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Affinity isolated peptide

Affinity isolated peptide


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What is affinity isolated peptides??
(I have not studied biology since last 8 years and now I am going through it because I need it for my research. So if someone can describe it in simple language it would be very helpful)


A peptide or protein can be purified by affinity chromatography. The principle is that the peptide has some substrate to which it will bind, retarding its progress through the column compared to the rest of the peptide population. A couple of typical examples are:

  • Using a His6 tag put on recombinant molecules, IIRC it binds to Ni2+ trapped in the chromatographic resin and is eluted with a chelator like EDTA.
  • Immunoaffinity chromatography, where you have a population of antibodies on the chromatographic resin which are specific to the protein that you want to purify (or alternatively having the immunogen bound to the resin so that you can purify the antibodies against it)

Mighty Wikipedia has a link about affinity chromatography here.


Quantification and Analysis of Proteins

Affinity Chromatography

Affinity chromatography uses the principle that the protein binds to a molecule for which it has specific affinity. This is because in most instances proteins carry out their biological activity through binding or complex formation with specific small molecules, or ligands. This small molecule can be immobilized through covalent attachment to the resin in a column ( Fig. 8.6 ). When the sample goes through the column, the protein of interest, in displaying affinity for its ligand, become bound and immobilized itself. The protein of interest is thus removed from the mixture of sample. Finally, the protein is dissociated or eluted from the resin by the addition of high concentrations of free ligand in solution. Because this method relies on the biological specificity of the protein of interest, it is a very efficient procedure. A typical example is the resins coupled to an antibody that recognizes a specific protein, or it may contain an unreactive analogue of an enzyme's substrate. The power of affinity chromatography lies in the specificity of binding between the affinity reagent on the resin and the molecule to be purified. As such, it is possible to design an affinity chromatography procedure to purify a protein in a single step.

Fig. 8.6 . Affinity chromatography to isolate molecules based upon ligand binding abilities.


TAP-tagging

The TAP tag consists of two Immunoglobulin G (IgG) binding domains from the Staphylococcus aureus surface protein, Protein A and a calmodulin-binding peptide (CBP). These two parts are separated by a short peptide which is a target for the site-specific TEV protease: A widely-available protease originally isolated from Tobacco Etch Virus (hence the name).

Your TAP-tagged protein of interest is initially isolated from cell lysate via IgG-coated beads, which are tightly bound by the protein A part of the tag. After washing the beads, the TAP-tagged protein (and its interactors) can be released from the beads by incubating with TEV protease. This cleaves the TAP tag, leaving the Protein A part bound to the beads, together with any non-specific IgG-binding proteins. Your favourite protein, plus the CBP half of the tag, is released from the beads. As it is still tagged with CBP, it can then be re-purified using Calmodulin resin, washed and eluted.

This two-step purification process greatly reduces the amount of non-specific binding you get in your protein purification. This is really important if, for example, you want to identify all the binding partners of your favourite protein by mass spec. By using two separate purification steps, you minimise the likelihood of spurious proteins contaminating your purification.

Since the first description of the TAP tag, tandem affinity purification has become widely used across an ever-expanding range of model systems. Hopefully this brief introduction will have given you an idea of the basic principles involved, and the advantages of using a two-stage protocol for purifying protein complexes.

For a more complete review of tandem affinity purification you could read: Puig, Caspary, Rigaut et al. (2001) Methods 24, 214-229. Alternatively, if you want to read the original description, see: Rigaut, Shevchenko, Rutz et al. (1999) Nature Biotechnology 17(10):1030-2.


A novel peptide isolated from garlic shows anticancer effect against leukemic cell lines via interaction with Bcl-2 family proteins

Dalina Tanyong, Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand.

Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Nakhon pathom, Thailand

Department of Medical Laboratory Sciences, Faculty of Allied Health Sciences, University of Jaffna, Jaffna, Sri Lanka

Center of Data Mining and Biomedical Informatics, Faculty of Medical Technology, Mahidol University, Nakhon pathom, Thailand

Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand

Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand

Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Nakhon pathom, Thailand

Dalina Tanyong, Department of Clinical Microscopy, Faculty of Medical Technology, Mahidol University, Nakhon Pathom 73170, Thailand.

