Cleavable detergents, also known as cleavable surfactants, [1] [2] are special surfactants (detergents) that are used in biochemistry and especially in proteomics to enhance protein denaturation and solubility. The detergent is rendered inactive by cleavage, usually under acidic conditions, in order to make the sample compatible with a following procedure or in order to selectively remove the cleavage products.
Applications for cleavable detergents include protease digestion of proteins such as in-gel digestion with trypsin after SDS PAGE and peptide extractions from electrophoresis gels. Cleavable detergents are mainly used in sample preparations for mass spectrometry.
PPS, available as PPS Silent Surfactant from Expedeon, is the abbreviation for sodium 3-(4-(1,1-bis(hexyloxy)ethyl)pyridinium-1-yl)propane-1-sulfonate. This acetalic detergent is split under acidic conditions into hexanol and the zwitterionic 3-acetyl-1-(3-sulfopropyl)pyridinium.
ProteaseMAX'is the brandname of Promega for sodium 3-((1-(furan-2-yl)undecyloxy)carbonylamino)propane-1-sulfonate. This cleavable detergent is sensitive to heat and acid and is degraded during a typical trypsin digestion into the uncharged lipophilic compound 1-(furan-2-yl)undecan-1-ol and the zwitterionic 3-aminopropane-1-sulfonic acid (homotaurine), which can be removed by C18 solid phase extraction during sample work-up.
RapiGest SF, the brand-name for sodium 3-[(2-methyl-2-undecyl-1,3-dioxolan-4-yl)methoxy]-1-propanesulfonate, is an acid-cleavable anionic detergent marketed by Waters Corporation and AOBIOUS INC.
MALDI matrix compounds such as α-cyano-4-hydroxycinnamic acid have been linked through a linker consisting of an unsymmetric formaldehyde acetals to dodecanol. [3] This type of cleavable detergent is inherently compatible with MALDI and does not have to be removed prior to analysis.
UV light- or fluoride-cleavable surfactants have also been developed but are not in current use. [4]
Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years. Proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion. Low pH or high temperatures can also cause proteolysis non-enzymatically.
Trypsin is a serine protease from the PA clan superfamily, found in the digestive system of many vertebrates, where it hydrolyzes proteins. Trypsin is formed in the small intestine when its proenzyme form, the trypsinogen produced by the pancreas, is activated. Trypsin cleaves peptide chains mainly at the carboxyl side of the amino acids lysine or arginine. It is used for numerous biotechnological processes. The process is commonly referred to as trypsin proteolysis or trypsinisation, and proteins that have been digested/treated with trypsin are said to have been trypsinized. Trypsin was discovered in 1876 by Wilhelm Kühne and was named from the Ancient Greek word for rubbing since it was first isolated by rubbing the pancreas with glycerin.
A protease is an enzyme that catalyzes proteolysis, the breakdown of proteins into smaller polypeptides or single amino acids. They do this by cleaving the peptide bonds within proteins by hydrolysis, a reaction where water breaks bonds. Proteases are involved in many biological functions, including digestion of eaten/swallowed proteins, protein catabolism, and cell signalling.
A detergent is a surfactant or a mixture of surfactants with cleansing properties in dilute solutions. These substances are usually alkylbenzenesulfonates, a family of compounds that are similar to soap but are more soluble in hard water, because the polar sulfonate is less likely than the polar carboxylate to bind to calcium and other ions found in hard water.
Surfactants are compounds that lower the surface tension between two liquids, between a gas and a liquid, or between a liquid and a solid. Surfactants may act as detergents, wetting agents, emulsifiers, foaming agents, and dispersants.
Serine proteases are enzymes that cleave peptide bonds in proteins, in which serine serves as the nucleophilic amino acid at the (enzyme's) active site. They are found ubiquitously in both eukaryotes and prokaryotes. Serine proteases fall into two broad categories based on their structure: chymotrypsin-like (trypsin-like) or subtilisin-like.
Protein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing of a protein provides sufficient information to identify it with reference to databases of protein sequences derived from the conceptual translation of genes.
Trypsinogen is the precursor form or zymogen of trypsin, a digestive enzyme. Produced by the pancreas, it is found in pancreatic juice, along with amylase, lipase, and chymotrypsinogen. It is activated by enterokinase, which is found in the intestinal mucosa, to form trypsin. Once activated, the trypsin can activate more trypsinogen into trypsin. Trypsin cleaves the peptide bond on the carboxyl side of basic amino acids such as arginine and lysine.
