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2.14: Proteomics - Biology

2.14: Proteomics - Biology



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Genome

One complete set of genes in an organism (a haploid set).

Except for occasional unrepaired damage to its DNA (= mutations), the genome is fixed.

Transcriptome

The most common definition: All the messenger RNA (mRNA) molecules transcribed from the genome.

Varies with the differentiated state of the cell and the activity of the transcription factors that turn gene transcription on (and off).

Speaking strictly, one would define the transcriptome as all the RNA molecules — which includes a wide variety of untranslated, nonprotein-encoding RNA — transcribed from the DNA of the genome. It is now thought that ~75% of our DNA is transcribed into RNA although only 1.5% of this is messenger RNA for protein synthesis.

Metabolome

All the metabolic machinery, e.g.,

  • enzymes
  • coenzymes
  • small metabolites, like
    • the intermediates in glycolysis and cellular respiration
    • nucleotides

present in a cell at a given time.

Varies with the differentiated state of the cell and its current activities.

Proteome

The proteome is the protein complement of the genome. It is quite a bit more complicated than the genome because a single gene can give rise to a number of different proteins through

  • alternative splicing of the pre-messenger RNAs (pre-mRNAs)
  • RNA editing of the pre-messenger RNAs
  • attachment of carbohydrate residues to form glycoproteins
  • addition of phosphate groups to some of the amino acids in the protein

While we humans probably have only some 21 thousand genes, we probably make at least 10 times that number of different proteins. The great majority of our genes produce pre-mRNAs that are alternatively-spliced.

The study of proteomics is important because proteins are responsible for both the structure and the functions of all living things. Genes are simply the instructions for making proteins. It is proteins that make life.

The set of proteins within a cell varies

  • from one differentiated cell type to another (e.g. red blood cell vs lymphocyte) and
  • from moment to moment, depending on the activities of the cell, e.g.,
    • getting ready to duplicate its genome;
    • repairing damage to its DNA;
    • responding to a newly-available nutrient or cytokine;
    • responding to the arrival of a hormone

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Diffusion, Active Transport and Osmosis: Grade 9 Understanding for IGCSE Biology 2.15 2.16

This post is going to describe some of the ways molecules can cross the cell membrane. (For Eton students revising for Trials, diffusion and active transport are found in the F block syllabus, osmosis comes in E Block)

Diffusion is the simplest to understand. Diffusion does not even need a cell membrane to occur. In the example below the dye molecules will move randomly in the solution. As the dye starts in one place, these random movements will mean that slowly spread out until an equilibrium is reached. This movement of the dye from the region of high concentration to the low concentration is called diffusion.

When considering diffusion into a cell, if the cell membrane is permeable to a particular molecule then the random movements of the molecule will mean that there will be a net (overall) movement from the higher concentration to the lower concentration down the concentration gradient.

Key Points about diffusion:

  • Always happens down a concentration gradient (from a high concentration to a lower one)
  • Never requires any energy from the cell – it is a passive process

Active Transport is a process that will move molecules into a cell against the concentration gradient – i.e. from a low concentration to a high concentration. This “pumping” of the molecules against the gradient requires energy from the cell and of course this energy comes from respiration.

You can see from the diagram above that active transport is working against the concentration gradient, is using energy from inside the cell (actually a molecule made in mitochondria in respiration called ATP) and that a specific transport protein is involved in the cell membrane. This protein will have a binding-site that is specific for a particular molecule and the solute molecule to be transported will collide with the transport protein due to random movement. Energy from the cell can cause the transport protein to change shape such that the solute is released on the other side of the membrane.

Can you think of another area of the iGCSE syllabus which features collisions between a specific binding-site on a protein and a certain other molecule? Linking ideas is a key characteristic of the A* Biologist!

Osmosis is the hardest of these processes to understand properly, especially as an iGCSE student when you are often told an over-simplified account that does not make sense…. Let’s try to simplify it in a way that does make sense.

Firstly it is only water molecules that can move by osmosis into and out of cells – never anything else. Indeed osmosis is the only way water can cross a membrane – it never moves by diffusion or active transport.

Osmosis is a passive process – it never needs any energy from the cell’s respiration and the only energy involved is the kinetic energy of the water molecules.

Osmosis can only occur through a partially permeable membrane. All cell membranes are partially permeable and this means they let small molecule like water through but prevent the diffusion of the larger solute molecules.

The water molecules on both sides of the membrane in the diagram above will be moving around randomly. They will occasionally hit one of the pores in the membrane and so pass across the membrane. This movement will be happening from left to right and from right to left.

The presence of the sucrose (solute) in the solution on the right means that some of the water molecules on that side of the membrane are less able to move. This is because they are temporarily attracted to the solute molecules by weak hydrogen bonds. So their kinetic energy is reduced and this makes them less likely to randomly collide with the pores in the membrane. The presence of the solute on the right means that water molecules on the left on average are more likely to collide with the membrane than the water molecules on the right and this leads to an overall movement from left to right. This net movement of water molecules from the dilute solution to the more concentrated solution through the partially permeable membrane is called osmosis.

