Name: atomic absorbance spectroscopy to measure intracellular zinc pools in mammalian cells
Uploaded: 2019-05-16T15:00:00
Description: Watch this Scientific Journal Video about Atomic Absorbance Spectroscopy to Measure Intracellular Zinc Pools in Mammalian Cells at JoVE.com

This work was supported by the Faculty Diversity Scholars Award from the University of Massachusetts Medical School to T.P.-B. N.N.-T. is supported by SEP-CONACYT, grant 279879. J.G.N is supported by the National Science Foundation Grant DBI 0959476. The authors are grateful to Dr. Daryl A. Bosco for providing the N2A cell line and to Daniella Cangussu for her technical support.

1. Mammalian cell culture
<ol>
	<li>General considerations
	<ol>
		<li>Follow the aseptic techniques for mammalian cell culture previously reviewed38.</li>
		<li>Maintain all cell lines in a humidified 5% CO2 incubator at 37 &#176;C. Cell culture conditions vary for each cell type. It is important to maintain appropriate culture conditions for each cell line used, as variations of these procedures will lead to aberrant phenotypes and failure of the cell culture.</li>
...

Atomic absorbance spectroscopy is a highly sensitive method for Zn quantification in small volume/mass biological samples. The described optimization of Zn measurement makes application of this method simple and guarantees ideal analytical conditions. Here, using GF-AAS, we determined the concentration of Zn in whole cells, and in cytosolic and nuclear fractions, from different cell lines. The results show that this technique renders comparable to those obtained by fluorescent probes and ICP-MS. For instance, several flu...

