Probing Native Protein Structures by Chemical Cross-linking, Mass Spectrometry, and Bioinformatics

Chemical cross-linking of reactive groups in native proteins and protein complexes in combination with the identification of cross-linked sites by mass spectrometry has been in use for more than a decade. Recent advances in instrumentation, cross-linking protocols, and analysis software have led to a renewed interest in this technique, which promises to provide important information about native protein structure and the topology of protein complexes. In this article, we discuss the critical steps of chemical cross-linking and its implications for (structural) biology: reagent design and cross-linking protocols, separation and mass spectrometric analysis of cross-linked samples, dedicated software for data analysis, and the use of cross-linking data for computational modeling. Finally, the impact of protein cross-linking on various biological disciplines is highlighted.The concept of protein cross-linking as a (bio)chemical tool to infer structural information about protein conformations and protein-protein interactions in combination with mass spectrometry was introduced at the end of the 1990s (1). In a seminal paper, Young et al. (1) used chemical cross-linking of lysine residues in bovine basic fibroblast growth factor FGF-2 (heparin-binding growth factor 2) to provide distance constraints for the computational derivation of the fold of this small (17-kDa) protein. FGF-2 was cross-linked with bis(sulfosuccinimidyl) suberate, purified by size exclusion chromatography, and digested with trypsin. Cross-linked peptides were separated by HPLC and analyzed on line by ESI-TOF and off line by MALDI-TOF mass spectrometry. Putative cross-links were then assigned based on their precursor masses, and some of them were verified by MALDI postsource decay. The authors could identify 15 cross-links that did not bridge directly adjacent lysines and therefore provided information on the three-dimensional structure of the protein. These data were used to assign FGF-2 to the β-trefoil family by excluding calculated models that did not fit the distance constraints.In the last decade, the application of protein cross-linking has expanded, first and foremost driven by developments in mass spectrometry as the method of choice for the high throughput identification of proteins and their modifications. Reviews by Back et al. (2), Sinz (3), and most recently Lee (4) give an overview on the evolution of the field. However, despite the progress that has undoubtedly been made, cross-linking is still considered a “niche” technique that has not (yet) lived up to its promises. High throughput generation of data supporting protein fold prediction and the determination of protein-protein interactions have not been realized routinely. There may be several reasons for that such as the necessity of access to high end mass spectrometers, the requirement of specialized reagents, and the need for tailored software. However, recent years have seen an increased interest in this technique, which is reflected in the literature and by the emergence of new reagents and software tools.Here, we present an overview of recent developments in methodology, instrumentation, and bioinformatics related to chemical cross-linking of proteins and the analysis of cross-linked peptides by mass spectrometry. Other cross-linking areas such as protein-DNA cross-linking, photoinduced cross-linking, or the characterization of disulfide bonds will not be covered in detail in this paper. We critically discuss advantages and limitations of different concepts and look beyond the immediate outcome of cross-linking experiments (putative interactions and/or distance constraints) and examine the potential role of chemical cross-linking in the analysis of protein interaction networks and, more generally, for structural and systems biology.     

Oligonucleotide-Mediated Au–Ag Core–Shell Nanoparticles

The bimetallic core–shell nanoparticles show unique plasmonic properties and their preparations and characterizations are currently under investigation. A new type of Au core–Ag shell (Au@Ag) nanoparticles is prepared by sandwiching the chemically attached Raman reporter molecules (RRMs) and a 12-base-long oligonucleotide between the 13 nm average size core-gold nanoparticles (AuNPs) and 9 nm and 21 nm average size of Ag shell. The synthesized Au@Ag nanoparticles are tested for their surface-enhanced Raman scattering (SERS) performance. It is found that the chemical attachment of the oligonucleotides along with the RRM improved the enhancement in Raman scattering more than one order of the magnitude with the Au@Ag nanoparticles with an average 9-nm shell thickness while the Au@Ag nanoparticles with 21 nm average shell thickness have poor SERS activity. A minimum enhancement factor of 1.0 × 10⁷ is estimated for the SERS active oligonucleotide-mediated Au@Ag nanoparticles. The approach may provide new routes for preparation of highly sensitive new generation of bimetallic core–shell nanoparticles.     