A sulfonic acid (or sulphonic acid) refers to a member of the class of organosulfur compounds with the general formula R−S(=O)2−OH, where R is an organic alkyl or aryl group and the S(=O)2(OH) group a sulfonyl hydroxide. As a substituent, it is known as a sulfo group. A sulfonic acid can be thought of as sulfuric acid with one hydroxyl group replaced by an organic substituent. The parent compound (with the organic substituent replaced by hydrogen) is the parent sulfonic acid, HS(=O)2(OH), a tautomer of sulfurous acid, S(=O)(OH)2. Salts or esters of sulfonic acids are called sulfonates.
Peptide mass fingerprinting (PMF) is an analytical technique for protein identification in which the unknown protein of interest is first cleaved into smaller peptides, whose absolute masses can be accurately measured with a mass spectrometer such as MALDI-TOF or ESI-TOF. The method was developed in 1993 by several groups independently. The peptide masses are compared to either a database containing known protein sequences or even the genome. This is achieved by using computer programs that translate the known genome of the organism into proteins, then theoretically cut the proteins into peptides, and calculate the absolute masses of the peptides from each protein. They then compare the masses of the peptides of the unknown protein to the theoretical peptide masses of each protein encoded in the genome. The results are statistically analyzed to find the best match.
In mass spectrometry, matrix-assisted laser desorption/ionization (MALDI) is an ionization technique that uses a laser energy absorbing matrix to create ions from large molecules with minimal fragmentation. It has been applied to the analysis of biomolecules and large organic molecules, which tend to be fragile and fragment when ionized by more conventional ionization methods. It is similar in character to electrospray ionization (ESI) in that both techniques are relatively soft ways of obtaining ions of large molecules in the gas phase, though MALDI typically produces far fewer multi-charged ions.
Hydroxysultaines are chemical compounds used in high-foaming shampoos, bath products and shower gels especially in conjunction with ether sulfates and alkyl sulfates. They are also used in industrial applications where high, stable foam is required. Chemically, hydroxysultaines are zwitterionic, typically containing covalently linked positive and negative ions.
CHAPS is a zwitterionic surfactant used in the laboratory to solubilize biological macromolecules such as proteins. It may be synthesized from cholic acid and is zwitterionic due to its quaternary ammonium and sulfonate groups; it is structurally similar to certain bile acids, such as taurodeoxycholic acid and taurochenodeoxycholic acid. It is used as a non-denaturing detergent in the process of protein purification and is especially useful in purifying membrane proteins, which are often sparingly soluble or insoluble in aqueous solution due to their native hydrophobicity.
Dodecylbenzene is an organic compound with the formula C12H25C6H5.Dodecylbenzene is a colorless liquid with a weak oily odor. Floats on water.
Protein mass spectrometry refers to the application of mass spectrometry to the study of proteins. Mass spectrometry is an important method for the accurate mass determination and characterization of proteins, and a variety of methods and instrumentations have been developed for its many uses. Its applications include the identification of proteins and their post-translational modifications, the elucidation of protein complexes, their subunits and functional interactions, as well as the global measurement of proteins in proteomics. It can also be used to localize proteins to the various organelles, and determine the interactions between different proteins as well as with membrane lipids.
The in-gel digestion step is a part of the sample preparation for the mass spectrometric identification of proteins in course of proteomic analysis. The method was introduced in 1992 by Rosenfeld. Innumerable modifications and improvements in the basic elements of the procedure remain.
1,3-Propane sultone is the organosulfur compound with the formula (CH2)3SO3. It is a cyclic sulfonate ester, a class of compounds called sultones. It is a readily melting colorless solid.
Terminal amine isotopic labeling of substrates (TAILS) is a method in quantitative proteomics that identifies the protein content of samples based on N-terminal fragments of each protein and detects differences in protein abundance among samples.
Alkylbenzene sulfonates are a class of anionic surfactants, consisting of a hydrophilic sulfonate head-group and a hydrophobic alkylbenzene tail-group. Along with sodium laureth sulfate they are one of the oldest and most widely used synthetic detergents and may be found in numerous personal-care products and household-care products . They were first introduced in the 1930s in the form of branched alkylbenzene sulfonates (BAS) however following environmental concerns these were replaced with linear alkylbenzene sulfonates (LAS) during the 1960s. Since then production has increased significantly from about 1 million tons in 1980, to around 3.5 million tons in 2016, making them most produced anionic surfactant after soaps.
Wastewater comes out of the laundry process with additional energy (heat), lint, soil, dyes, finishing agents, and other chemicals from detergents. Some laundry wastewater goes directly into the environment, due to the flaws of water infrastructure. The majority goes to sewage treatment plants before flowing into the environment. Some chemicals remain in the water after treatment, which may contaminate the water system. Some have argued they can be toxic to wildlife, or can lead to eutrophication.
