Protein methods

Last updated

Protein methods are the techniques used to study proteins. There are experimental methods for studying proteins (e.g., for detecting proteins, for isolating and purifying proteins, and for characterizing the structure and function of proteins [1] , often requiring that the protein first be purified). Computational methods typically use computer programs to analyze proteins. However, many experimental methods (e.g., mass spectrometry) require computational analysis of the raw data. [2]

Contents

Genetic methods

Experimental analysis of proteins typically requires expression and purification of proteins. Expression is achieved by manipulating DNA that encodes the protein(s) of interest. Hence, protein analysis usually requires DNA methods, especially cloning. Some examples of genetic methods include conceptual translation, Site-directed mutagenesis, using a fusion protein, and matching allele with disease states. [3] Some proteins have never been directly sequenced, however by translating codons from known mRNA sequences into amino acids by a method known as conceptual translation. (See genetic code.) Site-directed mutagenesis selectively introduces mutations that change the structure of a protein. [4] The function of parts of proteins can be better understood by studying the change in phenotype as a result of this change. Fusion proteins are made by inserting protein tags, such as the His-tag, to produce a modified protein that is easier to track. An example of this would be GFP-Snf2H which consists of a protein bound to a green fluorescent protein to form a hybrid protein. By analyzing DNA alleles can be identified as being associated with disease states, such as in calculation of LOD scores. [5]

Protein extraction from tissues

Protein extraction from tissues with tough extracellular matrices (e.g., biopsy samples, venous tissues, cartilage, skin) is often achieved in a laboratory setting by impact pulverization in liquid nitrogen. [6] Samples are frozen in liquid nitrogen and subsequently subjected to impact or mechanical grinding. [7] As water in the samples becomes very brittle at these temperature, the samples are often reduced to a collection of fine fragments, which can then be dissolved for protein extraction. Stainless steel devices known as tissue pulverizers are sometimes used for this purpose. Advantages of these devices include high levels of protein extraction from small, valuable samples, disadvantages include low-level cross-over contamination. [8]

Protein purification

Protein purification is a critical process in molecular biology and biochemistry, aimed at isolating a specific protein from a complex mixture, such as cell lysates or tissue extracts. [9] The goal is to obtain the protein in a pure form that retains its biological activity for further study, including functional assays, structural analysis, or therapeutic applications. The purification process typically involves several steps, including cell lysis, protein extraction, and a combination of chromatographic and electrophoretic techniques. [10]

Protein isolation

Protein isolation refers to the extraction of proteins from biological samples, which can include tissues, cells, or other materials. The process often begins with cell lysis, where the cellular membranes are disrupted to release proteins into a solution. This can be achieved through physical methods (e.g., sonication, homogenization) or chemical methods (e.g., detergents, enzymes). Following lysis, the mixture is usually clarified by centrifugation to remove cell debris and insoluble material, allowing soluble proteins to be collected for further purification.

Chromatography methods

Chromatography is a widely used technique for protein purification, allowing for the separation of proteins based on various properties, including charge, size, and binding affinity. Here are the main types of chromatography used in protein purification:

Ion Exchange Chromatography

Ion exchange chromatography separates proteins based on their net charge at a given pH. The stationary phase consists of charged resin beads that interact with oppositely charged proteins. As the sample passes through the column, proteins bind to the resin while unbound proteins are washed away. By gradually changing the ionic strength or pH of the elution buffer, bound proteins can be released in a controlled manner, allowing for effective separation.

Size-Exclusion Chromatography (Gel Filtration)

Size-exclusion chromatography separates proteins based on their size. The stationary phase is composed of porous beads that allow smaller molecules to enter the pores while larger molecules pass around them. As a result, larger proteins elute first, followed by smaller ones. This method is particularly useful for desalting or removing small contaminants from protein samples.

Affinity Chromatography

Affinity chromatography exploits the specific interactions between proteins and their ligands. A target protein is captured on a column containing a ligand that specifically binds to it, such as an antibody, enzyme substrate, or metal ion. After washing away non-specifically bound proteins, the target protein is eluted using a solution that disrupts the protein-ligand interaction. This method provides high specificity and is often used for purifying recombinant proteins that have affinity tags.

