Disulfide cross-links are where two cysteine residues form disulfide linkages.
Although they are part of primary protein structure, they begin to provide the framework for the 3-dimensional shape of the protein because they lower the entropy of the unfolded protein, and thus destabilize it.
Disulfide bonds form only between two cysteine residues because they have a sulfhydryl group as their side chain.
Creation of disulfide bridges is considered oxidative – the hydrogen atoms on both cysteine residues are lost.
Cysteine residues in a disulfide bond are called cystine.
As a biochemical corollary, consider that strong reducing reagents such as beta-mercaptoethanol and dithiotheitol (DTT) break disulfide linkages.
Ubiquitination is the addition of one or more ubiquitins to lysine residues; it requires a trio of proteins that add the ubiquitin to the lysine residue.
Ubiquitin is a small protein found in almost all tissues and its addition to a protein targets the protein for degradation.
Although many ubiquitins can be added to a single lysine residue, they are added one at a time.
Poly-ubiquitination is the addition of multiple ubiquitins to a single residue.
A single ubiquitin has a small hydrophobic patch on it and poly-ubiquitination creates a large hydrophobic strip that signals chaperones to move the protein to the proteasome.
Ubiquitination helps to rid the cell of unwanted, unneeded and misfolded proteins, which makes it a powerful tool for regulation of cellular processes.
ADP-ribosylation is the addition of ADP-ribose to arginine, glutamine, cysteine and diphthamide (a modified histidine) residues.
Ribose is the sugar component of RNA, and ADP is the de-phosphorylated form of ATP.
ADP-ribose is derived from NAD+ or nicotinamide adenine dinucleotide, a coenzyme found in all living cells that is important for electron transfer in metabolic reactions.
One or many ADP-ribose moieties can be added to a protein, and that ADP-ribosylation has important effects on gene regulation, DNA repair and cell survival.
Poly-ADP-ribose polymerases (PARPs) add poly ADP-ribose chains to proteins, and inhibition of PARP1 has been a potent anti-cancer therapeutic.
As a clinical correlation, bacterial toxins, such as those of cholera, pertussis, and diphtheria use ADP-ribosylation to permanently alter the function of proteins in infected cells.
Cholera toxin causes constant secretion of water to the lumen of the intestines, resulting in dehydration and diarrhea.
Glycosylation is the addition of sugars to asparagine, serine or threonine residues.
Single sugars, such as N-acetylglucosamine can be added, or branched chains of sugars can be added to these residues.
In N-linked glycosylation, sugars are added to the side chain amino group on asparagine.
In O-linked glycosylation, sugars are added to the side chain hydroxyl group of serine or threonine.
The addition of sugars is common on cell surface and secreted proteins because sugars make proteins more hydrophilic and therefore, more soluble.
Different glycosylation patterns found in different organisms aids the immune system's ability to identify foreign (and potentially pathogenic) entities.
Acetylation is the addition of acetyl groups to lysine residues and amino termini.
Lysine acetylation is another common modification of histones.
Lysine acetylation neutralizes the positive charge of amino group on the side chain, which, in histones, has an effect on its binding affinity for DNA; and can be used to turn genes on or off.
As a clinical correlation, acetylation is essential to the function of p53, which is silenced in many cancers.
Thus, small molecule cancer drugs have been developed that prevent deacetylation of p53 to keep it active (acetylated) to fight the cancer.
Methylation is the addition of methyl groups to lysine or arginine residues, both of which have positively charged side chains.
Arginine may have one or two methyl groups added to it, and lysine may have one, two, or three methyl groups added to it.
It doesn't affect the charge of the amino acid.
Because the methyl group is so small, it has few steric interactions.
Methylation seems to be a relatively minor modification (it neither affects the charge nor has steric interactions); however, it has quite an important functional effect.
Methylation is the most well-known modification of histones (the proteins around which DNA is wrapped), which affects the transcription of DNA.
Mono-, di-, and tri-methylation have been shown to have different meanings, and protein domains such as Tudor domains and PHD domains, can recognize and interpret these methylation states of lysine and arginine residues, giving a range of responses to them.