Transition and heavy metals, such as Zn, Cu, Mn, and Fe, are found naturally in the environment in both nutrients in food and pollutants. All living organisms require different amounts of these micronutrients; however, exposure to high levels is deleterious to organisms. Metal acquisition is mainly through the diet, but metals can also be inhaled or absorbed through the skin1,2,3,4,5. It is important to note that the presence of metals in atmospheric particles is increasing and has been largely associated with health risks. Due to anthropogenic activities, increased levels of heavy metals such as Ag, As, Cd, Cr, Hg, Ni, Fe, and Pb have been detected in atmospheric particulate matter, rainwater, and soil6,7. These metals have the potential to compete with essential physiological trace elements, particularly Zn and Fe, and they induce toxic effects by inactivating fundamental enzymes for biological processes.
The trace element Zn is redox neutral and behaves as a Lewis acid in biological reactions, which makes it a fundamental cofactor necessary for protein folding and catalytic activity in over 10% of mammalian proteins8,9,10; consequently, it is essential for diverse physiological functions8,11. However, like many trace elements, there is a delicate balance between these metals facilitating normal physiological function and causing toxicity. In mammals, Zn deficiencies lead to anemia, growth retardation, hypogonadism, skin abnormalities, diarrhea, alopecia, taste disorders, chronic inflammation, and impaired immune and neurological functions11,12,13,14,15,16,17,18. In excess, Zn is cytotoxic and impairs absorption of other essential metals such as copper19,20,21.
Additionally, some metals like Cu and Fe have the potential to participate in harmful reactions. Production of reactive oxygen species (ROS) via Fenton chemistry can interfere with the assembly of iron sulfur cluster proteins and alter lipid metabolism22,23,24. To prevent this damage, cells utilize metal-binding chaperones and transporters to prevent toxic effects. Undoubtedly, metal homeostasis must be tightly controlled to ensure that specific cell types maintain proper levels of metals. For this reason, there is a significant need to advance techniques for accurate measurement of trace metals in biological samples. In developing and mature organisms there exists a differential biological need for trace elements at the cellular level, at different developmental stages, and in normal and pathological conditions. Therefore, precise determination of tissue and systemic metal levels is necessary to understand organismal metal homeostasis.
Graphite furnace atomic absorption spectrometry (GF-AAS) is a highly sensitive technique used for small sample volumes, making it ideal to measure transition and heavy metals present in biological and environmental samples25,26,27,28. Moreover, due to high sensitivity of the technique, it has been shown to be appropriate for studying the fine transport properties of Na+/K+-ATPase and gastric H+/K+-ATPase using Xenopus oocytes as a model system29. In GF-AAS, the atomized elements within a sample absorb a wavelength of radiation emitted by a light source containing the metal of interest, with the absorbed radiation proportional to the concentration of the element. Elemental electronic excitation takes place upon absorption of ultraviolet or visible radiation in a quantized process unique for each chemical element. In a single electron process, the absorption of a photon involves an electron moving from a lower energy level to higher level within the atom and GF-AAS determines the amount of photons absorbed by the sample, which is proportional to the number of radiation absorbing elements atomized in the graphite tube.
The selectivity of this technique relies on the electronic structure of the atoms, in which each element has a specific absorption/emission spectral line. In the case of Zn, the absorbance wavelength is 213.9 nm and can be precisely distinguished from other metals. Overall, GF-AAS can be used to quantify Zn with adequate limits of detection (LOD) and high sensitivity and selectivity25. The changes in absorbed wavelength are integrated and presented as peaks of energy absorption at specific and isolated wavelengths. The concentration of the Zn in a given sample is usually calculated from a standard curve of known concentrations according to the Beer-Lambert law, in which the absorbance is directly proportional to the concentration of Zn in the sample. However, applying the Beer-Lambert equation to GF-AAS analyses also presents some complications. For instance, variations in the atomization and/or non-homogenous concentrations of the samples can affect the metal measurements.
The metal atomization required for GF AAS trace elemental analysis consists of three fundamental steps. The first step is desolvation, where the liquid solvent is evaporated; leaving dry compounds after the furnace reaches a temperature of around 100 &#176;C. Then, the compounds are vaporized by heating them from 800 to 1,400 &#176;C (depending on the element to be analyzed) and become a gas. Finally, the compounds in the gaseous state are atomized with temperatures that range from 1,500 to 2,500 &#176;C. As discussed above, increasing concentrations of a metal of interest will render proportional increases on the absorption detected by the GF-AAS, yet the furnace reduces the dynamic range of analysis, which is the working range of concentrations that can be determined by the instrument. Thus, the technique requires low concentrations and a careful determination of the dynamic range of the method by determining the LOD and limit of linearity (LOL) of the Beer-Lambert law. The LOD is the minimum quantity required for a substance to be detected, defined as three times the standard deviation of Zn in the matrix. The LOL is the maximum concentration that can be detected using Beer-Lambert law.
In this work, we describe a standard method to analyze the levels of Zn in whole cell extracts, cytoplasmic and nuclear fractions, and in proliferating and differentiating cultured cells (Figure 1). We adapted the rapid isolation of nuclei protocol to different cellular systems to prevent metal loss during sample preparation. The cellular models used were primary myoblasts derived from mouse satellite cells, murine neuroblastoma cells (N2A or Neuro2A), murine 3T3 L1 adipocytes, a human non-tumorigenic breast epithelial cell line (MCF10A), and epithelial Madin-Darby canine kidney (MDCK) cells. These cells were established from different lineages and are good models for investigating lineage specific variations of metal levels in vitro.
Primary myoblasts derived from mouse satellite cells constitute a well-suited in vitro model to investigate skeletal muscle differentiation. Proliferation of these cells is fast when cultured under high serum conditions. Differentiation into the muscular lineage is then induced by low serum conditions30. The murine neuroblastoma (N2A) established cell line was derived from the mouse neural crest. These cells present neuronal and amoeboid stem cell morphology. Upon differentiation stimulus, the N2A cells present several properties of neurons, such as neurofilaments. N2A cells are used to investigate Alzheimer&#39;s disease, neurite outgrowth, and neurotoxicity31,32,33. The 3T3-L1 murine pre-adipocytes established cell line is commonly used to investigate the metabolic and physiological changes associated with adipogenesis. These cells present a fibroblast-like morphology, but once stimulated for differentiation, they present enzymatic activation associated with lipid synthesis and triglycerides accumulation. This can be observed as morphological changes to produce cytoplasmic lipid droplets34,35. MCF10A is a non-tumor mammary epithelial cell line derived from a premenopausal woman with mammary fibrocystic disease36. It has been widely used for biochemical, molecular, and cellular studies related to mammary carcinogenesis such as proliferation, cell migration, and invasion. The Madin-Darby canine kidney (MDCK) epithelial cell line has been extensively used to investigate the properties and molecular events associated with the establishment of the epithelial phenotype. Upon reaching confluence, these cells become polarized and establish cell-cell adhesions, characteristics of mammalian epithelial tissues37.
To test the ability of AAS to measure the levels of Zn in mammalian cells, we analyzed whole and subcellular fractions (cytosol and nucleus) of these five cell lines. AAS measurements showed different concentrations of Zn in these cell types. Concentrations were lower in proliferating and differentiating primary myoblasts (4 to 7 nmol/mg of protein) and higher in the four established cell lines (ranging from 20 to 40 nmol/mg of protein). A small non-significant increase in Zn levels was detected in differentiating primary myoblasts and neuroblastoma cells when compared to proliferating cells. The opposite effect was detected in differentiated adipocytes. However, proliferating 3T3-L1 cells exhibited higher concentrations of the metal compared to differentiated cells. Importantly, in these three cell lines, subcellular fractionation showed that Zn is differentially distributed in the cytosol and nucleus according to the metabolic state of these cells. For instance, in proliferating myoblasts, N2A cells, and 3T3-L1 pre-adipocytes, a majority of the metal is localized to the nucleus. Upon induction of differentiation using specific cell treatments, Zn localized to the cytosol in these three cell types. Interestingly, both epithelial cell lines showed higher levels of Zn during proliferation compared to when reaching confluence, in which a characteristic tight monolayer was formed. In proliferating epithelial cells, the mammary cell line MCF10A had an equal Zn distribution between the cytosol and nucleus, while in the kidney-derived cell line, most of the metal was located in the nucleus. In these two cell types, when the cells reached confluence, Zn was predominantly located to the cytosol. These results demonstrate that GF-AAS is a highly sensitive and accurate technique for performing elemental analysis in low-yield samples. GF-AAS coupled with subcellular fractionation and can be adapted to investigate the levels of trace metal elements in different cell lines and tissues.

