G-protein-coupled receptor solubilization and purification for biophysical analysis and functional studies, in the total absence of detergent

G-protein coupled receptors (GPCRs) constitute the largest class of membrane proteins and are a major drug target. A serious obstacle to studying GPCR structure/function characteristics is the requirement to extract the receptors from their native environment in the plasma membrane, coupled with the inherent instability of GPCRs in the detergents required for their solubilization. In the present study, we report the first solubilization and purification of a functional GPCR [human adenosine A2A receptor (A2AR)], in the total absence of detergent at any stage, by exploiting spontaneous encapsulation by styrene maleic acid (SMA) co-polymer direct from the membrane into a nanoscale SMA lipid particle (SMALP). Furthermore, the A2AR-SMALP, generated from yeast (Pichia pastoris) or mammalian cells, exhibited increased thermostability (∼5°C) compared with detergent [DDM (n-dodecyl-β-D-maltopyranoside)]-solubilized A2AR controls. The A2AR-SMALP was also stable when stored for prolonged periods at 4°C and was resistant to multiple freeze-thaw cycles, in marked contrast with the detergent-solubilized receptor. These properties establish the potential for using GPCR-SMALP in receptor-based drug discovery assays. Moreover, in contrast with nanodiscs stabilized by scaffold proteins, the non-proteinaceous nature of the SMA polymer allowed unobscured biophysical characterization of the embedded receptor. Consequently, CD spectroscopy was used to relate changes in secondary structure to loss of ligand binding ([³H]ZM241385) capability. SMALP-solubilization of GPCRs, retaining the annular lipid environment, will enable a wide range of therapeutic targets to be prepared in native-like state to aid drug discovery and understanding of GPCR molecular mechanisms.