This diagram has the two solutions reversed so in which direction will osmosis happen here? Thats right from right to left. You can see the hydrogen bonds attracting water molecules to the solute – these are the ones that lower their kinetic energy overall.

You might even have been taught about osmosis with reference to the water potential of a solution. The water potential of a solution is just a measure of how much kinetic energy the water molecules in a solution possess. So a dilute solution will have a high water potential, a concentrated solution (with lots of dissolved solute) a lower water potential.

Osmosis is the

  • net movement of water
  • through a partially permeable membrane
  • from a solution with a high water potential (a dilute solution) to a solution with a lower water potential (a concentrated solution)

Biological examples

  • Oxygen diffuses from the air in the alveolus into the blood
  • Carbon Dioxide diffuses from the air spaces in the leaf into the palisade mesophyll cells of the leaf
  • Glucose diffuses from the blood into an actively-respiring muscle

Active Transport

  • Nitrates are pumped from the soil into root hair cells by active transport
  • In the kidney, glucose and other useful molecules are pumped from the nephron back into the blood by active transport.
  • In nerve cells, sodium and potassium ions are pumped across the cell membrane to set up the gradients needed for a nerve impulse
  • Water enters root hair cells from the soil by osmosis
  • In the kidney, water is reabsorbed from the nephron by osmosis.
  • In the large intestine, water is reabsorbed from the colon back into the blood by osmosis

There are many many more examples of each process, but this should be enough to be going on with…….


Population-specific design of de-immunized protein biotherapeutics

Immunogenicity is a major problem during the development of biotherapeutics since it can lead to rapid clearance of the drug and adverse reactions. The challenge for biotherapeutic design is therefore to identify mutants of the protein sequence that minimize immunogenicity in a target population whilst retaining pharmaceutical activity and protein function. Current approaches are moderately successful in designing sequences with reduced immunogenicity, but do not account for the varying frequencies of different human leucocyte antigen alleles in a specific population and in addition, since many designs are non-functional, require costly experimental post-screening. Here, we report a new method for de-immunization design using multi-objective combinatorial optimization. The method simultaneously optimizes the likelihood of a functional protein sequence at the same time as minimizing its immunogenicity tailored to a target population. We bypass the need for three-dimensional protein structure or molecular simulations to identify functional designs by automatically generating sequences using probabilistic models that have been used previously for mutation effect prediction and structure prediction. As proof-of-principle we designed sequences of the C2 domain of Factor VIII and tested them experimentally, resulting in a good correlation with the predicted immunogenicity of our model.

Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

(A) Contact map of Factor VIII’s C2 domain. The gray circles represent the…

(A) Immunogenicity screening for three…

(A) Immunogenicity screening for three DRB1 alleles (DRB1*15:01, DRB1*03:01 and DRB1*07:01) with TEPITOPEpan.…

Pareto front of de-immunized designs…

Pareto front of de-immunized designs in percent change compared to the wild type…

Fig 4. Evolutionary couplings-based model and FoldX…

Fig 4. Evolutionary couplings-based model and FoldX prediction correlations.

(A) Correlation of experimental and…

(A) Correlation of experimental and predicted immunogenicity of each peptide. The experimental immunogenicity…


Abstract

Redox-related plasma proteins are candidate reporters of protein signatures associated with endothelial structure/function. Thiol-proteins from protein disulfide isomerase (PDI) family are unexplored in this context. Here, we investigate the occurrence and physiological significance of a circulating pool of PDI in healthy humans. We validated an assay for detecting PDI in plasma of healthy individuals. Our results indicate high inter-individual (median = 330 pg/mL) but low intra-individual variability over time and repeated measurements. Remarkably, plasma PDI levels could discriminate between distinct plasma proteome signatures, with PDI-rich (>median) plasma differentially expressing proteins related to cell differentiation, protein processing, housekeeping functions and others, while PDI-poor plasma differentially displayed proteins associated with coagulation, inflammatory responses and immunoactivation. Platelet function was similar among individuals with PDI-rich vs. PDI-poor plasma. Remarkably, such protein signatures closely correlated with endothelial function and phenotype, since cultured endothelial cells incubated with PDI-poor or PDI-rich plasma recapitulated gene expression and secretome patterns in line with their corresponding plasma signatures. Furthermore, such signatures translated into functional responses, with PDI-poor plasma promoting impairment of endothelial adhesion to fibronectin and a disturbed pattern of wound-associated migration and recovery area. Patients with cardiovascular events had lower PDI levels vs. healthy individuals. This is the first study describing PDI levels as reporters of specific plasma proteome signatures directly promoting contrasting endothelial phenotypes and functional responses.