<table>
	<tbody>
		<tr>
			<td>3-isobutyl-1-methylxanthine</td>
			<td>Sigma Aldrich</td>
			<td>I5879</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic Acid</td>
			<td>Sigma Aldrich</td>
			<td>1005706</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti Brg1-antibody (G7)</td>
			<td>Santa Cruz biotechnologies</td>
			<td>sc-17796</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti b-tubulin-antibody (BT7R)</td>
			<td>Thermo Scientific</td>
			<td>MA5-16308</td>
			<td></td>
		</tr>
		<tr>
			<td>Bradford</td>
			<td>Biorad</td>
			<td>5000205</td>
			<td></td>
		</tr>
		<tr>
			<td>Dexamethasone</td>
			<td>Sigma Aldrich</td>
			<td>D4902</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle&#39;s Media (DMEM)</td>
			<td>ThermoFischer-Gibco</td>
			<td>11965092</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Modified Eagle&#39;s Media/Nutrient Mix (DMEM/F12)</td>
			<td>ThermoFischer-Gibco</td>
			<td>11320033</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s Phosphate Buffered Saline (DPBS)</td>
			<td>ThermoFischer-Gibco</td>
			<td>14190144</td>
			<td></td>
		</tr>
		<tr>
			<td>Epidemal Growth Factor (EGF)</td>
			<td>Sigma Aldrich</td>
			<td>E9644</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum (FBS)</td>
			<td>ThermoFischer-Gibco</td>
			<td>16000044</td>
			<td></td>
		</tr>
		<tr>
			<td>Fibroblastic Growth Factor-Basic (FGF) (AA 10-155)</td>
			<td>ThermoFischer-Gibco</td>
			<td>PHG0024</td>
			<td></td>
		</tr>
		<tr>
			<td>Horse serum</td>
			<td>ThermoFischer-Gibco</td>
			<td>16050122</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrocortisone</td>
			<td>Sigma Aldrich</td>
			<td>H0888</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrogen Peroxide (H2O2)</td>
			<td>Sigma Aldrich</td>
			<td>95321</td>
			<td></td>
		</tr>
		<tr>
			<td>Insulin</td>
			<td>Sigma Aldrich</td>
			<td>91077C</td>
			<td></td>
		</tr>
		<tr>
			<td>Insulin-Transferrin-Selenium-A</td>
			<td>ThermoFischer</td>
			<td>51300044</td>
			<td></td>
		</tr>
		<tr>
			<td>Nitric Acid (HNO3)</td>
			<td>Sigma Aldrich</td>
			<td>438073</td>
			<td></td>
		</tr>
		<tr>
			<td>Nonidet P-40 (NP-40)</td>
			<td>Thermo Scientific</td>
			<td>85125</td>
			<td></td>
		</tr>
		<tr>
			<td>OptiMEM (Reduced Serum Media)</td>
			<td>ThermoFischer-Gibco</td>
			<td>31985070</td>
			<td></td>
		</tr>
		<tr>
			<td>Penicillin-Streptomycin</td>
			<td>ThermoFischer-Gibco</td>
			<td>15140148</td>
			<td></td>
		</tr>
		<tr>
			<td>PureCol (Collagen)</td>
			<td>Advanced BioMatrix</td>
			<td>5005</td>
			<td></td>
		</tr>
		<tr>
			<td>Retionic Acid</td>
			<td>Sigma Aldrich</td>
			<td>PHR1187</td>
			<td></td>
		</tr>
		<tr>
			<td>Troglitazone</td>
			<td>Sigma Aldrich</td>
			<td>648469-M</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin-EDTA (0.25%), phenol red</td>
			<td>ThermoFischer-Gibco</td>
			<td>25200056</td>
			<td></td>
		</tr>
		<tr>
			<td>Zinc (Zn) Pure Single-Element Standard, 1,000 &#181;g/mL, 2% HNO3</td>
			<td>Perkin Elmer</td>
			<td>N9300168</td>
			<td></td>
		</tr>
		<tr>
			<td>Established Cell Lines</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>3T3-L1</td>
			<td>American Type Culture Collection</td>
			<td>CL-173</td>
			<td></td>
		</tr>
		<tr>
			<td>MCDK</td>
			<td>American Type Culture Collection</td>
			<td>CCL-34</td>
			<td></td>
		</tr>
		<tr>
			<td>MCF10A</td>
			<td>American Type Culture Collection</td>
			<td>CRL-10317</td>
			<td></td>
		</tr>
		<tr>
			<td>N2A</td>
			<td>American Type Culture Collection</td>
			<td>CCL-131</td>
			<td></td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Atomic Absortion spectrophotometer</td>
			<td>PerkinElmer</td>
			<td>Aanalyst 800</td>
			<td></td>
		</tr>
		<tr>
			<td>Bioruptor</td>
			<td>Diagnode</td>
			<td>UCD-200</td>
			<td></td>
		</tr>
	</tbody>
</table>

atomic absorbance spectroscopy to measure intracellular zinc pools in mammalian cells

Transition metals are essential micronutrients for organisms but can be toxic to cells at high concentrations by competing with physiological metals in proteins and generating redox stress. Pathological conditions that lead to metal depletion or accumulation are causal agents of different human diseases. Some examples include anemia, acrodermatitis enteropathica, and Wilson&#8217;s and Menkes&#8217; diseases. It is therefore important to be able to measure the levels and transport of transition metals in biological samples with high sensitivity and accuracy in order to facilitate research exploring how these elements contribute to normal physiological functions and toxicity. Zinc (Zn), for example, is a cofactor in many mammalian proteins, participates in signaling events, and is a secondary messenger in cells. In excess, Zn is toxic and can inhibit absorption of other metals, while in deficit, it can lead to a variety of potentially lethal conditions.

