus fruit peels enabled the identification of 127 compounds, revealing a predominance of monoterpenes. Limonene was the major constituent, and α‐pinene, β‐pinene, linalool and α‐terpineol were found in substantial quantities. Regarding the susceptibility of T. urticae, the Citrus oils and selected constituents were more effective by fumigation than residual contact. The C. reticulata oil was the most toxic by fumigation, and the C. limon oil was the most toxic by residual contact. The constituent α‐terpineol exhibited the highest toxicity with both methods. At a sublethal concentration, the oils and selected constituents had significant effects on the fecundity, feeding preference and oviposition of the mite. Citrus oils and their constituents are potentially useful for the future integrated management of T. urticae due to their lethal and sublethal properties. However, further studies are needed to evaluate the action of these essential oils against non‐target organisms and determine the cost–benefit ratio for the formulation of an acaricide harvested from agro‐industrial waste from citric fruit processing activities for use in the integrated control of T. urticae.     

Carbon “quantum” dots for bioapplications

Carbon “quantum” dots or carbon dots (CDots) exploit and enhance the intrinsic photoexcited state properties and processes of small carbon nanoparticles via effective nanoparticle surface passivation by chemical functionalization with organic species. The optical properties and photoinduced redox characteristics of CDots are competitive to those of established conventional semiconductor quantum dots and also fullerenes and other carbon nanomaterials. Highlighted here are major advances in the exploration of CDots for their serving as high-performance yet nontoxic fluorescence probes for one- and multi-photon bioimaging in vitro and in vivo, and for their uniquely potent antimicrobial function to inactivate effectively and efficiently some of the toughest bacterial pathogens and viruses under visible/natural or ambient light conditions. Opportunities and challenges in the further development of the CDots platform and related technologies are discussed.     

The Characterisation of Residual Strain in Ensis siliqua Shells

1 Introduction Molluscan species exhibit a range of morphologies associated with their particular function and habitat. The razor clam (Ensis siliqua) is a bivalve mollusc, usually found in fine sands, that burrows up to depths of 20 fathoms (～36 m)[1]. The species is found in several coastal regions of the British Isles, the Norwegian Sea, the Baltic south, the Iberian Peninsula, the Mediterranean and along the Atlantic coast of Morrocco[2]. The protec- tive outer shell, which is often …     

Two calanoids,two lakes,and a decade or two. An updated record and evaluation of occurrence and periodicity of Tropodiaptomus spectabilis and Metadiaptomus meridianus (Copepoda: Calanoida), and alternative stable states in two cascading impoundments

Episodic switching between Tropodiaptomus spectabilis and Metadiaptomus meridianus in L. Midmar (29° 30 S, 30° 12 E), and transitory seasonal alternation of these taxa in L. Albert Falls (29° 26 S, 30° 26 E) recorded in comparative studies of these inter-leading reservoirs between 1989 and 1999, along with historical records for Midmar extending back to 1978, are updated and re-evaluated in light of subsequent and additional findings. In the longer term, an `exclusive' occupancy by one or another species has been maintained in these and other inter-leading impoundments on the quasi-subtropical Mgeni River. Sympatry was invariably transitional. It lasted several months in the upper Midmar system, and where protracted over several years as in the downstream Albert Falls system, was effectively negated by seasonal separation of the taxa. Possible influences of parasitism, changes in water turbidity or pH, dependent or independent of inter-basin water transfers, and such water transfers themselves, are explored and rejected as proximate causes of species replacement. Because evidence for the existence of resting eggs was contradictory (respectively present and absent in preserved and live samples), emergence from diapause is considered an unlikely source of re-colonisation. The guild complement of invertebrate planktivores is comparable in both lakes, seemingly removing predation as a determinant factor. The comparability of food thresholds for various measures of demographic performance suggests remarkable similarity in the competitive potential of these species, which additionally show considerable niche overlap in terms of adult diet, and comparable vulnerability to ellobiopsid parasitism. Ecological separation is thus limited to differentiation of thermal optima, functional feeding biology of juvenile stages – especially nauplii, and sediment tolerance. Evidence now available supports previous arguments that species separations remain attributable largely to marginal species differences in thermal optima, mirrored in the pattern of seasonal separation during an episode of sympatry (1990 to early 1994) in the down-stream Albert Falls system. While no causal explanation can be substantiated from evidence gleaned during this decade of study, the species replacements observed in Midmar appear to reflect alternative stable states, induced by presently unknown factor(s), plausibly temperature, or improbably, human translocation. By contrast, alternative stable states are not manifest in Albert Falls, wherein the longer term, T. spectabilis seemingly represents the only stable state, a feature apparently shared by other warmer reservoirs down the Mgeni cascade. The unpredictability of chaotic dynamics precludes its analysis in this situation, while conversely, the system provides a unique model for meta-population analysis, related to uni-directionality of natural dispersal. However, the cost-effectiveness of continued monitoring for unforeseeable events poses a serious practical dilemma.     

Thermodynamic stability of ribonuclease A in alkylurea solutions and preferential solvation changes accompanying its thermal denaturation: a calorimetric and spectroscopic study

The effect of methylurea, N,N'-dimethylurea, ethylurea, and butylurea as well as guanidine hydrochloride (GuHCl), urea and pH on the thermal stability, structural properties, and preferential solvation changes accompanying the thermal unfolding of ribonuclease A (RNase A) has been investigated by differential scanning calorimetry (DSC), UV, and circular dichroism (CD) spectroscopy. The results show that the thermal stability of RNase A decreases with increasing concentration of denaturants and the size of the hydrophobic group substituted on the urea molecule. From CD measurements in the near- and far-UV range, it has been observed that the tertiary structure of RNase A melts at about 3 degrees C lower temperature than its secondary structure, which means that the hierarchy in structural building blocks exists for RNase A even at conditions at which according to DSC and UV measurements the RNase A unfolding can be interpreted in terms of a two-state approximation. The far-UV CD spectra also show that the final denatured states of RNase A at high temperatures in the presence of different denaturants including 4.5 M GuHCl are similar to each other but different from the one obtained in 4.5 M GuHCl at 25 degrees C. The concentration dependence of the preferential solvation change delta r23, expressed as the number of cosolvent molecules entering or leaving the solvation shell of the protein upon denaturation and calculated from DSC data, shows the same relative denaturation efficiency of alkylureas as other methods.