Editorial overview:new protein production tools for structural biology

Full text: The idea of producing proteins from recombinant DNA hatched almost half a century ago. In his PhD thesis, Peter Lobban foresaw the prospect of inserting foreign DNA (from any source, including mammalian cells) into the genome of a λ phage in order to detect and recover protein products from Escherichia coli [ 1 and 2]. Only a few years later, in 1977, Herbert Boyer and his colleagues succeeded in the first ever expression of a peptide-coding gene in E. coli — they produced recombinant somatostatin [ 3] followed shortly after by human insulin. The field has advanced enormously since those early days and today recombinant proteins have become indispensable in advancing research and development in all fields of the life sciences. Structural biology, in particular, has benefitted tremendously from recombinant protein biotechnology, and an overwhelming proportion of the entries in the Protein Data Bank (PDB) are based on heterologously expressed proteins. Nonetheless, synthesizing, purifying and stabilizing recombinant proteins can still be thoroughly challenging. For example, the soluble proteome is organized to a large part into multicomponent complexes (in humans often comprising ten or more subunits), posing critical challenges for recombinant production. A third of all proteins in cells are located in the membrane, and pose special challenges that require a more bespoke approach. Recent advances may now mean that even these most recalcitrant of proteins could become tenable structural biology targets on a more routine basis. In this special issue, we examine progress in key areas that suggests this is indeed the case. Our first contribution examines the importance of understanding quality control in the host cell during recombinant protein production, and pays particular attention to the synthesis of recombinant membrane proteins. A major challenge faced by any host cell factory is the balance it must strike between its own requirements for growth and the fact that its cellular machinery has essentially been hijacked by an expression construct. In this context, Bill and von der Haar examine emerging insights into the role of the dependent pathways of translation and protein folding in defining high-yielding recombinant membrane protein production experiments for the common prokaryotic and eukaryotic expression hosts. Rather than acting as isolated entities, many membrane proteins form complexes to carry out their functions. To understand their biological mechanisms, it is essential to study the molecular structure of the intact membrane protein assemblies. Recombinant production of membrane protein complexes is still a formidable, at times insurmountable, challenge. In these cases, extraction from natural sources is the only option to prepare samples for structural and functional studies. Zorman and co-workers, in our second contribution, provide an overview of recent advances in the production of multi-subunit membrane protein complexes and highlight recent achievements in membrane protein structural research brought about by state-of-the-art near-atomic resolution cryo-electron microscopy techniques. E. coli has been the dominant host cell for recombinant protein production. Nonetheless, eukaryotic expression systems, including yeasts, insect cells and mammalian cells, are increasingly gaining prominence in the field. The yeast species Pichia pastoris, is a well-established recombinant expression system for a number of applications, including the production of a range of different membrane proteins. Byrne reviews high-resolution structures that have been determined using this methylotroph as an expression host. Although it is not yet clear why P. pastoris is suited to producing such a wide range of membrane proteins, its ease of use and the availability of diverse tools that can be readily implemented in standard bioscience laboratories mean that it is likely to become an increasingly popular option in structural biology pipelines. The contribution by Columbus concludes the membrane protein section of this volume. In her overview of post-expression strategies, Columbus surveys the four most common biochemical approaches for the structural investigation of membrane proteins. Limited proteolysis has successfully aided structure determination of membrane proteins in many cases. Deglycosylation of membrane proteins following production and purification analysis has also facilitated membrane protein structure analysis. Moreover, chemical modifications, such as lysine methylation and cysteine alkylation, have proven their worth to facilitate crystallization of membrane proteins, as well as NMR investigations of membrane protein conformational sampling. Together these approaches have greatly facilitated the structure determination of more than 40 membrane proteins to date. It may be an advantage to produce a target protein in mammalian cells, especially if authentic post-translational modifications such as glycosylation are required for proper activity. Chinese Hamster Ovary (CHO) cells and Human Embryonic Kidney (HEK) 293 cell lines have emerged as excellent hosts for heterologous production. The generation of stable cell-lines is often an aspiration for synthesizing proteins expressed in mammalian cells, in particular if high volumetric yields are to be achieved. In his report, Buessow surveys recent structures of proteins produced using stable mammalian cells and summarizes both well-established and novel approaches to facilitate stable cell-line generation for structural biology applications. The ambition of many biologists is to observe a protein's structure in the native environment of the cell itself. Until recently, this seemed to be more of a dream than a reality. Advances in nuclear magnetic resonance (NMR) spectroscopy techniques, however, have now made possible the observation of mechanistic events at the molecular level of protein structure. Smith and colleagues, in an exciting contribution, review emerging ‘in-cell NMR’ techniques that demonstrate the potential to monitor biological activities by NMR in real time in native physiological environments. A current drawback of NMR as a structure determination tool derives from size limitations of the molecule under investigation and the structures of large proteins and their complexes are therefore typically intractable by NMR. A solution to this challenge is the use of selective isotope labeling of the target protein, which results in a marked reduction of the complexity of NMR spectra and allows dynamic processes even in very large proteins and even ribosomes to be investigated. Kerfah and co-workers introduce methyl-specific isotopic labeling as a molecular tool-box, and review its applications to the solution NMR analysis of large proteins. Tyagi and Lemke next examine single-molecule FRET and crosslinking following the co-translational incorporation of non-canonical amino acids (ncAAs); the goal here is to move beyond static snap-shots of proteins and their complexes and to observe them as dynamic entities. The encoding of ncAAs through codon-suppression technology allows biomolecules to be investigated with diverse structural biology methods. In their article, Tyagi and Lemke discuss these approaches and speculate on the design of improved host organisms for ‘integrative structural biology research’. Our volume concludes with two contributions that resolve particular bottlenecks in the protein structure determination pipeline. The contribution by Crepin and co-workers introduces the concept of polyproteins in contemporary structural biology. Polyproteins are widespread in nature. They represent long polypeptide chains in which individual smaller proteins with different biological function are covalently linked together. Highly specific proteases then tailor the polyprotein into its constituent proteins. Many viruses use polyproteins as a means of organizing their proteome. The concept of polyproteins has now been exploited successfully to produce hitherto inaccessible recombinant protein complexes. For instance, by means of a self-processing synthetic polyprotein, the influenza polymerase, a high-value drug target that had remained elusive for decades, has been produced, and its high-resolution structure determined. In the contribution by Desmyter and co-workers, a further, often imposing, bottleneck in high-resolution protein structure determination is addressed: The requirement to form stable three-dimensional crystal lattices that diffract incident X-ray radiation to high resolution. Nanobodies have proven to be uniquely useful as crystallization chaperones, to coax challenging targets into suitable crystal lattices. Desmyter and co-workers review the generation of nanobodies by immunization, and highlight the application of this powerful technology to the crystallography of important protein specimens including G protein-coupled receptors (GPCRs). Recombinant protein production has come a long way since Peter Lobban's hypothesis in the late 1960s, with recombinant proteins now a dominant force in structural biology. The contributions in this volume showcase an impressive array of inventive approaches that are being developed and implemented, ever increasing the scope of recombinant technology to facilitate the determination of elusive protein structures. Powerful new methods from synthetic biology are further accelerating progress. Structure determination is now reaching into the living cell with the ultimate goal of observing functional molecular architectures in action in their native physiological environment. We anticipate that even the most challenging protein assemblies will be tackled by recombinant technology in the near future.