Graphite furnace atomic absorption spectroscopy (GF-AAS) provides a highly sensitive and effective method for determining Zn and other transition metal concentrations in diverse biological samples. Electrothermal atomization via GF-AAS quantifies metals by atomizing small volumes of samples for subsequent selective absorption analysis using wavelength of excitation of the element of interest. Within the limits of linearity of the Beer-Lambert Law, the absorbance of light by the metal is directly proportional to concentration of the analyte. Compared to other methods of determining Zn content, GF-AAS detects both free and complexed Zn in proteins and possibly in small intracellular molecules with high sensitivity in small sample volumes. Moreover, GF-AAS is also more readily accessible than inductively coupled plasma mass spectrometry (ICP-MS) or synchrotron-based X-ray fluorescence. In this method, the systematic sample preparation of different cultured cell lines for analyses in a GF-AAS is described. Variations in this trace element were compared in both whole cell lysates and subcellular fractions of proliferating and differentiated cells as proof of principle.

We tested the ability of the GF-AAS to detect minute levels of Zn in mammalian cells (Figure 1). Thus, we cultured primary myoblasts derived from mouse satellite cells, and the established cell lines N2A (neuroblastoma derived), 3T3 L1 (adipocytes), MCF10A (breast epithelium), and MDCK cells (dog kidney epithelium). First, we isolated whole cell, cytosolic, and nuclear fractions of all these cell types and evaluated the purity of the fractions by western blot...

Watch this Scientific Journal Video about Atomic Absorbance Spectroscopy to Measure Intracellular Zinc Pools in Mammalian Cells at JoVE.com

Atomic Absorbance Spectroscopy to Measure Intracellular Zinc Pools in Mammalian Cells

Cultured primary or established cell lines are commonly used to address fundamental biological and mechanistic questions as an initial approach before using animal models. This protocol describes how to prepare whole cell extracts and subcellular fractions for studies of zinc (Zn) and other trace elements with atomic absorbance spectroscopy.

Transition metals are essential micronutrients for organisms but can be toxic to cells at high concentrations by competing with physiological metals in ...

