A proteo-liposome system for the analysis of the intracellular interactome of membrane proteins using amyloid precursor protein as a model

Transmembrane proteins play crucial roles in many important physiological processes. The intracellular domain of membrane proteins is key for their function by interacting with a wide variety of cytosolic proteins. It is therefore important to examine this interaction. A recently developed method to study these interactions, based on the use of liposomes as a model membrane, involves the covalent coupling of the cytoplasmic domains of membrane proteins to the liposome membrane. This allows for the analysis of interaction partners requiring both protein and membrane lipid binding. This thesis further establishes the liposome recruitment system and utilises it to examine the intracellular interactome of the amyloid precursor protein (APP), most well-known for its proteolytic cleavage that results in the production and accumulation of amyloid beta fragments, the main constituent of amyloid plaques in Alzheimer’s disease pathology. Despite this, the physiological function of APP remains largely unclear. Through the use of the proteo-liposome recruitment system two novel interactions of APP’s intracellular domain (AICD) are examined with a view to gaining a greater insight into APP’s physiological function. One of these novel interactions is between AICD and the mTOR complex, a serine/threonine protein kinase that integrates signals from nutrients and growth factors. The kinase domain of mTOR directly binds to AICD and the N-terminal amino acids of AICD are crucial for this interaction. The second novel interaction is between AICD and the endosomal PIKfyve complex, a lipid kinase involved in the production of phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2) from phosphatidylinositol-3-phosphate, which has a role in controlling ensdosome dynamics. The scaffold protein Vac14 of the PIKfyve complex binds directly to AICD and the C-terminus of AICD is important for its interaction with the PIKfyve complex. Using a recently developed intracellular PI(3,5)P2 probe it is shown that APP controls the formation of PI(3,5)P2 positive vesicular structures and that the PIKfyve complex is involved in the trafficking and degradation of APP. Both of these novel APP interactors have important implications of both APP function and Alzheimer’s disease. The proteo-liposome recruitment method is further validated through its use to examine the recruitment and assembly of the AP-2/clathrin coat from purified components to two membrane proteins containing different sorting motifs. Taken together this thesis highlights the proteo-liposome recruitment system as a valuable tool for the study of membrane proteins intracellular interactome. It allows for the mimicking of the protein in its native configuration therefore identifying weaker interactions that are not detected by more conventional methods and also detecting interactions that are mediated by membrane phospholipids.

Investigating the ability of antibodies to recognize specific oxidized protein epitopes

There is a growing awareness that inflammatory diseases have an oxidative pathology, which can result in specific oxidation of amino acids within proteins. Antibody-based techniques for detecting oxidative posttranslational modifications (oxPTMs) are often used to identify the level of protein oxidation. There are many commercially available antibodies but some uncertainty to the potential level of cross reactivity they exhibit; moreover little information regarding the specific target epitopes is available. The aim of this work was to investigate the potential of antibodies to distinguish between select peptides with and without oxPTMs. Two peptides, one containing chlorotyrosine (DY-Cl-EDQQKQLC) and the other an unmodified tyrosine (DYEDQQKQLC) were synthesized and complementary anti-sera were produced in sheep using standard procedures. The anti-sera were tested using a half-sandwich ELISA and the anti-serum raised against the chloro-tyrosine containing peptide showed increased binding to the chlorinated peptide, whereas the control anti-serum bound similarly to both peptides. This suggested that antibodies can discriminate between similar peptide sequences with and without an oxidative modification. A peptide (STSYGTGC) and its variants with chlorotyrosine or nitrotyrosine were produced. The anti-sera showed substantially less binding to these alternative peptides than to the original peptides the anti-sera were produced against. Work is ongoing to test commercially available antibodies against the synthetic peptides as a comparison to the anti-sera produced in sheep. In conclusion, the antisera were able to distinguish between oxidatively modified and unmodified peptides, and two different sequences around the modification site.