Protein Extraction and Solubilization

Protein extraction involves isolating proteins from complex biological samples while maintaining their functionality. It often requires a careful choice of extraction buffers that contain salts, detergents, or stabilizers to preserve protein structure and activity. The solubilization step is crucial for proteins that are membrane-bound or insoluble in aqueous solutions. Detergents such as Triton X-100 or SDS can be used to solubilize proteins from membranes by disrupting lipid bilayers, allowing for effective extraction.

Concentrating protein solutions

After initial purification, protein solutions may need to be concentrated to increase the protein's concentration for downstream applications. This can be achieved through various methods, including ultrafiltration, which uses semi-permeable membranes to separate proteins from smaller molecules and salts, and lyophilization (freeze-drying), which removes water and allows proteins to be stored in a stable form. Precipitation methods, such as ammonium sulfate precipitation, can also be employed to concentrate proteins by altering the solubility conditions.

Gel electrophoresis

Gel electrophoresis is a powerful analytical technique used to separate proteins based on their size and charge. Proteins are loaded onto a gel matrix, typically made of polyacrylamide or agarose, and an electric current is applied. The negatively charged proteins migrate towards the positive electrode, with smaller proteins moving faster through the gel matrix than larger ones. This method is crucial for assessing the purity and size of protein samples.

Gel electrophoresis under denaturing conditions

Denaturing gel electrophoresis, commonly performed using SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel electrophoresis), involves treating proteins with SDS, a detergent that denatures proteins and imparts a uniform negative charge. This allows proteins to be separated solely based on their molecular weight, providing a clear picture of the protein composition of a sample.

Gel electrophoresis under non-denaturing conditions

Non-denaturing gel electrophoresis allows proteins to maintain their native structure while being separated. This method is useful for studying protein-protein interactions and enzyme activities. Proteins migrate through the gel based on their size and charge, but their functional properties remain intact, making it ideal for analyzing native protein complexes.

2D gel electrophoresis

2D gel electrophoresis combines isoelectric focusing (IEF) and SDS-PAGE to achieve a high-resolution separation of proteins. In the first dimension, proteins are separated based on their isoelectric points (pI), while in the second dimension, they are separated by molecular weight. This technique allows for the analysis of complex protein mixtures, facilitating the identification of differentially expressed proteins in various conditions.

Electrofocusing

Electrofocusing is a specialized technique that separates proteins based on their isoelectric points in a pH gradient. As an electric field is applied, proteins migrate until they reach the point where their net charge is zero, effectively focusing them into narrow bands. This method provides high resolution and is often used in combination with other techniques for comprehensive protein analysis.

Detecting proteins

The considerably small size of protein macromolecules makes identification and quantification of unknown protein samples particularly difficult. Several reliable methods for quantifying protein have been developed to simplify the process. These methods include Warburg–Christian method, Lowry assay, and Bradford assay (all of which rely on absorbance properties of macromolecules). Bradford assay method uses a dye to bind to protein. Most commonly, Coomassie brilliant blue G-250 dye is used. When free of protein, the dye is red but once bound to protein it turns blue. [11] The dye-protein complex absorbs light maximally at the wavelength 595 nanometers and is sensitive for samples containing anywhere from 1 ug to 60 ug. Unlike Lowry and Warburg-Christian Methods, Bradford assays do not rely on Tryptophan and Tyrosine content in proteins which allows the method to be more accurate hypothetically. Lowry assay is similar to biuret assays, but it uses Folin reagent which is more accurate for quantification. Folin reagent is stable at only acidic conditions and the method is susceptible to skewing results depending on how much tryptophan and tyrosine is present in the examined protein. [12] The Folin reagent binds to tryptophan and tyrosine which means the concentration of the two amino acids affects the sensitivity of the method. The method is sensitive at concentration ranges similar to the Bradford method, but requires a minuscule amount more of protein. Warburg-Christian method screens proteins at their naturally occurring absorbance ranges. Most proteins absorb light very well at 280 nanometers due to the presence of tryptophan and tyrosine, but the method is susceptible to varying amounts of the amino acids it relies on.

More methods are listed below which link to more detailed accounts for their respective methods.

Non-specific methods that detect total protein only

Specific methods which can detect amount of a single protein

Protein structures

Interactions involving proteins

Protein–protein interactions

Protein–DNA interactions

Protein–RNA interactions

Computational methods

Other methods

See also

Bibliography

Related Research Articles

<span class="mw-page-title-main">Gel electrophoresis</span> Method for separation and analysis of biomolecules

Gel electrophoresis is a method for separation and analysis of biomacromolecules and their fragments, based on their size and charge. It is used in clinical chemistry to separate proteins by charge or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge.