Abstract

Leukemia is a group of cancer caused by the abnormal proliferation and differentiation of hematopoietic stem cells. Efforts geared toward effective therapeutic strategies with minimal side effects are underway. Peptides derived from natural resources have recently gained special attention as alternative chemotherapeutic agents due to their minimal adverse effects. In the present study, the aim was to isolate peptides from garlic (Allium sativum) and investigate their anticancer activity against leukemic cell lines. The protein extract of A. sativum was pepsin-digested to obtain protein hydrolysate followed by sequential purification methods. A novel anticancer peptide, VKLRSLLCS (VS-9), was identified and characterized by mass spectrometric analysis. The peptide was demonstrated to significantly inhibit the cell proliferation of MOLT-4 and K562 leukemic cell lines while exhibiting minimal inhibition against normal PBMC. Particularly, VS-9 could induce apoptosis and upregulate mRNA levels of caspase 3, caspase 8, caspase 9, and Bax while downregulating Bcl-2, Bcl-xL, and Bcl-w. Molecular docking of VS-9 with the anti-apoptotic Bcl-2 protein family suggested that VS-9 could bind the binding groove of the BH3 domain on target proteins. Protein–peptide interaction analysis by affinity chromatography and LC-MS/MS further showed that VS-9 could bind Bcl-2 proteins. Results suggest VS-9 as a potential garlic-derived novel anticancer peptide possessing apoptosis-inducing properties against leukemic cell lines via anti-apoptotic Bcl-2 protein family.

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Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.


Biochemical isolation of Argonaute protein complexes by Ago-APP

During microRNA (miRNA)-guided gene silencing, Argonaute (Ago) proteins interact with a member of the TNRC6/GW protein family. Here we used a short GW protein-derived peptide fused to GST and demonstrate that it binds to Ago proteins with high affinity. This allows for the simultaneous isolation of all Ago protein complexes expressed in diverse species to identify associated proteins, small RNAs, or target mRNAs. We refer to our method as "Ago protein Affinity Purification by Peptides" (Ago-APP). Furthermore, expression of this peptide competes for endogenous TNRC6 proteins, leading to global inhibition of miRNA function in mammalian cells.

Keywords: Argonaute GW proteins RNAi microRNAs small RNAs.

Conflict of interest statement

The authors declare no conflict of interest.

Figures

Precipitation of Ago complexes by…

Precipitation of Ago complexes by Ago-APP. ( A ) Schematic representation of the…

Isolation and characterization of Ago…

Isolation and characterization of Ago complexes from different species. ( A ) Ago-APP…

Ago-APP can be used for simultaneous PAR–CLIP of human Ago1–4. ( A )…

T6B peptide expression inhibits endogenous…

T6B peptide expression inhibits endogenous miRNA-guided gene silencing. ( A ) Luciferase assays…


Sequential peptide affinity purification system for the systematic isolation and identification of protein complexes from Escherichia coli

Biochemical purification of affinity-tagged proteins in combination with mass spectrometry methods is increasingly seen as a cornerstone of systems biology, as it allows for the systematic genome-scale characterization of macromolecular protein complexes, representing demarcated sets of stably interacting protein partners. Accurate and sensitive identification of both the specific and shared polypeptide components of distinct complexes requires purification to near homogeneity. To this end, a sequential peptide affinity (SPA) purification system was developed to enable the rapid and efficient isolation of native Escherichia coli protein complexes (J Proteome Res 3:463-468, 2004). SPA purification makes use of a dual-affinity tag, consisting of three modified FLAG sequences (3X FLAG) and a calmodulin binding peptide (CBP), spaced by a cleavage site for tobacco etch virus (TEV) protease (J Proteome Res 3:463-468, 2004). Using the lambda-phage Red homologous recombination system (PNAS 97:5978-5983, 2000), a DNA cassette, encoding the SPA-tag and a selectable marker flanked by gene-specific targeting sequences, is introduced into a selected locus in the E. coli chromosome so as to create a C-terminal fusion with the protein of interest. This procedure aims for near-endogenous levels of tagged protein production in the recombinant bacteria to avoid spurious, non-specific protein associations (J Proteome Res 3:463-468, 2004). In this chapter, we describe a detailed, optimized protocol for the tagging, purification, and subsequent mass spectrometry-based identification of the subunits of even low-abundance bacterial protein complexes isolated as part of an ongoing large-scale proteomic study in E. coli (Nature 433:531-537, 2005).