The redoxomics of PTEN: walking a fine line between damage and signaling:mass spectrometry-based approaches to study the effect of oxidation on PTEN function, structure, and protein-protein interactions

The research described in this PhD thesis focuses on proteomics approaches to study the effect of oxidation on the modification status and protein-protein interactions of PTEN, a redox-sensitive phosphatase involved in a number of cellular processes including metabolism, apoptosis, cell proliferation, and survival. While direct evidence of a redox regulation of PTEN and its downstream signaling has been reported, the effect of cellular oxidative stress or direct PTEN oxidation on PTEN structure and interactome is still poorly defined. In a first study, GST-tagged PTEN was directly oxidized over a range of hypochlorous acid (HOCl) concentration, assayed for phosphatase activity, and oxidative post-translational modifications (oxPTMs) were quantified using LC-MS/MS-based label-free methods. In a second study, GSTtagged PTEN was prepared in a reduced and reversibly H2O2-oxidized form, immobilized on a resin support and incubated with HCT116 cell lysate to capture PTEN interacting proteins, which were analyzed by LC-MS/MS and comparatively quantified using label-free methods. In parallel experiments, HCT116 cells transfected with a GFP-tagged PTEN were treated with H2O2 and PTENinteracting proteins immunoprecipitated using standard methods. Several high abundance HOCl-induced oxPTMs were mapped, including those taking place at amino acids known to be important for PTEN phosphatase activity and protein-protein interactions, such as Met35, Tyr155, Tyr240 and Tyr315. A PTEN redox interactome was also characterized, which identified a number of PTEN-interacting proteins that vary with the reversible inactivation of PTEN caused by H2O2 oxidation. These included new PTEN interactors as well as the redox proteins peroxiredoxin-1 (Prdx1) and thioredoxin (Trx), which are known to be involved in the recycling of PTEN active site following H2O2-induced reversible inactivation. The results suggest that the oxidative modification of PTEN causes functional alterations in PTEN structure and interactome, with fundamental implications for the PTEN signaling role in many cellular processes, such as those involved in the pathophysiology of disease and ageing.

The thermodynamics and statistical mechanics of protein folding

The physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding. ^

Whole body and splanchnic amino acid metabolism in sheep during an acute endotoxin challenge

Acknowledgements The expertise of A. Graham Calder and Susan Anderson for the various stable isotope analyses is gratefully recognised. Ngaire Dennison is also thanked for her surgical expertise with the trans-splanchnic tissue catheter preparations. This study was supported by funds provided to the Rowett Institute of Nutrition and Health, University of Aberdeen and Biomathematics and Statistics Scotland by the Rural and Environment Science and Analytical Services Division of the Scottish Government. S. O. H. was a recipient of a FoRST (NZ) award to study abroad.

Evolution of protein bound Maillard reaction end-products and free Amadori compounds in low lactose milk in presence of fructosamine oxidase I

Thermal treatments and storage influence milk quality, particularly in low lactose milk as the higher concentration of reducing sugars can lead to the increased formation of the Maillard reaction products (MRPs). The control of the Amadori products (APs) formation is the key step to mitigate the Maillard reaction (MR) in milk. The use of fructosamine oxidases, (Faox) provided promising results. In this paper, the effects of Faox I were evaluated by monitoring the concentration of free and bound MRPs in low lactose milk during shelf life. Results showed that the enzyme reduced the formation of protein-bound MRPs down to 79% after six days at 37 °C. Faox I lowered the glycation of almost all the free amino acids resulting effective on basic and polar amino acids. Data here reported corroborate previous findings on the potentiality of Faox enzymes in controlling the early stage of the MR in foods.

Circulating leukocyte heat shock protein 70 (HSP70) and oxidative stress markers in rats after a bout of exhaustive exercise

A novel method to measure oxidative stress resulting from exhaustive exercise in rats is presented. In this new procedure we evaluated the erythrocyte antioxidant enzymes, catalase ( CAT) and glutathione reductase (GR), the plasma oxidative attack markers, reactive carbonyl derivatives (RCD) and thiobarbituric reactive substances (TBARS). Muscular tissue damage was evaluated by monitoring plasma creatine kinase (CK) and plasma taurine ( Tau) concentrations. Also, we monitored total sulphydryl groups (TSG) and uric acid (UA), and the level of the 70 kDa heat shock protein (HSP70) in leukocytes as a marker of oxidative stress. In the study we found a correspondence between erythrocyte CAT and GR activities and leukocyte HSP70 levels, principally 3 h after the acute exercise, and this suggested an integrated mechanism of antioxidant defense. The increase in levels of plasma Tau was coincident with the increasing plasma levels of CK and TBARS, principally after two hours of exercise. Thus tissue damage occurred before the expression of any anti-oxidant system markers and the monitoring of Tau, CK or TBARS may be important for the estimation of oxidative stress during exhaustive exercise. Furthermore, the integrated analyses could be of value in a clinical setting to quantify the extent of oxidative stress risk and reduce the need to perform muscle biopsies as a tool of clinical evaluation.