<span class="mw-page-title-main">Proteomics</span> Large-scale study of proteins

Proteomics is the large-scale study of proteins. Proteins are vital macromolecules of all living organisms, with many functions such as the formation of structural fibers of muscle tissue, enzymatic digestion of food, or synthesis and replication of DNA. In addition, other kinds of proteins include antibodies that protect an organism from infection, and hormones that send important signals throughout the body.

<span class="mw-page-title-main">Western blot</span> Analytical technique used in molecular biology

The western blot, or western blotting, is a widely used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract. Besides detecting the proteins, this technique is also utilized to visualize, distinguish, and quantify the different proteins in a complicated protein combination.

<span class="mw-page-title-main">Glycome</span> Complete set of all sugars, free or bound, in an organism.

A glycome is the entire complement or complete set of all sugars, whether free or chemically bound in more complex molecules, of an organism. An alternative definition is the entirety of carbohydrates in a cell. The glycome may in fact be one of the most complex entities in nature. "Glycomics, analogous to genomics and proteomics, is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology.

Protein purification is a series of processes intended to isolate one or a few proteins from a complex mixture, usually cells, tissues or whole organisms. Protein purification is vital for the specification of the function, structure and interactions of the protein of interest. The purification process may separate the protein and non-protein parts of the mixture, and finally separate the desired protein from all other proteins. Ideally, to study a protein of interest, it must be separated from other components of the cell so that contaminants will not interfere in the examination of the protein of interest's structure and function. Separation of one protein from all others is typically the most laborious aspect of protein purification. Separation steps usually exploit differences in protein size, physico-chemical properties, binding affinity and biological activity. The pure result may be termed protein isolate.

Affinity chromatography is a method of separating a biomolecule from a mixture, based on a highly specific macromolecular binding interaction between the biomolecule and another substance. The specific type of binding interaction depends on the biomolecule of interest; antigen and antibody, enzyme and substrate, receptor and ligand, or protein and nucleic acid binding interactions are frequently exploited for isolation of various biomolecules. Affinity chromatography is useful for its high selectivity and resolution of separation, compared to other chromatographic methods.

A protein microarray is a high-throughput method used to track the interactions and activities of proteins, and to determine their function, and determining function on a large scale. Its main advantage lies in the fact that large numbers of proteins can be tracked in parallel. The chip consists of a support surface such as a glass slide, nitrocellulose membrane, bead, or microtitre plate, to which an array of capture proteins is bound. Probe molecules, typically labeled with a fluorescent dye, are added to the array. Any reaction between the probe and the immobilised protein emits a fluorescent signal that is read by a laser scanner. Protein microarrays are rapid, automated, economical, and highly sensitive, consuming small quantities of samples and reagents. The concept and methodology of protein microarrays was first introduced and illustrated in antibody microarrays in 1983 in a scientific publication and a series of patents. The high-throughput technology behind the protein microarray was relatively easy to develop since it is based on the technology developed for DNA microarrays, which have become the most widely used microarrays.

<span class="mw-page-title-main">Southwestern blot</span> Molecular biology technique

The southwestern blot, is a lab technique that involves identifying as well as characterizing DNA-binding proteins by their ability to bind to specific oligonucleotide probes. Determination of molecular weight of proteins binding to DNA is also made possible by the technique. The name originates from a combination of ideas underlying Southern blotting and Western blotting techniques of which they detect DNA and protein respectively. Similar to other types of blotting, proteins are separated by SDS-PAGE and are subsequently transferred to nitrocellulose membranes. Thereafter southwestern blotting begins to vary with regards to procedure as since the first blotting’s, many more have been proposed and discovered with goals of enhancing results. Former protocols were hampered by the need for large amounts of proteins and their susceptibility to degradation while being isolated.

<span class="mw-page-title-main">Dot blot</span> Technique for protein detection

A dot blot is a technique in molecular biology used to detect proteins. It represents a simplification of the western blot method, with the exception that the proteins to be detected are not first separated by electrophoresis. Instead, the sample is applied directly on a membrane in a single spot, and the blotting procedure is performed.

<span class="mw-page-title-main">Immunoproteomics</span> Study of large set of protein

Immunoproteomics is the study of large sets of proteins (proteomics) involved in the immune response.