Biosorption of Copper(II) by Live and Dried Biomass of the White Rot Fungi Phanerochaete chrysosporium and Funalia trogii

Biosorption is an innovative and alternative technology to remove heavy metal pollutants from aqueous solution using live, inactive and dead biomasses such as algae, bacteria and fungi. In this study, live and dried biomass of Phanerochaete chrysosporium and Funalia trogii was applied as heavy metal adsorbent material. Biosorption of copper(II) cations in aqueous solution by live and dried biomass of Phanerochaete chrysosporium and Funalia trogii was investigated to study the effects of initial heavy metal concentration, pH, temperature, contact time, agitation rate and amount of fungus. Copper(II) was taken up quickly by fungal biomass (live or dried) during the first 15 min and the most important factor which affected the copper adsorption by live and dried biomass was the pH value. An initial pH of around 5.0 allowed for an optimum adsorption performance. Live biomass of two white rot fungi showed a high copper adsorption capacity compared with dried biomass. Copper(II) uptake was found to be independent of temperature in the range of 20–45 °C. The initial metal ion concentration (10–300 mg/L) significantly influenced the biosorption capacity of these fungi. The results indicate that a biosorption as high as 40–60 % by live and dried biomass can be obtained under optimum conditions.     

From refugia to contact: Pine processionary moth hybrid zone in a complex biogeographic setting

Contact zones occur at the crossroad between specific dispersal routes and are facilitated by biogeographic discontinuities. Here, we focused on two Lepidoptera sister species that come in contact near the Turkish Straits System (TSS). We aimed to infer their phylogeographic histories in the Eastern Mediterranean and finely analyze their co‐occurrence and hybridization patterns in this biogeographic context. We used molecular mitochondrial and nuclear markers to study 224 individuals from 42 localities. We used discordances between markers and complementary assignment methods to identify and map hybrids and parental individuals. We confirmed the parapatric distribution of Thaumetopoea pityocampa (Lepidoptera: Notodontidae) in the west and Thaumetopoea wilkinsoni in the east and identified a narrow contact zone. We identified several glacial refugia of T. wilkinsoni in southern Turkey with a strong east–west differentiation in this species. Unexpectedly, T. pityocampa crossed the TSS and occur in northern Aegean Turkey and some eastern Greek islands. We found robust evidence of introgression between the two species in a restricted zone in northwestern Turkey, but we did not identify any F₁ individuals. The identified hybrid zone was mostly bimodal. The distributions and genetic patterns of the studied species were strongly influenced both by the Quaternary climatic oscillations and the complex geological history of the Aegean region. T. pityocampa and T. wilkinsoni survived the last glacial maximum in disjoint refugia and met in western Turkey at the edge of the recolonization routes. Expanding population of T. wilkinsoni constrained T. pityocampa to the western Turkish shore. Additionally, we found evidence of recurrent introgression by T. wilkinsoni males in several T. pityocampa populations. Our results suggest that some prezygotic isolation mechanisms, such as differences in timing of the adult emergences, might be a driver of the isolation between the sister species.     

Derivation,characterization and expansion of fetal chondrocytes on different microcarriers

Fetal chondrocytes (FCs) have recently been identified as an alternative cell source for cartilage tissue engineering applications because of their partially chondrogenically differentiated phenotype and developmental plasticity. In this study, chondrocytes derived from fetal bovine cartilage were characterized and then cultured on commercially available Cytodex-1 and Biosilon microcarriers and thermosensitive poly(hydroxyethylmethacrylate)-poly(N-isopropylacrylamide) (PHEMA-PNIPAAm) beads produced by us. Growth kinetics of FCs were estimated by means of specific growth rate and metabolic activity assay. Cell detachment from thermosensitive microcarriers was induced by cold treatment at 4 °C for 20 min or enzymatic treatment was applied for the detachment of cells from Cytodex-1 and Biosilon. Although attachment efficiency and proliferation of FCs on PHEMA-PNIPAAm beads were lower than that of commercial Cytodex-1 and Biosilon microcarriers, these beads also supported growth of FCs. Detached cells from thermosensitive beads by cold induction exhibited a normal proliferative activity. Our results indicated that Cytodex-1 microcarrier was the most suitable material for the production of FCs in high capacity, however, ‘thermosensitive microcarrier model’ could be considered as an attractive solution to the process scale up for cartilage tissue engineering by improving surface characteristics of PHEMA-PNIPAAm beads.     

IMPROVED Candida methylica FORMATE DEHYDROGENASE FERMENTATION THROUGH STATISTICAL OPTIMIZATION OF LOW-COST CULTURE MEDIA

NAD⁺-dependent formate dehydrogenase (FDH, EC 1.2.1.2) is of use in the regeneration of NAD(P)H coenzymes, and therefore has strong potential for practical application in chemical and medical industries. A low-cost production of recombinant Escherichia coli (E. coli) containing FDH from Candida methylica (cmFDH) was optimized in molasses-based medium by using response surface methodology (RSM) based on central composite design (CCD). The beet molasses as a sole carbon source, (NH₄)₂HPO₄ as a nitrogen and phosphorus source, KH₂PO₄ as a buffer agent, and Mg₂SO₄ · 7H₂O as a magnesium and sulfur source were used as variables in the medium. The optimum medium composition was found to be 34.694 g L^?1 of reducing sugar (equivalent to molasses solution), 8.536 g L^?1 of (NH₄)₂HPO₄, 3.073 g L^?1 of KH₂PO₄, and 1.707 g L^?1 of Mg₂SO₄ · 7H₂O. Molasses-based culture medium increased the yield of cmFDH about three times compared to LB medium. The currently developed media has the potential to be used in industrial bioprocesses with low-cost production.     