NUTRITIONAL AND AMINO ACID ANALYSIS OF RAW, PARTIALLY FERMENTED AND COMPLETELY FERMENTED LOCUST BEAN ( Parkia biglobosa ) SEEDS

The nutritional and amino acid analysis of raw and fermented seeds of Parkia biglobosa were carried out. Parameters investigated include moisture, crude protein, crude fat, ash, crude fibre and mineral contents; and the effect of the degree of fermentation on these parameters was also investigated. The amino acid compositions of all the samples were evaluated and amino acid quality determined by calculating amino acid scores and the predicted protein efficiency ratio (P-PER). Results showed that the proximate composition was significantly affected by fermentation, although there was little difference between the parameters for the partially fermented and completely fermented samples. Based on dry matter percentage, protein content was in the 39.77 – 43.74 % range while crude fibre ranged between 5.55 – 7.42 %. The ash content was lowest in the raw sample (2.34 %), while the fermented samples had ash contents between 4.27 and 8.33 % for the fully fermented and the partially fermented seeds, respectively. The fat content increased from 8.65 % in the raw seed to 24.4 % and 27.6 % for the partially and completely fermented samples, respectively. Results of the amino acid analysis showed that the partially fermented sample had the lowest quantities of all amino acids determined and had lysine as the limiting amino acid, whereas the raw and completely fermented samples had very similar amino acid profile with amino acid scores of 100, indicating that there are no limiting amino acids. All the samples were rich in essential amino acids. The P-PER also showed that the partially fermented sample had the lowest protein efficiency while the raw seed had the highest. Mineral contents generally increased from the raw, through the partially fermented, to the completely fermented seeds and results showed the samples to be good sources of potassium (K), calcium (Ca), manganese (Mn) and copper (Cu) in addition to being complementary sources of other metals. Locust bean seed does not accumulate lead and is, therefore, safe for consumption without the potential of food poisoning.

Protein disulfide isomerase as a target for besnoitiosis therapy : molecular characterization and studies of its role in infection and host immune response

Tese de Doutoramento em Ciências Veterinárias na especialidade de Sanidade Animal

Incorporation of dietary nitrogen from fish meal and pea meal ( Pisum sativum ) in muscle tissue of Pacific white shrimp ( Litopenaeus vannamei ) fed low protein compound diets

Stable isotope analyses were applied to explore the relative dietary nitrogen contributions from fish meal and pea meal (Pisum sativum) to muscle tissue of Pacific white shrimp postlarvae (141 ± 31 mg) fed low protein diets having different proportions of both ingredients as the sole dietary protein sources. A negative control diet was formulated to contain 100% pea meal and six more isoproteic diets to have decreasing levels of pea meal-derived nitrogen: 95%, 85%, 70%, 55%, 40% and 0% of the initial level. Growth rates were negatively correlated to dietary pea protein inclusion due to progressive essential amino acid deficiencies (sulphur amino acids, threonine, lysine, histidine). The nitrogen turnover rate significantly increased in muscle tissue of shrimps fed diets having high levels of pea meal; however, contrary to observations from a previous study using soy protein, the relative contributions of dietary nitrogen from pea meal to shrimp muscle tissue were equal or higher than expected contributions established by the dietary formulations. Results highlight the effectiveness of stable isotope analysis in assessing the nutritional contributions of alternative ingredients for aquaculture feeds and the potential suitability of pea as a source of protein (provided the diets are nutritionally balanced)

Prediction of peptide and protein propensity for amyloid formation

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Amino acid composition of processed fish silage using different raw materials

The objective was to evaluate amino acid composition of silages produced from three raw materials. Commercial marine fish waste, commercial freshwater fish waste, and tilapia filleting residue were used to produce fish silage by acid digestion (20 ml/kg formic acid and 20 ml/kg sulfuric acid) and anaerobic fermentation (50 g/kg Lactobacillus plantarum, 150 g/kg sugar cane molasses). Protein content and amino acid composition were determined for raw materials and silage. Marine fish waste had higher crude protein content (776.7 g/kg) compared to freshwater fish waste (496.2 g/kg) and tilapia filleting residue (429.9 g/kg). All silages lacked up to three amino acids for each product according to FAO standards for essential amino acids. However, considering as the limiting factor only the amino acids below the 30% minimum requirement for fish in general, all products were satisfactory with respect to essential amino acids. Therefore, the results suggest that all products investigated are appropriate for use in balanced fish diets. (C) 2003 Elsevier B.V. B.V. All rights reserved.

