REFOLDdb: a new and sustainable gateway to experimental protocols for protein refolding

Background

More than 7000 papers related to “protein refolding” have been published to date, with approximately 300 reports each year during the last decade. Whilst some of these papers provide experimental protocols for protein refolding, a survey in the structural life science communities showed a necessity for a comprehensive database for refolding techniques. We therefore have developed a new resource – “REFOLDdb” that collects refolding techniques into a single, searchable repository to help researchers develop refolding protocols for proteins of interest.

Results

We based our resource on the existing REFOLD database, which has not been updated since 2009. We redesigned the data format to be more concise, allowing consistent representations among data entries compared with the original REFOLD database. The remodeled data architecture enhances the search efficiency and improves the sustainability of the database. After an exhaustive literature search we added experimental refolding protocols from reports published 2009 to early 2017. In addition to this new data, we fully converted and integrated existing REFOLD data into our new resource. REFOLDdb contains 1877 entries as of March 17^th, 2017, and is freely available at http://p4d-info.nig.ac.jp/refolddb/.

Conclusion

REFOLDdb is a unique database for the life sciences research community, providing annotated information for designing new refolding protocols and customizing existing methodologies. We envisage that this resource will find wide utility across broad disciplines that rely on the production of pure, active, recombinant proteins. Furthermore, the database also provides a useful overview of the recent trends and statistics in refolding technology development.

     

MODBASE, a database of annotated comparative protein structure models

MODBASE (http://guitar.rockefeller.edu/modbase) is a relational database of annotated comparative protein structure models for all available protein sequences matched to at least one known protein structure. The models are calculated by MODPIPE, an automated modeling pipeline that relies on PSI-BLAST, IMPALA and MODELLER. MODBASE uses the MySQL relational database management system for flexible and efficient querying, and the MODVIEW Netscape plugin for viewing and manipulating multiple sequences and structures. It is updated regularly to reflect the growth of the protein sequence and structure databases, as well as improvements in the software for calculating the models. For ease of access, MODBASE is organized into different datasets. The largest dataset contains models for domains in 304 517 out of 539 171 unique protein sequences in the complete TrEMBL database (23 March 2001); only models based on significant alignments (PSI-BLAST E-value < 10^–4) and models assessed to have the correct fold are included. Other datasets include models for target selection and structure-based annotation by the New York Structural Genomics Research Consortium, models for prediction of genes in the Drosophila melanogaster genome, models for structure determination of several ribosomal particles and models calculated by the MODWEB comparative modeling web server.     

Toxicity of three acaricides to Tetranychus urticae (Tetranychidae: Acari) and Orius insidiosus (Anthocoridae: Hemiptera)

Management for twospotted spider mite, Tetranychus urticae Koch, populations in peanut, Arachis hypogaea L., relies on acaricides. The outcomes of acaricide applications are most predictable when complete information on their toxicity and specificity is available. Specifically, the degrees to which acaricides impact different stages of T. urticae and natural enemies combined determine the overall efficacy of an acaricide application. The objectives of this study were to determine stage-specific direct and residual efficacies of three acaricides (fenpropathrin, etoxazole, and propargite) against T. urticae, and the direct and residual toxicity of the acaricides to Orius insidiosus (Say) adults. Direct toxicity of acaricides to T. urticae was measured on peanut cuttings. All acaricide treatments caused significant mortality to a mixed stage population of T. urticae, and mortality did not differ among the acaricides 7 d after treatment. When toxicity to eggs was tested, the proportion of eggs that hatched for all acaricide treatments was significantly lower than the control, with etoxazole and propargite causing 100% mortality. Exposure to acaricide residues caused < 30% mortality of T. urticae adults 1 and 2 d after treatment and was not significantly different from the control. Fenpropathrin and propargite caused 100% mortality and etoxazole caused > 50% mortality of O. insidious adults after direct exposure to the acaricides. Residual toxicity of acaricides to O. insidiosus adults varied but remained toxic to O. insidiosus longer than to T. urticae. Fenpropathrin had the longest residual effect on O. insidiosus adults, causing > 95% mortality after 14 d; etoxazole and propargite caused < 30% mortality after 14 d.     