A cell-permeable tool for analysing APP intracellular domain function and manipulation of PIKfyve activity

The mechanisms for regulating PIKfyve complex activity are currently emerging. The PIKfyve complex, consisting of the phosphoinositide kinase PIKfyve (also known as FAB1), VAC14 and FIG4, is required for the production of phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2). PIKfyve function is required for homeostasis of the endo/lysosomal system and is crucially implicated in neuronal function and integrity, as loss of function mutations in the PIKfyve complex lead to neurodegeneration in mouse models and human patients. Our recent work has shown that the intracellular domain of the Amyloid Precursor Protein (APP), a molecule central to the aetiology of Alzheimer's disease binds to VAC14 and enhances PIKfyve function. Here we utilise this recent advance to create an easy-to-use tool for increasing PIKfyve activity in cells. We fused APP's intracellular domain (AICD) to the HIV TAT domain, a cell permeable peptide allowing proteins to penetrate cells. The resultant TAT-AICD fusion protein is cell permeable and triggers an increase of PI(3,5)P2. Using the PI(3,5)P2 specific GFP-ML1Nx2 probe we show that cell-permeable AICD alters PI(3,5)P2 dynamics. TAT-AICD also provides partial protection from pharmacological inhibition of PIKfyve. All three lines of evidence show that the APP intracellular domain activates the PIKfyve complex in cells, a finding that is important for our understanding of the mechanism of neurodegeneration in Alzheimer's disease.

Immunological protein-protein interactions:a critical reflection

Life, and the biochemistry of which it is ultimately comprised, is built from the interactions of proteins, and the study of protein-protein interactions is fast becoming a central feature of molecular bioscience. This is as true of immunobiology as it is of other areas of the wider biological milieu. Protein-protein interactions within an immunological setting comprise both the kind familiar from other areas of biology and instantiations of protein-protein interactions special to the immune arena. Of the generic kind of protein-protein interaction, co-stimulatory receptors, such as CD28, and the interaction of accessory proteins, such as CD4 or CD8, are amongst the most prevalent and apposite of examples. The key examples of special immunological instantiations of protein-protein interactions are the binding of antigens by antibodies and the formation of peptide-MHC-TCR complexes; both prime examples of vital molecular recognition events mediated by protein-protein interactions. In this brief review, and within the context of this burgeoning field, we examine immunological protein-protein interactions, focussing on the problematic nature of defining such interactions. © 2011 by Nova Science Publishers, Inc. All rights reserved.

Contact-mediated control of radial migration of corneal epithelial cells

We thank Darrin Sheppard and other staff at the University of Aberdeen Medical Research Facility for specialist technical assistance. We thank Patsy D. Goast for overnight microscope monitoring. This work was performed under the Biotechnology and Bioscience Research Council Grant number BB/E015840/1 to JMC.