Isolation, cloning, and overexpression of a chitinase gene fragment from the hyperthermophilic archaeon Thermococcus chitonophagus: semi-denaturing purification of the recombinant peptide and investigation of its relation with other chitinases

A 189-bp sequence was isolated from the hyperthermophilic archaeon Thermococcus chitonophagus and was found to present strong homology with a large number of chitinase genes from a variety of organisms and particularly with the chitinaseA gene from Pyrococcus kodakaraensis (Pk-chiA). This fragment was subcloned to an expression vector and overexpressed in Escherichia coli. The E. coli BLR21(DE3)pLysS transformant, harbouring the gene on the pET-31b plasmid vector, was found to overproduce the target protein at high levels. The 63 aminoacid-long peptide was efficiently purified to homogeneity, with a one-step, semi-denaturing affinity chromatography, on a metal chelation resin and was used for the production of a specific, polyclonal antibody from rabbits. The produced antibody was demonstrated to display strong and specific affinity for the chitinase A from Serratia marcescens (Sm-chiA), as well as the membrane-bound chitinase70 from Thermococcus chitonophagus (Tc-Chi70). The strong sequence homology, in combination with the demonstrated specific immunochemical affinity, indicates that the isolated peptide is part of a chitinolytic enzyme of T. chitonophagus. In particular, it could belong to the membrane-bound chi70, or to a distinct chitinase, coded by a different gene, or even by the same gene, following post-transcriptional or post-translational modifications.


Individual protein immunoprecipitation (IP) Edit

Involves using an antibody that is specific for a known protein to isolate that particular protein out of a solution containing many different proteins. These solutions will often be in the form of a crude lysate of a plant or animal tissue. Other sample types could be body fluids or other samples of biological origin.

Protein complex immunoprecipitation (Co-IP) Edit

Immunoprecipitation of intact protein complexes (i.e. antigen along with any proteins or ligands that are bound to it) is known as co-immunoprecipitation (Co-IP). Co-IP works by selecting an antibody that targets a known protein that is believed to be a member of a larger complex of proteins. By targeting this known member with an antibody it may become possible to pull the entire protein complex out of solution and thereby identify unknown members of the complex.

This works when the proteins involved in the complex bind to each other tightly, making it possible to pull multiple members of the complex out of solution by latching onto one member with an antibody. This concept of pulling protein complexes out of solution is sometimes referred to as a "pull-down". Co-IP is a powerful technique that is used regularly by molecular biologists to analyze protein–protein interactions.

  • A particular antibody often selects for a subpopulation of its target protein that has the epitope exposed, thus failing to identify any proteins in complexes that hide the epitope. This can be seen in that it is rarely possible to precipitate even half of a given protein from a sample with a single antibody, even when a large excess of antibody is used.
  • As successive rounds of targeting and immunoprecipitations take place, the number of identified proteins may continue to grow. The identified proteins may not ever exist in a single complex at a given time, but may instead represent a network of proteins interacting with one another at different times for different purposes.
  • Repeating the experiment by targeting different members of the protein complex allows the researcher to double-check the result. Each round of pull-downs should result in the recovery of both the original known protein as well as other previously identified members of the complex (and even new additional members). By repeating the immunoprecipitation in this way, the researcher verifies that each identified member of the protein complex was a valid identification. If a particular protein can only be recovered by targeting one of the known members but not by targeting other of the known members then that protein's status as a member of the complex may be subject to question.

Chromatin immunoprecipitation (ChIP) Edit

Chromatin immunoprecipitation (ChIP) is a method used to determine the location of DNA binding sites on the genome for a particular protein of interest. This technique gives a picture of the protein–DNA interactions that occur inside the nucleus of living cells or tissues. The in vivo nature of this method is in contrast to other approaches traditionally employed to answer the same questions.