Scents and scents-ability: pollution disrupts chemical social recognition and shoaling in fish

Chemical cues are of enormous importance in mediating the behaviour of animals, enabling them to navigate throughout their habitats, to detect the presence of predators or prey and for social recognition-identifying and discriminating between conspecifics. In many species of freshwater fish, social recognition is known to be based primarily on chemical cues. Such recognition mechanisms are vulnerable to disruption by the presence of anthropogenic contaminants in the aquatic environment. Here we show that acute exposure to low, environmentally relevant dosages of the ubiquitous contaminant, 4-nonylphenol, can seriously affect social recognition and ultimately social organization in fishes. A 1 hour 0.5 microgl-1 dose was sufficient to alter the response of members of a shoaling fish species (juvenile banded killifish, Fundulus diaphanus) to conspecific chemical cues. Dosages of 1-2 microgl-1 caused killifish to orient away from dosed conspecifics, in both a flow channel and an arena. Given the overall importance of shoaling as an adaptive strategy against predators and for locating food, it is likely that its disruption by anthropogenic contaminants would have serious implications for fishes' fitness.     

Parasites ofSpodoptera exigua,S. eridania [Lep.: Noctuidae] andHerpetogramma bipunctalis [Lep.: Pyralidae] collected fromAmaranthus hybridus in field corn

Three species of lepidopterous larvae were collected fromAmaranthus hybridus L. growing in field corn during 1975 and 1976 at Hastings, Florida.Spodoptera exigua (Hubner) was the predominant species in May.Spodoptera eridania (Cramer) was predominant in June andHerpetogramma bipunctalis (F.) in July and August. Nine native species of parasites, representing theBraconidae, Eulophidae, Ichneumonidae andTachinidae, emerged from these larvae.Meteorus autographae Muesebeck emerged from bothS. exigua andS. eridania. TheTachinidae, Winthemia rufopicta (Bigot),Eucelatori rubentis (Coquillett) andLespensia sp., emerged from mixtures ofS. exigua andS. eridania. Apanteles marginiventris (Cresson),Temelucha sp., andChelonus texanus Cresson emerged from bothS. exigua andH. bipunctalis larvae, andEuplectrus platyhypenae Howard andOphion sp. emerged fromS. eridania. All the species of parasites from the lepidopterous larvae that feed onAmaranthus hybridus are also reported as parasites ofS. frugiperda, a serious pest of corn. Therefore these larvae onA. hybridus may be a source of the parasites found attackingS. frugiperda.     

Identification of the NADH-NAD+ transhydrogenase peptide of the mitochondrial NADH-CoQ reductase (Complex I). A photodependent labeling study utilizing arylazido-beta-alanyl NAD+

Incubation of Complex I (NADH-CoQ reductase) of ox heart mitochondria at 4 degrees C in the presence of 0.5 M NaClO4 followed by ammonium sulfate fractionation of the solubilized proteins results in the isolation of a resolved preparation still capable of catalyzing NADH-NAD+ transhydrogenation but having only low levels of NADH dehydrogenase activity. A number of NAD(H) analogues, including the photoaffinity probes, arylazido-beta-alanyl NAD+ (A3'-O-[3-[N-(4-azido-2-nitrophenyl)amino]propionyl]NAD+ and arylazido-beta-alanyl AcPyAD+ (A3'-O-[3-[N-(4-azido-2-nitrophenyl)amino]propionyl]AcPyAD+ can be utilized as substrates for transhydrogenation in this preparation. A further incubation (10 min) of the resolved NADH-NAD+ transhydrogenase in the presence of 0.5 M NaClO4, but now at 30 degrees C, results in the complete loss of this transhydrogenase activity. Photoaffinity labeling experiments utilizing arylazido-[3-3H]beta-alanyl NAD+ and arylazido-[3-3H]beta-alanyl AcPyAD+ with the resolved NADH-NAD+ transhydrogenase preparation prior to and following NaClO4 (30 degrees C) treatment indicates that the 42,000 molecular weight component of Complex I is the pyridine nucleotide binding site responsible for the major NADH-NAD+ (DD) transhydrogenase activity of Complex I.     