The role of transition metals in mammalian development is largely underestimated. Emerging evidence shows that metal homeostasis continues to change according to the developmental stage of cells and tissues. Moreover, the specific cellular destinations of metals also varietal in development, and of course, it's challenging to identify their location.To date, different analytical techniques have been developed to quantify metals, but most are expensive or inaccessible. Intensive research is focused to improve metal determinations in a more accessible and efficient manner. Graphite furnace atomic absorption spectroscopy, GF-AAS, has two main advantages.It provides low limits of detection for zinc, allowing for accurate trace zinc analysis. It is also a technique that does not require high volumes of sample, microliters of solution tend to be enough to carry out the analysis. The combination of these two advantages make GF-AAS ideal to analyze trace elements in low volume samples.Several human pathological conditions are related to metal misbalances. Some examples are anemia, acrodermatitis enteropathica, and Wilson's and Menkes'diseases. Therefore, it is important to develop efficient and reliable methods to measure the levels of transition metals in biological samples with high sensitivity and accuracy.GF-AAS is an excellent example on a technology that facilitates a determination of any given metal in normal physiological conditions, and in pathogenic cases. The method is very versatile. It can be applied to many systems and many elements can be analysis using GF-AAS.The challenges are to establish the method limit of detection in reality, making sure that the samples fall within this limit. Given the fact that the volume of samples is low, there is not a lot of room for testing, so carefully examination of data needs to take place since the very beginning. After the first analysis of samples, we need to establish what's the dilution factor needed to bring the samples to the limits required for quantification.Be sure that you are able to fractionate the nuclei properly before going to the AAS. Western blots are always good validation prior to the spectroscopic analysis. While GF-AAS requires low volumes, intracellular pools are in low volumes already.That gives little room for testing. The first measurements need to be carefully done and examined, so sample treatment can be minimized to just one dilution factor. To begin, culture the cells of interest in 55 square centimeter plates.Use a vacuum trap to aspirate the culture media. Be sure to remove all traces of media. Use ice cold PBS free of calcium and magnesium to rinse the cells from the desired time points, or culture conditions, three times.Then add one milliliter of ice cold PBS to the plate, and scrape the cells off the plate. Transfer the cell suspensions to a 1.5 milliliter microcentrifuge tube, and keep it on ice. Centrifuge for 10 seconds at 10, 000 times G, and remove the supernatant by aspiration.If metal analysis of cytoplasmic and nuclear fractions is desired, resuspend the cell pellet in 400 microliters of ice cold PBS containing 0.1%NP-40, a non-ionic detergent. Transfer 100 microliters to a new microcentrifuge tube as the whole cell sample, and store it at minus 20 degrees celsius. To isolate nuclei, use a P1000 micropipette tip to pipette the 400 microliter cell suspension up and down five to 10 times on ice.Then, extract five microliters of the cell suspension and transfer it to a microscope glass slide. Place the five microliters under a light microscope using a 40 times objective to verify the nuclei integrity. Centrifuge the remaining 395 microliter cell lysate suspension for 10 seconds at 10, 000 times G.Transfer the supernatant containing the cytosolic fraction to a new microcentrifuge tube.Next, add 500 microliters of the PBS containing 0.1%NP-40 to rinse the pellet with the nuclear fraction, and centrifuge for 10 seconds at 10, 000 times G.Remove the supernatant, and resuspend the pellet containing the nuclei in 100 microliters of the same solution. To lyse the cells, use a Bioruptor to sonicate the whole cell and nuclei containing solution three times, each for five minutes. Proceed to perform quality control of the purity of the fractions by western blot, using antibodies specific for either the nuclear or cytosolic fractions.First, add an equal volume of concentrated nitric acid of trace metal grade to the whole cell, cytoplasmic and nuclear fractions containing 100, 500 and 100 microliters of cell suspension in 1.5 milliliter microcentrifuge tubes, and place them in a thermal block at 80 degrees celsius to mineralize the cell culture for one hour. After that, take out the tubes from the thermal block and place them in a rack to continue the acid digestion overnight at 20 degrees celsius. Stop the reaction by adding 30%of the sample volume of hydrogen peroxide.Bring the sample volume to 500 microliters with 18 mega Ohm purified water. Next, in a 15 milliliter Falcon tube dilute analytical grade standard nitric oxide in purified water at 18 mega Ohms to prepare two volume percent nitric acid solution as the blank solution during calibration. Then, use the two volume percent nitric acid solution to dilute a commercially available 1, 000 ppm zinc stock solution with a concentration of 1, 000 parts per billion.Prepare working standard solutions from the 1, 000 part per million zinc standard solution, the 1, 000 part per billion solution, then dilute it to 5, 8, 10, 15, 20, and 25 ppb directly with 2 volume percent nitric acid solution. Place one milliliter of 0.1%magnesium nitrate matrix modifier into polypropylene sample cups, and then load the cups into the autosampler carousel. Program the atomic absorption spectrometer to automatically add five microliters of the matrix modifier to the zinc standards and the blank.Set the same optimized condition on the atomic absorption spectrometer for the standard solutions and the samples, with introduction flow rate at 250 milliliters per minute, injection temperature at 20 degrees celsius, and graphite furnace temperature reaching 1, 800 degrees celsius in four step processes. All the standards and samples of a single experiment should be measured at the same time to avoid mistakes due to calibration differences or evaporation. Optimize the lamp C-HCL to a current of 20 amps, wavelength of 213.9 nanometers, and slit of 0.7 nanometers.Pipette the samples in polypropylene sample cups, and place them into the autosampler carousel. The lower limit of detection of zinc is 0.01 parts per billion. By increasing the concentration of the standards, the upper limit of detection of zinc is determined to be 20 parts per billion.After a zinc standard curve is obtained, measure the mineralized samples to determine metal content. If the data obtained is beyond the limit of detection, dilute the samples with 18 mega Ohm purified water treated with 0.1%analytical grade nitric acid. In this rapid isolation of nuclei protocol, a representative western blot from differentiating primary myoblasts shows the purity of subcellular fractions.The chromatin remodeler enzyme Brg1 was used to identify the nuclear fraction, and tubulin was used to identify the cytosolic fraction. This figure shows representative light micrographs for proliferating and differentiated or confluent monolayers of each cell type, and the corresponding zinc content in whole cell extracts, cytosolic and nuclear fractions. All the cell lines analyzed in this study showed zinc concentrations in the nanomolar range.Differentiated primary myotubes exhibited higher levels of zinc than proliferating cells. A similar subcellular distribution of zinc was detected in the neuroblastoma derived cell line N2A. On the other hand, the established 3T3-L1 cell line exhibited higher levels of zinc when the pre-adipocytes were proliferating than when they were induced or differentiated.MCF10A cells showed equal levels of zinc between cytosolic and nuclear fractions in proliferating cells. Once MCF10A cells reach confluence, a 40%decrease in whole cell zinc levels was detected, and the metal was found to be most concentrated in the cytosolic fraction. Graphite furnace atomic absorption spectrometry is a highly sensitive technique to measure transition and heavy metals in biological and environmental samples.Special care and cleanliness in the preparation of subcellular fractions should be taken, as minimal contamination will likely interfere with the analysis, due to the sensitivity of the equipment. Given the low volumes and trace levels of metals in every experiment, it is difficult to think of a better and more accurate technique to measure zinc than GF-AAS. There are no current techniques that can provide the limits of detection and low volume required at the relatively low cost of GF-AAS.Graphite furnace atomic absorption spectrometry is accurate, sensitive, cost-effective, and accessible. This analytical technique will continue to improve as elemental detection technologies continues to advance. Future application for detection of zinc and other metals by GF-AAS will include organs, tissues obtained from animal models, and biopsies from patients with disease associated with systemic metal imbalances.Nitric acid is an extremely corrosive acid capable of causing severe chemical burns very rapidly. This chemical can also react violently with certain compounds such as metallic powders. Because of the hazard posed by nitric acid, it's important to take strict safety measures whenever handling nitric acid.When handling nitric acid we strongly recommend you wear safety chemical glasses, face shield for splash protection, gloves, and approved vapor respiration if ventilation is not adequate.