The principle underpinning this assay is that DNA-binding proteins (including transcription factors and histones) in living cells can be cross-linked to the DNA that they are binding. By using an antibody that is specific to a putative DNA binding protein, one can immunoprecipitate the protein–DNA complex out of cellular lysates. The crosslinking is often accomplished by applying formaldehyde to the cells (or tissue), although it is sometimes advantageous to use a more defined and consistent crosslinker such as di-tert-butyl peroxide (DTBP). Following crosslinking, the cells are lysed and the DNA is broken into pieces 0.2–1.0 kb in length by sonication. At this point the immunoprecipitation is performed resulting in the purification of protein–DNA complexes. The purified protein–DNA complexes are then heated to reverse the formaldehyde cross-linking of the protein and DNA complexes, allowing the DNA to be separated from the proteins. The identity and quantity of the DNA fragments isolated can then be determined by polymerase chain reaction (PCR). The limitation of performing PCR on the isolated fragments is that one must have an idea which genomic region is being targeted in order to generate the correct PCR primers. Sometimes this limitation is circumvented simply by cloning the isolated genomic DNA into a plasmid vector and then using primers that are specific to the cloning region of that vector. Alternatively, when one wants to find where the protein binds on a genome-wide scale, ChIP-sequencing is used and has recently emerged as a standard technology that can localize protein binding sites in a high-throughput, cost-effective fashion, allowing also for the characterization of the cistrome. Previously, DNA microarray was also used (ChIP-on-chip or ChIP-chip).

RNP immunoprecipitation (RIP) Edit

Similar to chromatin immunoprecipitation (ChIP) outlined above, but rather than targeting DNA binding proteins as in ChIP, an RNP immunoprecipitation targets ribonucleoproteins (RNPs). [1] Live cells are first lysed and then the target protein and associated RNA are immunoprecipitated using an antibody targeting the protein of interest. The purified RNA-protein complexes can be separated by performing an RNA extraction and the identity of the RNA can be determined by cDNA sequencing [2] or RT-PCR. Some variants of RIP, such as PAR-CLIP include cross-linking steps, which then require less careful lysis conditions.

Tagged proteins Edit

One of the major technical hurdles with immunoprecipitation is the great difficulty in generating an antibody that specifically targets a single known protein. To get around this obstacle, many groups will engineer tags onto either the C- or N- terminal end of the protein of interest. The advantage here is that the same tag can be used time and again on many different proteins and the researcher can use the same antibody each time. The advantages with using tagged proteins are so great that this technique has become commonplace for all types of immunoprecipitation including all of the types of IP detailed above. Examples of tags in use are the green fluorescent protein (GFP) tag, glutathione-S-transferase (GST) tag and the FLAG-tag tag. While the use of a tag to enable pull-downs is convenient, it raises some concerns regarding biological relevance because the tag itself may either obscure native interactions or introduce new and unnatural interactions.

The two general methods for immunoprecipitation are the direct capture method and the indirect capture method.

Direct Edit

Antibodies that are specific for a particular protein (or group of proteins) are immobilized on a solid-phase substrate such as superparamagnetic microbeads or on microscopic agarose (non-magnetic) beads. The beads with bound antibodies are then added to the protein mixture, and the proteins that are targeted by the antibodies are captured onto the beads via the antibodies in other words, they become immunoprecipitated.

Indirect Edit

Antibodies that are specific for a particular protein, or a group of proteins, are added directly to the mixture of protein. The antibodies have not been attached to a solid-phase support yet. The antibodies are free to float around the protein mixture and bind their targets. As time passes, beads coated in Protein A/G are added to the mixture of antibody and protein. At this point, the antibodies, which are now bound to their targets, will stick to the beads.

From this point on, the direct and indirect protocols converge because the samples now have the same ingredients. Both methods give the same end-result with the protein or protein complexes bound to the antibodies which themselves are immobilized onto the beads.

Selection Edit

An indirect approach is sometimes preferred when the concentration of the protein target is low or when the specific affinity of the antibody for the protein is weak. The indirect method is also used when the binding kinetics of the antibody to the protein is slow for a variety of reasons. In most situations, the direct method is the default, and the preferred, choice.