Acute activation of de novo sphingolipid biosynthesis upon heat shock causes an accumulation of ceramide and subsequent dephosphorylation of SR proteins

Recent studies are beginning to implicate sphingolipids in the heat stress response. In the yeast Saccharomyces cerevisiae, heat stress has been shown to activate de novo biosynthesis of sphingolipids, whereas in mammalian cells the sphingolipid ceramide has been implicated in the heat shock responses. In the current study, we found an increase in the ceramide mass of Molt-4 cells in response to heat shock, corroborating findings in HL-60 cells. Increased ceramide was determined to be from de novo biosynthesis by two major lines of evidence. First, the accumulation of ceramide was dependent upon the activities of both ceramide synthase and serine palmitoyltransferase. Second, pulse labeling studies demonstrated increased production of ceramide through the de novo biosynthetic pathway. Significantly, the de novo sphingolipid biosynthetic pathway was acutely induced upon heat shock, which resulted in a 2-fold increased flux in newly made ceramides within 1-2 min of exposure to 42.5 degrees C. Functionally, heat shock induced the dephosphorylation of the SR proteins, and this effect was demonstrated to be dependent upon the accumulation of de novo-produced ceramides. Thus, these studies disclose an evolutionary conserved activation of the de novo pathway in response to heat shock. Moreover, SR dephosphorylation is emerging as a specific downstream target of accumulation of newly made ceramides in mammalian cells.     

A modified two-step phage display selection for isolation of polycystin-1 ligands

The identification of proteins that interact with polycystin-1, the product of the autosomal dominant polycystic kidney disease gene, is an important step towards understanding the molecular pathogenesis of the disease. We have developed a two-step approach for the efficient identification of potential polycystin-1 ligands using the T7 phage display system. The first enrichment step of 4–5 rounds of biopanning is followed by a second step of reverse protein overlay assay. Thus, the sequencing efforts are minimized to the analysis of only positive rather than randomly chosen clones from the enriched population as in the standard phage display approach. Most importantly, the modified approach immediately provides the confirmation of the specificity of interaction and discriminates between strong and weak interactions. Here we present several potential interactors with distinct regions of polycystin-1, representing high-affinity binding partners. Electronic Publication     

Subsurface hydrology and degree of burial affect mass loss and invertebrate colonisation of leaves in a woodland stream

SUMMARY 1. In deciduous forest streams, fallen leaves form a large component of the total organic matter budget, and many leaves become buried within stream sediments. We examined the processing of buried leaves as compared with those at the surface, and the influence of subsurface hydrology on processing rates.
2. Leaf packs were secured on the streambed surface or buried 10 cm deep in upwelling and downwelling reaches of a second-order stream in Michigan, U.S.A. Mass loss and invertebrate colonisation were measured from October to February.
3. Leaves buried in upwelling reaches lost mass more slowly (exponential decay coefficient, k =−0.0097) than did leaves from the other treatments (buried downwelling: −0.017; surface upwelling: −0.022; surface downwelling: −0.021).
4. Initially, more invertebrates colonised surface leaf packs than buried packs. During the remainder of the study, however, hydrology had a greater effect on invertebrate abundance than did burial, as more invertebrates were found in packs in downwelling reaches than in upwelling reaches.
5. Local subsurface hydrology and degree of burial, factors rarely considered in studies of detritus processing, can significantly influence mass loss and invertebrate colonisation of fallen leaves in streams. Furthermore, because of slower processing, subsurface zones may function as organic matter reservoirs that gradually 'spiral' carbon to downstream subsurface and surface habitats.