Next generation e-learning platform: virtual laboratory simulations

Bioscience subjects require a significant amount of training in laboratory techniques to produce highly skilled science graduates. Many techniques which are currently used in diagnostic, research and industrial laboratories require expensive equipment for single users; examples of which include next generation sequencing, quantitative PCR, mass spectrometry and other analytical techniques. The cost of the machines, reagents and limited access frequently preclude undergraduate students from using such cutting edge techniques. In addition to cost and availability, the time taken for analytical runs on equipment such as High Performance Liquid Chromatography (HPLC) does not necessarily fit with the limitations of timetabling. Understanding the theory underlying these techniques without the accompanying practical classes can be unexciting for students. One alternative from wet laboratory provision is to use virtual simulations of such practical which enable students to see the machines and interact with them to generate data. The Faculty of Science and Technology at the University of Westminster has provided all second and third year undergraduate students with iPads so that these students all have access to a mobile device to assist with learning. We have purchased licences from Labster to access a range of virtual laboratory simulations. These virtual laboratories are fully equipped and require student responses to multiple answer questions in order to progress through the experiment. In a pilot study to look at the feasibility of the Labster virtual laboratory simulations with the iPad devices; second year Biological Science students (n=36) worked through the Labster HPLC simulation on iPads. The virtual HPLC simulation enabled students to optimise the conditions for the separation of drugs. Answers to Multiple choice questions were necessary to progress through the simulation, these focussed on the underlying principles of the HPLC technique. Following the virtual laboratory simulation students went to a real HPLC in the analytical suite in order to separate of asprin, caffeine and paracetamol. In a survey 100% of students (n=36) in this cohort agreed that the Labster virtual simulation had helped them to understand HPLC. In free text responses one student commented that "The terminology is very clear and I enjoyed using Labster very much”. One member of staff commented that “there was a very good knowledge interaction with the virtual practical”.

Working with people affected by cancer – Phase 1 of a mixed methods exploration of practitioner perspectives in nutritional therapy

Introduction - Nutritional therapy (NT) is a bioscience-based branch of complementary and alternative medicine (CAM) with National Occupational Standards (NOS) and accredited training courses which include compulsory clinical training. Approximately 900 practitioners are registered with the voluntary regulator, the Complementary and Natural Healthcare Council (CNHC), but the number of unregulated practitioners is unknown. Cancer is a leading cause of death worldwide; nutrition and lifestyle factors may affect recurrence and survival rates. Many cancer patients and survivors seek individualised advice on diet and use of supplements and appropriately skilled nutritional therapy practitioners (NTP) may be well-placed to safely provide this advice. Little is known of NTPs’ perspectives on working with people affected by cancer; this study seeks to explore their views on training, use of evidence and other resources, to support the development of safe evidence-based practice in this important clinical area. Methods – An on-line anonymised questionnaire collected data from participants recruited from all UK registered NTPs. Recruitment was facilitated by the British Association for Applied Nutrition and Nutritional Therapy (BANT). Quantitative data on practitioner characteristics, years in practice, other therapies practiced and work with cancer clients were collected. Qualitative data on types of evidence used, barriers to practice and perceived training and support needs when working with clients with cancer, were collected and analysed. SPSS was used to produce descriptive statistics. Preliminary Results – 274/888 (31%) of registered NTPs participated. 61% respondents had accredited NT qualifications of which 46% were at degree or post-graduate level. 73% (202) participants indicated they also had other higher education qualifications, including 153 (56%) at degree or above. When asked to describe their position on cancer work, 17% respondents (40/238) indicated no interest, and 35% (84/238) respondents already work with cancer clients (cancer practitioners - CP). A further 48% (114/238) respondents expressed interest in starting cancer work, and typically requested specialist training and practice guidelines to support this area of clinical practice. Cancer practitioners (CP) rated searches of peer-reviewed literature as most useful for information to support practice, whereas commercial product information was rated least useful. CPs requested engagement with mainstream medicine, more access to research evidence and professional recognition to facilitate and support work with cancer clients. A need for professional networking, mentorship and/or supervision was noted by CP and non-CP respondents, which is of interest since 81% all participants worked as sole practitioners exclusively or as part of their practice, <1% worked within the NHS. Discussion & Conclusions – This is the first detailed documentation of NTP perspectives on cancer work. A number of areas have been identified for further detailed evidence to be collected using focus groups and interviews, including detailed training needs, communication with mainstream cancer professionals, access to research evidence, and professional recognition. This work will inform and support the development of professional practice guidelines for NT and inform the development of specialist training and other resources.