Agarose Edit

Historically the solid-phase support for immunoprecipitation used by the majority of scientists has been highly-porous agarose beads (also known as agarose resins or slurries). The advantage of this technology is a very high potential binding capacity, as virtually the entire sponge-like structure of the agarose particle (50 to 150μm in size) is available for binding antibodies (which will in turn bind the target proteins) and the use of standard laboratory equipment for all aspects of the IP protocol without the need for any specialized equipment. The advantage of an extremely high binding capacity must be carefully balanced with the quantity of antibody that the researcher is prepared to use to coat the agarose beads. Because antibodies can be a cost-limiting factor, it is best to calculate backward from the amount of protein that needs to be captured (depending upon the analysis to be performed downstream), to the amount of antibody that is required to bind that quantity of protein (with a small excess added in order to account for inefficiencies of the system), and back still further to the quantity of agarose that is needed to bind that particular quantity of antibody. In cases where antibody saturation is not required, this technology is unmatched in its ability to capture extremely large quantities of captured target proteins. The caveat here is that the "high capacity advantage" can become a "high capacity disadvantage" that is manifested when the enormous binding capacity of the sepharose/agarose beads is not completely saturated with antibodies. It often happens that the amount of antibody available to the researcher for their immunoprecipitation experiment is less than sufficient to saturate the agarose beads to be used in the immunoprecipitation. In these cases the researcher can end up with agarose particles that are only partially coated with antibodies, and the portion of the binding capacity of the agarose beads that is not coated with antibody is then free to bind anything that will stick, resulting in an elevated background signal due to non-specific binding of lysate components to the beads, which can make data interpretation difficult. While some may argue that for these reasons it is prudent to match the quantity of agarose (in terms of binding capacity) to the quantity of antibody that one wishes to be bound for the immunoprecipitation, a simple way to reduce the issue of non-specific binding to agarose beads and increase specificity is to preclear the lysate, which for any immunoprecipitation is highly recommended. [3] [4]

Preclearing Edit

Lysates are complex mixtures of proteins, lipids, carbohydrates and nucleic acids, and one must assume that some amount of non-specific binding to the IP antibody, Protein A/G or the beaded support will occur and negatively affect the detection of the immunoprecipitated target(s). In most cases, preclearing the lysate at the start of each immunoprecipitation experiment (see step 2 in the "protocol" section below) [5] is a way to remove potentially reactive components from the cell lysate prior to the immunoprecipitation to prevent the non-specific binding of these components to the IP beads or antibody. The basic preclearing procedure is described below, wherein the lysate is incubated with beads alone, which are then removed and discarded prior to the immunoprecipitation. [5] This approach, though, does not account for non-specific binding to the IP antibody, which can be considerable. Therefore, an alternative method of preclearing is to incubate the protein mixture with exactly the same components that will be used in the immunoprecipitation, except that a non-target, irrelevant antibody of the same antibody subclass as the IP antibody is used instead of the IP antibody itself. [4] This approach attempts to use as close to the exact IP conditions and components as the actual immunoprecipitation to remove any non-specific cell constituent without capturing the target protein (unless, of course, the target protein non-specifically binds to some other IP component, which should be properly controlled for by analyzing the discarded beads used to preclear the lysate). The target protein can then be immunoprecipitated with the reduced risk of non-specific binding interfering with data interpretation.

Superparamagnetic beads Edit

While the vast majority of immunoprecipitations are performed with agarose beads, the use of superparamagnetic beads for immunoprecipitation is a newer approach that is gaining in popularity as an alternative to agarose beads for IP applications. Unlike agarose, magnetic beads are solid and can be spherical, depending on the type of bead, and antibody binding is limited to the surface of each bead. While these beads do not have the advantage of a porous center to increase the binding capacity, magnetic beads are significantly smaller than agarose beads (1 to 4μm), and the greater number of magnetic beads per volume than agarose beads collectively gives magnetic beads an effective surface area-to-volume ratio for optimum antibody binding.

Commercially available magnetic beads can be separated based by size uniformity into monodisperse and polydisperse beads. Monodisperse beads, also called microbeads, exhibit exact uniformity, and therefore all beads exhibit identical physical characteristics, including the binding capacity and the level of attraction to magnets. Polydisperse beads, while similar in size to monodisperse beads, show a wide range in size variability (1 to 4μm) that can influence their binding capacity and magnetic capture. Although both types of beads are commercially available for immunoprecipitation applications, the higher quality monodisperse superparamagnetic beads are more ideal for automatic protocols because of their consistent size, shape and performance. Monodisperse and polydisperse superparamagnetic beads are offered by many companies, including Invitrogen, Thermo Scientific, and Millipore.