atomic-absorbance-spectroscopy-to-measure-intracellular-zinc-pools

Research

JoVE Journal

Biochemistry

Protein Complex Affinity Capture from Cryomilled Mammalian Cells

Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this technique is also frequently referred to as immunoprecipitation. Affinity capture can be applied in a bench-scale and in a high-throughput context. When coupled with protein mass spectrometry, affinity capture has proven to be a workhorse of interactome analysis. Although there are potentially many ways to execute the numerous steps involved, the following protocols implement our favored methods. Two features are distinctive: the use of cryomilled cell powder to produce cell extracts, and antibody-coupled paramagnetic beads as the affinity medium. In many cases, we have obtained superior results to those obtained with more conventional affinity capture practices. Cryomilling avoids numerous problems associated with other forms of cell breakage. It provides efficient breakage of the material, while avoiding denaturation issues associated with heating or foaming. It retains the native protein concentration up to the point of extraction, mitigating macromolecular dissociation. It reduces the time extracted proteins spend in solution, limiting deleterious enzymatic activities, and it may reduce the non-specific adsorption of proteins by the affinity medium. Micron-scale magnetic affinity media have become more commonplace over the last several years, increasingly replacing the traditional agarose- and Sepharose-based media. Primary benefits of magnetic media include typically lower non-specific protein adsorption; no size exclusion limit because protein complex binding occurs on the bead surface rather than within pores; and ease of manipulation and handling using magnets.

Here we describe protocols to disrupt mammalian cells by solid-state milling at a cryogenic temperature, produce a cell extract from the resulting cell powder, and isolate protein complexes of interest by affinity capture upon antibody-coupled micron-scale paramagnetic beads.

Affinity capture is an effective technique for isolating endogenous protein complexes for further study. When used in conjunction with an antibody, this ...

Atomic Scale Structural Studies of Macromolecular Assemblies by Solid-state Nuclear Magnetic Resonance Spectroscopy

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the propagation of neurodegenerative disorders. Such assemblies consist in multiple protein subunits organized in a non-covalent way to form large macromolecular objects that can execute a variety of cellular functions or cause detrimental consequences. Atomic insights into the assembly mechanisms and the functioning of those macromolecular assemblies remain often scarce since their inherent insolubility and non-crystallinity often drastically reduces the quality of the data obtained from most techniques used in structural biology, such as X-ray crystallography and solution Nuclear Magnetic Resonance (NMR). We here present magic-angle spinning solid-state NMR spectroscopy (SSNMR) as a powerful method to investigate structures of macromolecular assemblies at atomic resolution. SSNMR can reveal atomic details on the assembled complex without size and solubility limitations. The protocol presented here describes the essential steps from the production of 13C/15N isotope-labeled macromolecular protein assemblies to the acquisition of standard SSNMR spectra and their analysis and interpretation. As an example, we show the pipeline of a SSNMR structural analysis of a filamentous protein assembly.

Structures of supramolecular protein assemblies at atomic resolution are of high relevance because of their crucial roles in a variety of biological phenomena. Herein, we present a protocol to perform high-resolution structural studies on insoluble and non-crystalline macromolecular protein assemblies by magic-angle spinning solid-state nuclear magnetic resonance spectroscopy (MAS SSNMR).

Supramolecular protein assemblies play fundamental roles in biological processes ranging from host-pathogen interaction, viral infection to the ...

Quantitative Immunofluorescence to Measure Global Localized Translation

The mechanisms regulating mRNA translation are involved in various biological processes, such as germ line development, cell differentiation, and organogenesis, as well as in multiple diseases. Numerous publications have convincingly shown that specific mechanisms tightly regulate mRNA translation. Increased interest in the translation-induced regulation of protein expression has led to the development of novel methods to study and follow de novo protein synthesis in cellulo. However, most of these methods are complex, making them costly and often limiting the number of mRNA targets that can be studied. This manuscript proposes a method that requires only basic reagents and a confocal fluorescence imaging system to measure and visualize the changes in mRNA translation that occur in any cell line under various conditions. This method was recently used to show localized translation in the subcellular structures of adherent cells over a short period of time, thus offering the possibility of visualizing de novo translation for a short period during a variety of biological processes or of validating changes in translational activity in response to specific stimuli.

This manuscript describes a method to visualize and quantify localized translation events in subcellular compartments. The approach proposed in this manuscript requires a basic confocal imaging system and reagents and is rapid and cost-effective.

The mechanisms regulating mRNA translation are involved in various biological processes, such as germ line development, cell differentiation, and ...