Age‐associated microRNA expression in human peripheral blood is associated with all‐cause mortality and age‐related traits

Recent studies provide evidence of correlations of DNA methylation and expression of protein‐coding genes with human aging. The relations of microRNA expression with age and age‐related clinical outcomes have not been characterized thoroughly. We explored associations of age with whole‐blood microRNA expression in 5221 adults and identified 127 microRNAs that were differentially expressed by age at P < 3.3 × 10^?4 (Bonferroni‐corrected). Most microRNAs were underexpressed in older individuals. Integrative analysis of microRNA and mRNA expression revealed changes in age‐associated mRNA expression possibly driven by age‐associated microRNAs in pathways that involve RNA processing, translation, and immune function. We fitted a linear model to predict ‘microRNA age’ that incorporated expression levels of 80 microRNAs. MicroRNA age correlated modestly with predicted age from DNA methylation (r = 0.3) and mRNA expression (r = 0.2), suggesting that microRNA age may complement mRNA and epigenetic age prediction models. We used the difference between microRNA age and chronological age as a biomarker of accelerated aging (Δage) and found that Δage was associated with all‐cause mortality (hazards ratio 1.1 per year difference, P = 4.2 × 10^?5 adjusted for sex and chronological age). Additionally, Δage was associated with coronary heart disease, hypertension, blood pressure, and glucose levels. In conclusion, we constructed a microRNA age prediction model based on whole‐blood microRNA expression profiling. Age‐associated microRNAs and their targets have potential utility to detect accelerated aging and to predict risks for age‐related diseases.     

Reproductive biology of little tunny,Euthynnus alletteratus (Rafinesque), from the north‐eastern Mediterranean Sea

The study aimed at identifying spawning season and potential year classes reaching maturity in the north‐eastern Mediterranean, an area where little information on tuna spawning is available. Gonads (60 ovaries and 36 testis) were obtained from little tunny, Euthynnus alletteratus. The fish were caught between November 2002 and May 2005 in the north‐eastern Mediterranean Sea. The ovaries were histologically examined to determine the reproductive conditions and developmental stages of oocytes. Seven females sampled in May, July, and August were sexually mature (stage III or IV). The gonado‐somatic index (GSI) indicated that spawning generally occurred between May and September. The most intensive spawning period was observed between July and August. The sex ratio was calculated as 1 : 1.7 M/F (total n = 96). The length and weight relationship was calculated with W = 0.038 L^2.77, ages from year I to IV being included in the analysis.     

Molecular and agro-morphological characterization of ancient wheat landraces of turkey

Background

Turkey is one of the important gene centers for many crop species. In this research, some ancient wheats such as tetraploid and diploid hulled wheats together with hexaploid tir wheats (Triticum aestivum ssp. leucospermum Korn.) landraces mainly adapted to harsh winter conditions of Eastern Anatolian region of Turkey were characterized at agro-morphological and molecular level. Totally 50 hulled wheat population from Kastamonu, Konya and Kayseri provinces and 15 tir wheats from Kars provinces of Turkey were in-situ collected for characterization in 2013. Some quantitative and qualitative traits of each population were determined.

Results

Twenty three hulled wheat population collected from Kastamonu province were distinguished into nine emmer and 14 einkorn wheats at morphological level. Additionally, Konya, Kayseri and Kars population were characterized as einkorn, emmer and tir wheat, respectively. Among the evaluated traits, protein ratios of hulled wheats were strikingly higher than registered cultivars. All the populations were also examined by molecular level by using fluorescently labelled 11 polymorphic SSRs primers. The primers exhibited 104 bands, ranging from 6 to 16 with a mean value 9.45 per loci. The clustering analysis separated the germplasm into two clusters which were also divided into two subclusters based on genetic similarity coefficient. Sixty-five population and five checks were analyzed to estimate mean number of alleles (N), expected and observed heterozygoties (He and Ho), polymorphism information content (PIC), Wright fix index (F), genetic deviation from Hardy-Weinberg expectation (Fit-Fis) and genetic variation (Fst) were determined as 9.45, 0.71, 0.07, 0.67, 0.90, 0.39, 0.87 and 0.39, respectively. A clear genetic deviation from Hardy – Weinberg expectation was observed among population in particular. These results showed considerable genetic variation among landraces rather than within population.

Conclusions

These molecular information has revealed genetically diverse einkorn, emmer wheat and tir wheat population could be used as parents for further breeding studies in both Turkey and abroad. Furthermore, the molecular analysis has also generally discriminated the germplasm into ploidy level.