Agarose vs. magnetic beads Edit

Proponents of magnetic beads claim that the beads exhibit a faster rate of protein binding [6] [7] [8] over agarose beads for immunoprecipitation applications, although standard agarose bead-based immunoprecipitations have been performed in 1 hour. [4] Claims have also been made that magnetic beads are better for immunoprecipitating extremely large protein complexes because of the complete lack of an upper size limit for such complexes, [6] [7] [9] although there is no unbiased evidence stating this claim. The nature of magnetic bead technology does result in less sample handling [7] due to the reduced physical stress on samples of magnetic separation versus repeated centrifugation when using agarose, which may contribute greatly to increasing the yield of labile (fragile) protein complexes. [7] [8] [9] Additional factors, though, such as the binding capacity, cost of the reagent, the requirement of extra equipment and the capability to automate IP processes should be considered in the selection of an immunoprecipitation support.

Binding capacity Edit

Proponents of both agarose and magnetic beads can argue whether the vast difference in the binding capacities of the two beads favors one particular type of bead. In a bead-to-bead comparison, agarose beads have significantly greater surface area and therefore a greater binding capacity than magnetic beads due to the large bead size and sponge-like structure. But the variable pore size of the agarose causes a potential upper size limit that may affect the binding of extremely large proteins or protein complexes to internal binding sites, and therefore magnetic beads may be better suited for immunoprecipitating large proteins or protein complexes than agarose beads, although there is a lack of independent comparative evidence that proves either case.

Some argue that the significantly greater binding capacity of agarose beads may be a disadvantage because of the larger capacity of non-specific binding. Others may argue for the use of magnetic beads because of the greater quantity of antibody required to saturate the total binding capacity of agarose beads, which would obviously be an economical disadvantage of using agarose. While these arguments are correct outside the context of their practical use, these lines of reasoning ignore two key aspects of the principle of immunoprecipitation that demonstrates that the decision to use agarose or magnetic beads is not simply determined by binding capacity.

First, non-specific binding is not limited to the antibody-binding sites on the immobilized support any surface of the antibody or component of the immunoprecipitation reaction can bind to nonspecific lysate constituents, and therefore nonspecific binding will still occur even when completely saturated beads are used. This is why it is important to preclear the sample before the immunoprecipitation is performed.

Second, the ability to capture the target protein is directly dependent upon the amount of immobilized antibody used, and therefore, in a side-by-side comparison of agarose and magnetic bead immunoprecipitation, the most protein that either support can capture is limited by the amount of antibody added. So the decision to saturate any type of support depends on the amount of protein required, as described above in the Agarose section of this page.

Cost Edit

The price of using either type of support is a key determining factor in using agarose or magnetic beads for immunoprecipitation applications. A typical first-glance calculation on the cost of magnetic beads compared to sepharose beads may make the sepharose beads appear less expensive. But magnetic beads may be competitively priced compared to agarose for analytical-scale immunoprecipitations depending on the IP method used and the volume of beads required per IP reaction.

Using the traditional batch method of immunoprecipitation as listed below, where all components are added to a tube during the IP reaction, the physical handling characteristics of agarose beads necessitate a minimum quantity of beads for each IP experiment (typically in the range of 25 to 50μl beads per IP). This is because sepharose beads must be concentrated at the bottom of the tube by centrifugation and the supernatant removed after each incubation, wash, etc. This imposes absolute physical limitations on the process, as pellets of agarose beads less than 25 to 50μl are difficult if not impossible to visually identify at the bottom of the tube. With magnetic beads, there is no minimum quantity of beads required due to magnetic handling, and therefore, depending on the target antigen and IP antibody, it is possible to use considerably less magnetic beads.

Conversely, spin columns may be employed instead of normal microfuge tubes to significantly reduce the amount of agarose beads required per reaction. Spin columns contain a filter that allows all IP components except the beads to flow through using a brief centrifugation and therefore provide a method to use significantly less agarose beads with minimal loss.

Equipment Edit

As mentioned above, only standard laboratory equipment is required for the use of agarose beads in immunoprecipitation applications, while high-power magnets are required for magnetic bead-based IP reactions. While the magnetic capture equipment may be cost-prohibitive, the rapid completion of immunoprecipitations using magnetic beads may be a financially beneficial approach when grants are due, because a 30-minute protocol with magnetic beads compared to overnight incubation at 4 °C with agarose beads may result in more data generated in a shorter length of time. [6] [7] [8]

Automation Edit

An added benefit of using magnetic beads is that automated immunoprecipitation devices are becoming more readily available. These devices not only reduce the amount of work and time to perform an IP, but they can also be used for high-throughput applications.