Force Spectroscopy of Single Protein Molecules Using an Atomic Force Microscope

The determination of the folding process of proteins from their amino acid sequence to their native 3D structure is an important problem in biology. Atomic force microscopy (AFM) can address this problem by enabling stretching and relaxation of single protein molecules, which gives direct evidence of specific unfolding and refolding characteristics. AFM-based single-molecule force-spectroscopy (AFM-SMFS) provides a means to consistently measure high-energy conformations in proteins that are not possible in traditional bulk (biochemical) measurements. Although numerous papers were published to show principles of AFM-SMFS, it is not easy to conduct SMFS experiments due to a lack of an exhaustively complete protocol. In this study, we briefly illustrate the principles of AFM and extensively detail the protocols, procedures, and data analysis as a guideline to achieve good results from SMFS experiments. We demonstrate representative SMFS results of single protein mechanical unfolding measurements and we provide troubleshooting strategies for some commonly encountered problems.

We describe the detailed procedures and strategies to measure the mechanical properties and mechanical unfolding pathways of single protein molecules using an atomic force microscope. We also show representative results as a reference for selection and justification of good single protein molecule recordings.

The determination of the folding process of proteins from their amino acid sequence to their native 3D structure is an important problem in biology. ...

Dissipative Microgravimetry to Study the Binding Dynamics of the Phospholipid Binding Protein Annexin A2 to Solid-supported Lipid Bilayers Using a Quartz Resonator

The dissipative quartz crystal microbalance technique is a simple and label-free approach to measure simultaneously the mass uptake and viscoelastic properties of the absorbed/immobilized mass on sensor surfaces, allowing the measurements of the interaction of proteins with solid-supported surfaces, such as lipid bilayers, in real-time and with a high sensitivity. Annexins are a highly conserved group of phospholipid-binding proteins that interact reversibly with the negatively charged headgroups via the coordination of calcium ions. Here, we describe a protocol that was employed to quantitatively analyze the binding of annexin A2 (AnxA2) to planar lipid bilayers prepared on the surface of a quartz sensor. This protocol is optimized to obtain robust and reproducible data and includes a detailed step-by-step description. The method can be applied to other membrane-binding proteins and bilayer compositions.

Here, we present an experimental protocol that can be employed to determine the binding affinities and mode of interaction of label-free phospholipid-binding protein annexin A2 with immobilized solid-supported bilayers (SLB) by simultaneously measuring the mass uptake and the viscoelastic properties of the protein annexin A2.

The dissipative quartz crystal microbalance technique is a simple and label-free approach to measure simultaneously the mass uptake and viscoelastic ...

A Strategy to Identify Compounds that Affect Cell Growth and Survival in Cultured Mammalian Cells at Low-to-Moderate Throughput

Cytotoxicity is a critical parameter that needs to be quantified when studying drugs that may have therapeutic benefits. Because of this, many drug screening assays utilize cytotoxicity as one of the critical characteristics to be profiled for individual compounds. Cells in culture are a useful model to assess cytotoxicity before proceeding to follow up on promising lead compounds in more costly and labor-intensive animal models. We describe a strategy to identify compounds that affect cell growth in a tdTomato expressing human neural stem cells (NSC) line. The strategy uses two complementary assays to assess cell number. One assay works via the reduction of 3-(4,5-dimethylthizol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) to formazan as a proxy for cell number and the other directly counts the tdTomato expressing NSCs. The two assays can be performed simultaneously in a single experiment and are not labor intensive, rapid, and inexpensive. The strategy described in this demonstration tested 57 compounds in an exploratory primary screen for toxicity in a 96-well plate format. Three of the hits were characterized further in a six-point dose response using the same assay set-up as the primary screen. In addition to providing excellent corroboration for toxicity, comparison of results from the two assays may be effective in identifying compounds affecting other aspects of cell growth.

It is often necessary to assess the potential cytotoxicity of a set of compounds on cultured cells. Here, we describe a strategy to reliably screen for toxic compounds in a 96-well format.

Cytotoxicity is a critical parameter that needs to be quantified when studying drugs that may have therapeutic benefits. Because of this, many drug ...

Density Gradient Ultracentrifugation for Investigating Endocytic Recycling in Mammalian Cells

Endosomal trafficking is an essential cellular process that regulates a broad range of biological events. Proteins are internalized from the plasma membrane and then transported to the early endosomes. The internalized proteins could be transited to the lysosome for degradation or recycled back to the plasma membrane. A robust endocytic recycling pathway is required to balance the removal of membrane materials from endocytosis. Various proteins are reported to regulate the pathway, including ADP-ribosylation factor 6 (ARF6). Density gradient ultracentrifugation is a classical method for cell fractionation. After the centrifugation, organelles are sedimented at their isopycnic surface. The fractions are collected and used for other downstream applications. Described here is a protocol to obtain a recycling endosome-containing fraction from transfected mammalian cells using density gradient ultracentrifugation. The isolated fractions were subjected to standard Western blotting for analyzing their protein contents. By employing this method, we identified that the plasma membrane targeting of engulfment and cell motility 1 (ELMO1), a Ras-related C3 botulinum toxin substrate 1 (Rac1) guanine nucleotide exchange factor, is through ARF6-mediated endocytic recycling.

This paper aims to present a protocol for preparing recycling endosomes from mammalian cells using sucrose density gradient ultracentrifugation.

Endosomal trafficking is an essential cellular process that regulates a broad range of biological events. Proteins are internalized from the plasma ...