Anti-MDR and antitumoral action of acetylsalicylic acid on leukaemic cells

ASA (acetylsalicylic acid) is an NSAID (non-steroidal anti-inflammatory drug). ASA has gained attention as a potential chemopreventive and chemotherapeutic agent for several neoplasms. The aim of this study was to analyse the possible antitumoural effects of ASA in two erythroleukaemic cell lines, with or without the MDR (multidrug resistance) phenotype. The mechanism of action of different concentrations of ASA were compared in K562 (non-MDR) and Lucena (MDR) cells by analysing cell viability, apoptosis and necrosis, intracellular ROS (reactive oxygen species) formation and bcl-2, p53 and cox-2 gene expression. ASA inhibited the cellular proliferation or induced toxicity in K562 and Lucena cell lines, irrespective of the MDR phenotype. The ASA treatment provoked death by apoptosis and necrosis in K562 cells and only by necrosis in Lucena cells. ASA also showed antioxidant activity in both cell lines. The bcl-2, p53 and cox-2 genes in both cell lines treated with ASA seem to exhibit different patterns of expression. However, normal lymphocytes treated with the same ASA concentrations were more resistant than tumoral cells. The results of this work show that both cell lines responded to treatment with ASA, demonstrating a possible antitumoral and anti-MDR role for this drug.

Lipid oxidation kinetics of ozone-processed shrimp during iced storage using peroxide value measurements

In this research, in situ generated ozone exposure/wash cycles of 1, 3, and 5 min applied to shrimp samples either before (BIS) or during iced storage (DIS) has been used to study the lipid oxidation kinetics using the peroxide values (PV). The induction period (IP) as well as PV at end of the IP (PVIP) have been obtained. The rate constants (k) as well as half-lives (t1/2) of hydroperoxides formation for different oxidation stages were calculated. The results showed that both IP and PVIP were lower with BIS (IP between 4.35±0.09 and 5.08±0.23 days; PVIP between 2.92±0.06 and 3.40±0.18 mEq kg−1) compared with DIS (IP between 5.92±0.12 and 6.14±0.09 days; PVIP between 4.49±0.17 and 4.56±0.10 mEq kg−1). The k value for DIS seemed to be the greater compared to BIS. In addition, whilst decreases and increases in t1/2 were found at propagation, respectively, for BIS and DIS, decreases and increases were only found at the induction of oxidation stage(s) for BIS. Further, the PV of ozone-processed samples would fit first order lipid oxidation kinetics independent of duration of ozone exposures. For the first time, PV measurements and fundamental kinetic principles have been used to describe how increasing ozone exposures positively affects the different oxidation stages responsible for the formation of hydroperoxides in ozone-processed shrimp.

Produção de biomassa e composição química de adubos verdes cultivados no Vale do Ribeira

The contribution of green manure to soil improvement and crop production depends primarily on biomass production and its chemical composition, which vary depending on the species, region and growing season. The aim of this research was to evaluate the chemical composition of biomass produced by green manures in Vale do Ribeira, São Paulo, Brazil. In order to develop this research, was carried an experiment in Pariquera-Acu, in 2006/2007, in completely randomized blocks design with four treatments (three green manure and spontaneous vegetation) and five replications. At 30, 60, 90 and 120 after sowing samples were collected in 1m(2) of the shoots and determined fresh and dry, and chemical composition biomass. Sunhemp, pigeon pea and mucuna produced, in decreasing order, the largest quantities of biomass and were more efficient than the spontaneous vegetation. The biomass produced by green manure had higher quality than that produced by spontaneous vegetation. Sunhemp and pigeon pea have a higher proportion of dry matter in stems which have low N, high C/N and L/N ratio, variables indicating slow decomposition of residues. The analysis of dry matter partitioned to better indication of the chemical composition of the residues and the prevision of the availability of nutrients in the soil.