2.14: Proteomics - Biology

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Intracellular location of the multidomain protein CAD in mammalian cells

The first three steps of mammalian de novo pyrimidine biosynthesis are catalyzed by the multifunctional protein CAD, consisting of glutamine-dependent carbamylphosphate synthetase, aspartate transcarbamylase, and dihydroorotase. The intracellular distribution of CAD in two hamster cell lines, BHK 21 and BHK 165-23 (a strain in which the CAD gene was selectively amplified), was determined by differential centrifugation and by two different cytochemical immunolocalization methods. Ammonia-dependent carbamylphosphate synthetase I was found in both cell types at a concentration of 0.01% of the total cell protein, so its distribution was also determined as a control for possible cross-reactivity of the CAD antibody probes and as a mitochondrial marker. CAD was localized in the cytoplasmic compartment and almost completely excluded from the nucleus. A punctate staining pattern suggested that it was not uniformly dispersed throughout the cytosol (unlike typical soluble proteins) but was associated with subcellular organelles. Although there was a slight tendency for CAD to be localized in the vicinity of the nuclear envelope, the amount of staining was much less than expected from differential centrifugation, which showed that 30% of the protein was found in the nuclear fraction. No interactions with other subcellular components could be detected by centrifugation. It is possible, however, that CAD is associated with subcellular structures that cosediment with the nuclei. Despite a 150-fold increase in CAD concentration in the over-producing cells, the distribution of the protein was unaltered. CAD was not concentrated near the mitochondria where the next enzyme of the de novo pathway, dihydroorotate dehydrogenase, is localized, which indicates that the intermediate dihydroorotate is not channeled, but rather dissociates from CAD and diffuses through the bulk cellular fluid.— C haparian , M. G. E vans , D. R. Intracellular location of the multi-domain protein CAD in mammalian cells. FASEB J. 2: 2982-2989 1988.


Protein kinases 1988: a current perspective

Howard Hughes Medical Institute and the Section of Diabetes and Metabolism, Division of Endocrinology, Metabolism and Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina, 27710 USA

Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York, 10021 USA

Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia, 30322 USA

Howard Hughes Medical Institute and the Section of Diabetes and Metabolism, Division of Endocrinology, Metabolism and Genetics, Department of Medicine, Duke University Medical Center, Durham, North Carolina, 27710 USA

Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, New York, 10021 USA

Department of Pharmacology, Emory University School of Medicine, Atlanta, Georgia, 30322 USA

Abstract

This review focuses on several recent developments in the field of protein kinases. In the area of protein serine/threonine kinases, much has been learned recently about protein kinase C structure and function. Novel lipid mediators, both stimulatory and inhibitory, have been discovered, and kinase has been shown to be an increasingly large family of gene products. Heterogeneity of cellular localization and function has been documented. Calcium/calmodulin-dependent protein kinases are now believed to consist of at least five enzymes, which range from those with extreme substrate specificity such as phosphorylase kinase and myosin light-chain kinases to calcium calmodulin kinase II, with several known substrates. Several of these enzymes appear to be important in synaptic transmission and, for calcium/calmodulin kinase III, in the regulation of protein synthesis. Several new examples of pseudosubstrate prototopes as endogenous kinase inhibitors have been described, including regions intrinsic to kinase primary sequences, which could serve as constitutive inhibitors of enzyme activity. In the field of protein tyrosine kinases, new enzyme species are being discovered at a rapid rate. There are several well-documented examples of kinase autophosphorylation on tyrosine leading to stimulation of catalytic activity. For the growth factor receptors with intrinsic protein tyrosine kinase activity, it now seems clear that kinase catalytic activity is necessary for most hormone effects on cells, with the general exceptions of ligand binding and, possibly, receptor cycling. Finally, several groups have recently described a close association between protein tyrosine kinases and a phosphatidylinositol kinase activity, a link that might eventually explain some of the initial steps in signal transduction that occur after kinase activation.— B lackshear , R J. N airn , A. C. Kuo, J. F. Protein kinases 1988: a current perspective. FASEB J. 2: 2957-2969 1988.


Proteomics of human mitochondria

Proteomics have passed through a tremendous development in the recent years by the development of ever more sensitive, fast and precise mass spectrometry methods. The dramatically increased research in the biology of mitochondria and their prominent involvement in all kinds of diseases and ageing has benefitted from mitochondrial proteomics. We here review substantial findings and progress of proteomic analyses of human cells and tissues in the recent past. One challenge for investigations of human samples is the ethically and medically founded limited access to human material. The increased sensitivity of mass spectrometry technology aids in lowering this hurdle and new approaches like generation of induced pluripotent cells from somatic cells allow to produce patient-specific cellular disease models with great potential. We describe which human sample types are accessible, review the status of the catalog of human mitochondrial proteins and discuss proteins with dual localization in mitochondria and other cellular compartments. We describe the status and developments of pertinent mass spectrometric strategies, and the use of databases and bioinformatics. Using selected illustrative examples, we draw a picture of the role of proteomic analyses for the many disease contexts from inherited disorders caused by mutation in mitochondrial proteins to complex diseases like cancer, type 2 diabetes and neurodegenerative diseases. Finally, we speculate on the future role of proteomics in research on human mitochondria and pinpoint fields where the evolving technologies will be exploited.

Keywords: Mass spectrometry Mitochondrial diseases Mitochondrial medicine Mitochondrial proteins Proteomics.