Summary Edit

While clear benefits of using magnetic beads include the increased reaction speed, more gentle sample handling and the potential for automation, the choice of using agarose or magnetic beads based on the binding capacity of the support medium and the cost of the product may depend on the protein of interest and the IP method used. As with all assays, empirical testing is required to determine which method is optimal for a given application.

Background Edit

Once the solid substrate bead technology has been chosen, antibodies are coupled to the beads and the antibody-coated-beads can be added to the heterogeneous protein sample (e.g. homogenized tissue). At this point, antibodies that are immobilized to the beads will bind to the proteins that they specifically recognize. Once this has occurred the immunoprecipitation portion of the protocol is actually complete, as the specific proteins of interest are bound to the antibodies that are themselves immobilized to the beads. Separation of the immunocomplexes from the lysate is an extremely important series of steps, because the protein(s) must remain bound to each other (in the case of co-IP) and bound to the antibody during the wash steps to remove non-bound proteins and reduce background.

When working with agarose beads, the beads must be pelleted out of the sample by briefly spinning in a centrifuge with forces between 600–3,000 x g (times the standard gravitational force). This step may be performed in a standard microcentrifuge tube, but for faster separation, greater consistency and higher recoveries, the process is often performed in small spin columns with a pore size that allows liquid, but not agarose beads, to pass through. After centrifugation, the agarose beads will form a very loose fluffy pellet at the bottom of the tube. The supernatant containing contaminants can be carefully removed so as not to disturb the beads. The wash buffer can then be added to the beads and after mixing, the beads are again separated by centrifugation.

With superparamagnetic beads, the sample is placed in a magnetic field so that the beads can collect on the side of the tube. This procedure is generally complete in approximately 30 seconds, and the remaining (unwanted) liquid is pipetted away. Washes are accomplished by resuspending the beads (off the magnet) with the washing solution and then concentrating the beads back on the tube wall (by placing the tube back on the magnet). The washing is generally repeated several times to ensure adequate removal of contaminants. If the superparamagnetic beads are homogeneous in size and the magnet has been designed properly, the beads will concentrate uniformly on the side of the tube and the washing solution can be easily and completely removed.

After washing, the precipitated protein(s) are eluted and analyzed by gel electrophoresis, mass spectrometry, western blotting, or any number of other methods for identifying constituents in the complex. Protocol times for immunoprecipitation vary greatly due to a variety of factors, with protocol times increasing with the number of washes necessary or with the slower reaction kinetics of porous agarose beads.


Engineering antibody therapeutics

Therapeutic Abs come from critical screenings of in vivo and in vitro methods.

Bispecific Abs increase specificity and broaden the range of therapeutic MOA.

Optimized Ab leads undergo HFA, affinity maturation, and developability assessment.

Fc optimization is critical for antibody pharmacokinetics and pharmacodynamics.

The successful introduction of antibody-based protein therapeutics into the arsenal of treatments for patients has within a few decades fostered intense innovation in the production and engineering of antibodies. Reviewed here are the methods currently used to produce antibodies along with how our knowledge of the structural and functional characterization of immunoglobulins has resulted in the engineering of antibodies to produce protein therapeutics with unique properties, both biological and biophysical, that are leading to novel therapeutic approaches. Antibody engineering includes the introduction of the antibody combining site (variable regions) into a host of architectures including bi and multi-specific formats that further impact the therapeutic properties leading to further advantages and successes in patient treatment.


Chemical and Synthetic Biology Approaches To Understand Cellular Functions - Part C

Hemlata Dwivedi-Agnihotri , . Arun K. Shukla , in Methods in Enzymology , 2020

2.2 Reagents for capture and detection of biotinylated proteins

Pre-cast or manually prepared acrylamide gels for SDS-PAGE

Suitable power supply and SDS-PAGE apparatus

Protein molecular weight marker

Chemicals for different buffers (Tris–HCl, Glycine, Methanol, Tween-20, Hydrochloric acid)


Watch the video: Kyddiekafka - Isolated Toxic Affinity EP Free Download (July 2022).


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