Dual-Color Fluorescence Cross-Correlation Spectroscopy to Study Protein-Protein Interaction and Protein Dynamics in Live Cells

We present a protocol and workflow to perform live cell dual-color fluorescence cross-correlation spectroscopy (FCCS) combined with F&#246;rster Resonance Energy transfer (FRET) to study membrane receptor dynamics in live cells using modern fluorescence labeling techniques. In dual-color FCCS, where the fluctuations in fluorescence intensity represent the dynamic &#34;fingerprint&#34; of the respective fluorescent biomolecule, we can probe co-diffusion or binding of the receptors. FRET, with its high sensitivity to molecular distances, serves as a well-known &#34;nanoruler&#34; to monitor intramolecular changes. Taken together, conformational changes and key parameters such as local receptor concentrations and mobility constants become accessible in cellular settings.
Quantitative fluorescence approaches are challenging in cells due to high noise levels and the vulnerability of the sample. Here we show how to perform this experiment, including the calibration steps using dual-color labeled &#946;2-adrenergic receptor (&#946;2AR) labeled with eGFP and SNAP-tag-TAMRA. A step-by-step data analysis procedure is provided using open-source software and templates that are easy to customize.
Our guideline enables researchers to unravel molecular interactions of biomolecules in live cells in situ with high reliability despite the limited signal-to-noise levels in live cell experiments. The operational window of FRET and particularly FCCS at low concentrations allows quantitative analysis at near-physiological conditions.

We present an experimental protocol and data analysis workflow to perform live cell dual-color fluorescence cross correlation spectroscopy (FCCS) combined with F&#246;rster Resonance Energy transfer (FRET) to study membrane receptor dynamics in live cells using modern fluorescence labeling techniques.

We present a protocol and workflow to perform live cell dual-color fluorescence cross-correlation spectroscopy (FCCS) combined with F&#246;rster Resonance ...

Purification of Ubiquitinated p53 Proteins from Mammalian Cells

Ubiquitination is a type of posttranslational modification that regulates not only the stability but also the localization and function of a substrate protein. The ubiquitination process occurs intracellularly in eukaryotes and regulates almost all basic cellular biological processes. Purification of ubiquitinated proteins aids the investigation of the role of ubiquitination in controlling the function of substrate proteins. Here, a step-by-step procedure to purify ubiquitinated proteins in mammalian cells is described with the p53 tumor suppressor protein as an example. Ubiquitinated p53 proteins were purified under stringent nondenaturing and denaturing conditions. Total cellular Flag-tagged p53 protein was purified with anti-Flag antibody-conjugated agarose under nondenaturing conditions. Alternatively, total cellular His-tagged ubiquitinated protein was purified using nickel-charged resin under denaturing conditions. Ubiquitinated p53 proteins in the eluates were successfully detected with specific antibodies. Using this procedure, the ubiquitinated forms of a given protein can be efficiently purified from mammalian cells, facilitating studies on the roles of ubiquitination in regulating protein function.

The protocol describes a step-by-step method to purify ubiquitinated proteins from mammalian cells using the p53 tumor suppressor protein as an example. Ubiquitinated p53 proteins were purified from cells under stringent nondenaturing and denaturing conditions.

Ubiquitination is a type of posttranslational modification that regulates not only the stability but also the localization and function of a substrate ...

Inner Mitochondrial Membrane Sensitivity to Na+ Reveals Partially Segmented Functional CoQ Pools

Ubiquinone (CoQ) pools in the inner mitochondrial membrane (IMM) are partially segmented to either complex I or FAD-dependent enzymes. Such subdivision can be easily assessed by a comparative assay using NADH or succinate as electron donors in frozen-thawed mitochondria, in which cytochrome c (cyt c) reduction is measured. The assay relies on the effect of Na+ on the IMM, decreasing its fluidity. Here, we present a protocol to measure NADH-cyt c oxidoreductase activity and succinate-cyt c oxidoreductase activities in the presence of NaCl or KCl. The reactions, which rely on the mixture of reagents in a cuvette in a stepwise manner, are measured spectrophotometrically during 4 min in the presence of Na+ or K+. The same mixture is performed in parallel in the presence of the specific enzyme inhibitors in order to subtract the unspecific change in absorbance. NADH-cyt c oxidoreductase activity does not decrease in the presence of any of these cations. However, succinate-cyt c oxidoreductase activity decreases in the presence of NaCl. This simple experiment highlights: 1) the effect of Na+ in decreasing IMM fluidity and CoQ transfer; 2) that supercomplex I+III2 protects ubiquinone (CoQ) transfer from being affected by lowering IMM fluidity; 3) that CoQ transfer between CI and CIII is functionally different from CoQ transfer between CII and CIII. These facts support the existence of functionally differentiated CoQ pools in the IMM and show that they can be regulated by the changing Na+ environment of mitochondria.

Inner Mitochondrial Membrane Sensitivity to Na+ Reveals Partially Segmented Functional CoQ Pools

This protocol describes a comparative assay, using mitochondrial complex activities CI+CIII and CII+CIII in the presence or absence of Na+, to study the existence of partially segmented functional CoQ pools.

Ubiquinone (CoQ) pools in the inner mitochondrial membrane (IMM) are partially segmented to either complex I or FAD-dependent enzymes. Such subdivision ...