Surface-enhanced laser desorption/ionization (SELDI) is a soft ionization method in mass spectrometry (MS) used for the analysis of protein mixtures. It is a variation of matrix-assisted laser desorption/ionization (MALDI). In MALDI, the sample is mixed with a matrix material and applied to a metal plate before irradiation by a laser, whereas in SELDI, proteins of interest in a sample become bound to a surface before MS analysis. The sample surface is a key component in the purification, desorption, and ionization of the sample. SELDI is typically used with time-of-flight (TOF) mass spectrometers and is used to detect proteins in tissue samples, blood, urine, or other clinical samples, however, SELDI technology can potentially be used in any application by simply modifying the sample surface.

Phosphoproteomics is a branch of proteomics that identifies, catalogs, and characterizes proteins containing a phosphate group as a posttranslational modification. Phosphorylation is a key reversible modification that regulates protein function, subcellular localization, complex formation, degradation of proteins and therefore cell signaling networks. With all of these modification results, it is estimated that between 30–65% of all proteins may be phosphorylated, some multiple times. Based on statistical estimates from many datasets, 230,000, 156,000 and 40,000 phosphorylation sites should exist in human, mouse, and yeast, respectively.

<span class="mw-page-title-main">Electroblotting</span>

Electroblotting is a method in molecular biology/biochemistry/immunogenetics to transfer proteins or nucleic acids onto a membrane by using PVDF or nitrocellulose, after gel electrophoresis. The protein or nucleic acid can then be further analyzed using probes such as specific antibodies, ligands like lectins, or stains. This method can be used with all polyacrylamide and agarose gels. An alternative technique for transferring proteins from a gel is capillary blotting.

<span class="mw-page-title-main">Affinity electrophoresis</span>

Affinity electrophoresis is a general name for many analytical methods used in biochemistry and biotechnology. Both qualitative and quantitative information may be obtained through affinity electrophoresis. Cross electrophoresis, the first affinity electrophoresis method, was created by Nakamura et al. Enzyme-substrate complexes have been detected using cross electrophoresis. The methods include the so-called electrophoretic mobility shift assay, charge shift electrophoresis and affinity capillary electrophoresis. The methods are based on changes in the electrophoretic pattern of molecules through biospecific interaction or complex formation. The interaction or binding of a molecule, charged or uncharged, will normally change the electrophoretic properties of a molecule. Membrane proteins may be identified by a shift in mobility induced by a charged detergent. Nucleic acids or nucleic acid fragments may be characterized by their affinity to other molecules. The methods have been used for estimation of binding constants, as for instance in lectin affinity electrophoresis or characterization of molecules with specific features like glycan content or ligand binding. For enzymes and other ligand-binding proteins, one-dimensional electrophoresis similar to counter electrophoresis or to "rocket immunoelectrophoresis", affinity electrophoresis may be used as an alternative quantification of the protein. Some of the methods are similar to affinity chromatography by use of immobilized ligands.

Bioanalysis is a sub-discipline of analytical chemistry covering the quantitative measurement of xenobiotics and biotics in biological systems.

<span class="mw-page-title-main">Yessotoxin</span> Chemical compound

Yessotoxins are a group of lipophilic, sulfur bearing polyether toxins that are related to ciguatoxins. They are produced by a variety of dinoflagellates, most notably Lingulodinium polyedrum and Gonyaulax spinifera.

A thermal shift assay (TSA) measures changes in the thermal denaturation temperature and hence stability of a protein under varying conditions such as variations in drug concentration, buffer formulation, redox potential, or sequence mutation. The most common method for measuring protein thermal shifts is differential scanning fluorimetry (DSF). DSF methodology includes techniques such as nanoDSF, which relies on the intrinsic fluorescence from native tryptophan or tyrosine residues, and Thermofluor, which utilizes extrinsic fluorogenic dyes.

A ligand binding assay (LBA) is an assay, or an analytic procedure, which relies on the binding of ligand molecules to receptors, antibodies or other macromolecules. A detection method is used to determine the presence and amount of the ligand-receptor complexes formed, and this is usually determined electrochemically or through a fluorescence detection method. This type of analytic test can be used to test for the presence of target molecules in a sample that are known to bind to the receptor.