Biotechnological approaches to valorize alternative protein source, waste and by-products from food industries

The PhD research project was a striking example of the enhancement of milling by-product and alternative protein sources from house cricket (Acheta domesticus), conceived as sustainable and renewable sources, to produce innovative food products. During milling processing of wheat and rye, several by-products with high technological and functional potential, are produced. The use of selected microbial consortia, allowed to obtain a pre-fermented ingredient for use in the bakery. The pre-ferments obtained were characterized by a high technological, functional and nutritional value, also interesting from a nutraceutical point of view. Bakery products obtained by the addition of pre-fermented ingredients were characterized by a greater quantity of aromatic molecules and an increase in SCFA, antioxidant activity, total amino acids and total phenols resulting in positive effect on the functionality. Moreover, the industrial scaling-up of pre-ferment and innovative bakery goods production, developed in this research, underlined the technological applicability of pre-fermented ingredients on a large scale. Moreover, the identification of innovative protein sources, can address the request of new sustainable ingredients able to less impact on the environment and to satisfy the food global demand. To upscale the insect production and ensure food safety of insect-based products, biotechnological formulations based on Acheta domesticus powder were optimized. The use of Yarrowia lipolytica in the biotechnological transformation of cricket powder led to the achievement of a cricket-based food ingredient characterized by a reduced content of chitin and an increase of antimicrobial and health-promoting molecules. The innovative bakery products containing cricket-based hydrolysates from Y. lipolytica possessed specific sensory, qualitative and functional characteristics to the final product. Moreover, the combination of Y. lipolytica hydrolysis and baking showed promising results regarding a reduced allergenicity in cricket-based baked products. Thus, the hydrolysate of cricket powder may represent a versatile and promising ingredient in the production of innovative foods.

New Interaction Partners For Nek4.1 And Nek4.2 Isoforms: From The Dna Damage Response To Rna Splicing.

Neks are serine-threonine kinases that are similar to NIMA, a protein found in Aspergillus nidulans which is essential for cell division. In humans there are eleven Neks which are involved in different biological functions besides the cell cycle control. Nek4 is one of the largest members of the Nek family and has been related to the primary cilia formation and in DNA damage response. However, its substrates and interaction partners are still unknown. In an attempt to better understand the role of Nek4, we performed an interactomics study to find new biological processes in which Nek4 is involved. We also described a novel Nek4 isoform which lacks a region of 46 amino acids derived from an insertion of an Alu sequence and showed the interactomics profile of these two Nek4 proteins. Isoform 1 and isoform 2 of Nek4 were expressed in human cells and after an immunoprecipitation followed by mass spectrometry, 474 interacting proteins were identified for isoform 1 and 149 for isoform 2 of Nek4. About 68% of isoform 2 potential interactors (102 proteins) are common between the two Nek4 isoforms. Our results reinforce Nek4 involvement in the DNA damage response, cilia maintenance and microtubule stabilization, and raise the possibility of new functional contexts, including apoptosis signaling, stress response, translation, protein quality control and, most intriguingly, RNA splicing. We show for the first time an unexpected difference between both Nek4 isoforms in RNA splicing control. Among the interacting partners, we found important proteins such as ANT3, Whirlin, PCNA, 14-3-3ε, SRSF1, SRSF2, SRPK1 and hNRNPs proteins. This study provides new insights into Nek4 functions, identifying new interaction partners and further suggests an interesting difference between isoform 1 and isoform 2 of this kinase. Nek4 isoform 1 may have similar roles compared to other Neks and these roles are not all preserved in isoform 2. Besides, in some processes, both isoforms showed opposite effects, indicating a possible fine controlled regulation.

Formação das substâncias de reserva durante o desenvolvimento de sementes de urucum (Bixa orellana L. - Bixaceae)

Annatto seeds do not germinate during early stages of their development because of insufficient reserve substances. In situ analysis showed that the principal reserves are proteins and starch, deposited in endosperm cells. During the early stages of development, the starch grains were elliptic, because amylose was the minor component. During development, these grains became more spherical due to an increase in amylose relative to amylopectin. Endosperm cells do not contain protein bodies, but they accumulate proteins dispersed in the cytoplasm. At the final stage of development the proteins became compacted due to the dehydration of the seeds wich is part of the global process of orthodox seeds maturation. Natural fluorescence revealed aromatic amino acids, principally tryptophan and tyrosine in the proteins. The seeds reached their maximum dry weight after moisture contents had declined to around 60%. At this point the seeds presented maximum germination capacity.