Resistência do solo à penetração e ao cisalhamento em diversos usos do solo em áreas de preservação permanente

The soil resistance to penetration and shear can be used as indicators of soil compaction and to indicate the susceptibility of a soil to erosion. The objective of this study was to quantify and compare the impact provided by different land uses in a haplic cambissol in areas of permanent preservation, from the soil resistance to penetration and shear. The experimental area was located in an area of permanent preservation, the sub-basin of the Ribeira Iguape River - SP, with different land uses: banana cultivation - CBAN, degraded pasture - PDEG, silvopastoral system - MPIS and native forest - MNAT. The test for resistance to penetration was accomplished with a digital penetrometer compaction of manual effort, to a depth of 40 cm. The soil shear strength was determined by Vane Test at a depth between 0 and 5 cm. The degraded pasture was similar to native forest, with less resistance to penetration. The banana cultivation and silvopastoral system were the land uses with the highest resistance to penetration, bringing serious risk of erosion in areas of permanent preservation. The soil under native forest had lower shear strength. The cultivation of bananas, degraded pasture and silvopastoral system were the land uses with higher shear strength of soil, indicating that the use of these soils in areas of permanent preservation is promoting the same compression.

Minerals and vitamin B9 in dried plants vs. infusions: assessing absorption dynamics of minerals by membrane dialysis tandem in vitro digestion

Vitamins and mineral elements are among the most important phytochemicals due to their important role in the maintenance of human health. Despite these components had already been studied in different plant species, their full characterization in several wild species is still scarce. In addition, the knowledge regarding the in vivo effects of phytochemicals, particularly their bioaccessibility, is still scarce. Accordingly, a membrane dialysis process was used to simulate gastrointestinal conditions in order to assess the potential bioaccessibility of mineral elements in different preparations of Achillea millefolium (yarrow), Laurus nobilis (laurel) and Taraxacum sect. Ruderalia (dandelion). The retention/passage dynamics was evaluated using a cellulose membrane with 34 mm pore. Dandelion showed the highest levels of all studied mineral elements (except zinc) independently of the used formulations (dried plant or infusion), but yarrow was the only species yielding minerals after the dialysis step, either in dried form, or as infusion. In fact, the ability of each evaluated element to cross the dialysis membrane showed significant differences, being also highly dependent on the plant species. Regarding the potential use of these plants as complementary vitamin B9 sources, the detected values were much lower in the infusions, most likely due to the thermolability effect.

Isolamento e caracterização biológica e bioquímica de um activador do factor x da coagulação presente no veneno da serpente Bothrops erythromelas

Dissertação de Mestrado Integrado em Medicina Veterinária

Bioecology of Spodoptera frugiperda (Smith, 1757) in different cover crops.

The objective of this work was to evaluate the biological variables of Spodoptera frugiperda on species of cover crops. The experiments were conducted in laboratory and greenhouse using the following species: sunflower (Helianthus annuus), sun hemp (Crotalaria juncea), brachiaria (Urochloa decumbens e Urochloa ruziziensis), millet (Pennisetum americanum), black oat (Avena stringosa), white lupin (Lupinus albus), forage turnip (Rafanus sativus) and maize (Zea mays). In laboratory the S. frugiperda larval survival varied from 57%, on L. albus, to 93% on H. annuus and the survival of the pre-imaginal phase varied from 45% on U. decumbens to 81.6% on Z. mays. On C. juncea the larval biomass was lower and the development period of the young and larval stage was higher. The adaptation index was less on C. juncea in greenhouse and laboratory. In greenhouse the larval survival at 14 days was similar for all plants and at 21 days was the lowest on C. juncea. There was less accumulation of biomass at 14 days on C. juncea and at 21 days on C. juncea and A. stringosa. Regarding damage, C. juncea presented less susceptibility to Spodoptera frugiperda attack, which together with the other evaluated parameters, indicated this plant as the most appropriate for soil cover before cultivation of maize.