The northwestern blot, also known as the northwestern assay, is a hybrid analytical technique of the western blot and the northern blot, and is used in molecular biology to detect interactions between RNA and proteins. A related technique, the western blot, is used to detect a protein of interest that involves transferring proteins that are separated by gel electrophoresis onto a nitrocellulose membrane. A colored precipitate clusters along the band on the membrane containing a particular target protein. A northern blot is a similar analytical technique that, instead of detecting a protein of interest, is used to study gene expression by detection of RNA on a similar membrane. The northwestern blot combines the two techniques, and specifically involves the identification of labeled RNA that interact with proteins that are immobilized on a similar nitrocellulose membrane.

<span class="mw-page-title-main">SDS-PAGE</span> Biochemical technique

SDS-PAGE is a discontinuous electrophoretic system developed by Ulrich K. Laemmli which is commonly used as a method to separate proteins with molecular masses between 5 and 250 kDa. The combined use of sodium dodecyl sulfate and polyacrylamide gel eliminates the influence of structure and charge, and proteins are separated by differences in their size. At least up to 2012, the publication describing it was the most frequently cited paper by a single author, and the second most cited overall.

References

  1. ↑ Walkup, Ward G.; Kennedy, Mary B. (April 2015). "Protein Purification Using PDZ Affinity Chromatography". Current Protocols in Protein Science. 80 (1). doi:10.1002/0471140864.ps0910s80. ISSN   1934-3655.
  2. ↑ Otwinowski, Zbyszek; Minor, Wladek (1997), "[20] Processing of X-ray diffraction data collected in oscillation mode", Methods in Enzymology, Elsevier, pp. 307–326, ISBN   978-0-12-182177-7 , retrieved 2024-10-29
  3. ↑ Malke, H. (1984). "T. Maniatis, E. F. Fritsch and J. Sambrook, Molecular Cloning: A Laboratory Manual, X + 545 S., 61 Abb., 28 Tab. Cold Spring Harbor, N. Y. 1982. Cold Spring Harbor Laboratory". Zeitschrift für allgemeine Mikrobiologie. 24 (1): 32–32. doi:10.1002/jobm.3630240107. ISSN   0044-2208.
  4. ↑ Hagen, Fred K. (2011-12-26), "Proteoglycan: Site Mapping and Site-Directed Mutagenesis", Methods in Molecular Biology, Totowa, NJ: Humana Press, pp. 23–34, ISBN   978-1-61779-497-1 , retrieved 2024-10-29
  5. ↑ Kossiakoff, Anthony A. (June 1983). "Neutron Protein Crystallography: Advances in Methods and Applications". Annual Review of Biophysics and Bioengineering. 12 (1): 159–182. doi:10.1146/annurev.bb.12.060183.001111. ISSN   0084-6589.
  6. ↑ Ganapathy‐Kanniappan, Shanmugasundaram (2019-01-31). "pI Determination of Native Proteins In Biological Samples". Current Protocols in Protein Science. 96 (1). doi:10.1002/cpps.85. ISSN   1934-3655.
  7. ↑ "Erratum". Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology. 1037 (2): 263. February 1990. doi:10.1016/0167-4838(90)90294-p. ISSN   0167-4838.
  8. ↑ Kato, Takeo; Katayama, Emiko; Matsubara, Sueno; Omi, Yuko; Matsuda, Tsukasa (2000-07-25). "Release of Allergenic Proteins from Rice Grains Induced by High Hydrostatic Pressure". Journal of Agricultural and Food Chemistry. 48 (8): 3124–3129. doi:10.1021/jf000180w. ISSN   0021-8561.
  9. ↑ Janson, Jan‐Christer, ed. (2011-03-07). Protein Purification. Methods of Biochemical Analysis. Wiley. ISBN   978-0-471-74661-4.
  10. ↑ Hajizadeh, Solmaz; Mattiasson, Bo (2015), "Cryogels with Affinity Ligands as Tools in Protein Purification", Methods in Molecular Biology, New York, NY: Springer New York, pp. 183–200, ISBN   978-1-4939-2446-2 , retrieved 2024-10-29
  11. ↑ Bradford, Marion M. (May 1976). "A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding". Analytical Biochemistry. 72 (1–2): 248–254. doi:10.1016/0003-2697(76)90527-3. ISSN   0003-2697.
  12. ↑ Lowry, OliverH.; Rosebrough, NiraJ.; Farr, A. Lewis; Randall, RoseJ. (November 1951). "Protein Measurement With the Folin Phenol Reagent". Journal of Biological Chemistry. 193 (1): 265–275. doi:10.1016/s0021-9258(19)52451-6. ISSN   0021-9258.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.