In biochemistry, denaturation is a process in which proteins or nucleic acids lose folded structure present in their native state due to various factors, including application of some external stress or compound, such as a strong acid or base, a concentrated inorganic salt, an organic solvent, agitation and radiation, or heat. If proteins in a living cell are denatured, this results in disruption of cell activity and possibly cell death. Protein denaturation is also a consequence of cell death. Denatured proteins can exhibit a wide range of characteristics, from conformational change and loss of solubility or dissociation of cofactors to aggregation due to the exposure of hydrophobic groups. The loss of solubility as a result of denaturation is called coagulation. Denatured proteins lose their 3D structure, and therefore, cannot function.
Cysteine is a semiessential proteinogenic amino acid with the formula HOOC−CH(−NH2)−CH2−SH. The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile. Cysteine is chiral, but both D and L-cysteine are found in nature. L‑Cysteine is a protein monomer in all biota, and D-cysteine acts as a signaling molecule in mammalian nervous systems. Cysteine is named after its discovery in urine, which comes from the urinary bladder or cyst, from Greek κύστη kýsti, "bladder".
In chemistry, a disulfide is a compound containing a R−S−S−R′ functional group or the S2−
2 anion. The linkage is also called an SS-bond or sometimes a disulfide bridge and usually derived from two thiol groups.
Glutathione is an organic compound with the chemical formula HOCOCH(NH2)CH2CH2CONHCH(CH2SH)CONHCH2COOH. It is an antioxidant in plants, animals, fungi, and some bacteria and archaea. Glutathione is capable of preventing damage to important cellular components caused by sources such as reactive oxygen species, free radicals, peroxides, lipid peroxides, and heavy metals. It is a tripeptide with a gamma peptide linkage between the carboxyl group of the glutamate side chain and cysteine. The carboxyl group of the cysteine residue is attached by normal peptide linkage to glycine.
In organic chemistry, a thiol, or thiol derivative, is any organosulfur compound of the form R−SH, where R represents an alkyl or other organic substituent. The −SH functional group itself is referred to as either a thiol group or a sulfhydryl group, or a sulfanyl group. Thiols are the sulfur analogue of alcohols, and the word is a blend of "thio-" with "alcohol".
Cystine is the oxidized derivative of the amino acid cysteine and has the formula (SCH2CH(NH2)CO2H)2. It is a white solid that is poorly soluble in water. As a residue in proteins, cystine serves two functions: a site of redox reactions and a mechanical linkage that allows proteins to retain their three-dimensional structure.
In molecular biology, post-translational modification (PTM) is the covalent process of changing proteins following protein biosynthesis. PTMs may involve enzymes or occur spontaneously. Proteins are created by ribosomes, which translate mRNA into polypeptide chains, which may then change to form the mature protein product. PTMs are important components in cell signalling, as for example when prohormones are converted to hormones.
Protein disulfide isomerase, or PDI, is an enzyme in the endoplasmic reticulum (ER) in eukaryotes and the periplasm of bacteria that catalyzes the formation and breakage of disulfide bonds between cysteine residues within proteins as they fold. This allows proteins to quickly find the correct arrangement of disulfide bonds in their fully folded state, and therefore the enzyme acts to catalyze protein folding.
Dithiothreitol (DTT) is an organosulfur compound with the formula (CH CH2SH)2. A colorless compound, it is classified as a dithiol and a diol. DTT is redox reagent also known as Cleland's reagent, after W. Wallace Cleland. The reagent is commonly used in its racemic form. Its name derives from the four-carbon sugar, threose. DTT has an epimeric ('sister') compound, dithioerythritol (DTE).
Iodoacetamide (IAA) is an organic compound with the chemical formula ICH2CONH2. It is an alkylating agent used for peptide mapping purposes. Its actions are similar to those of iodoacetate. It is commonly used to bind covalently with the thiol group of cysteine so the protein cannot form disulfide bonds. It is also used in ubiquitin studies as an inhibitor of deubiquitinase enzymes (DUBs) because it alkylates the cysteine residues at the DUB active site.
2-Mercaptoethanol (also β-mercaptoethanol, BME, 2BME, 2-ME or β-met) is the chemical compound with the formula HOCH2CH2SH. ME or βME, as it is commonly abbreviated, is used to reduce disulfide bonds and can act as a biological antioxidant by scavenging hydroxyl radicals (amongst others). It is widely used because the hydroxyl group confers solubility in water and lowers the volatility. Due to its diminished vapor pressure, its odor, while unpleasant, is less objectionable than related thiols.
Sulfur assimilation is the process by which living organisms incorporate sulfur into their biological molecules. In plants, sulfate is absorbed by the roots and then transported to the chloroplasts by the transipration stream where the sulfur are reduced to sulfide with the help of a series of enzymatic reactions. Furthermore, the reduced sulfur is incorporated into cysteine, an amino acid that is a precursor to many other sulfur-containing compounds. In animals, sulfur assimilation occurs primarily through the diet, as animals cannot produce sulfur-containing compounds directly. Sulfur is incorporated into amino acids such as cysteine and methionine, which are used to build proteins and other important molecules.
Dithioerythritol (DTE) is a sulfur containing sugar alcohol derived from the corresponding 4-carbon monosaccharide erythrose. It is an epimer of dithiothreitol (DTT). The molecular formula for DTE is C4H10O2S2.
Peroxiredoxins are a ubiquitous family of antioxidant enzymes that also control cytokine-induced peroxide levels and thereby mediate signal transduction in mammalian cells. The family members in humans are PRDX1, PRDX2, PRDX3, PRDX4, PRDX5, and PRDX6. The physiological importance of peroxiredoxins is indicated by their relative abundance. Their function is the reduction of peroxides, specifically hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite.
Bioconjugation is a chemical strategy to form a stable covalent link between two molecules, at least one of which is a biomolecule.
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.
Chymopapain is a proteolytic enzyme isolated from the latex of papaya. It is a cysteine protease which belongs to the papain-like protease (PLCP) group. Because of its proteolytic activity, it is the main molecule in the process of chemonucleolysis, used in some procedures like the treatment of herniated lower lumbar discs in the spine by a nonsurgical method.
In chemistry, a selenosulfide refers to distinct classes of inorganic and organic compounds containing sulfur and selenium. The organic derivatives contain Se-S bonds, whereas the inorganic derivatives are more variable.
S-(2-Aminoethyl)isothiourea dihydrobromide, commonly knwn as AET, is a isothiouronium-group-containing reducing agent with textbook uses as a disulfide reducing agent. Though it does not have a free thiol group (-SH) like 2-mercaptoethanol and dithiothreitol (DTT), it reacts with water to decompose transiently into thiol intermediates that acts on disulfide in a manner to these containing free -SH groups.
Dithiobutylamine (DTBA) is a reducing agent intended as an alternative for DTT in biochemical uses. It was designed to be easily synthesized in non-racemic form, to have a lower pKa, and to have a low disulfide E°′ reduction potential. It was rationally designed & reported in 2012. It is commercially available.
