Posttranslational chemical modification

The elements of protein structure are divided into four classes primary, secondary, tertiary, and quaternary. Primary structure refers to the linear sequence of amino acids linked by amide bonds along protein chains. These polymer chains vary in length from a few amino acid residues (oligopeptides) to molecules containing 2000 or more amino acids. Most proteins are from 100 to 500 amino acid residues in length. One or more of each of 20 natural amino acids may be present in each protein molecule. In some cases the amino acids undergo posttranslational chemical modification, which introduces still more variety into protein structure. 

Table 1 A catalog of posttranslational chemical modifications of the histone proteins...

Reversible phosphorylation of proteins on serine, threonine and tyrosine residues by protein kinases and phosphatases represents the principal mechanism of signal transduction events that control a multitude of cellular processes (see ref. 1 and 2 for detained reviews). Phosphorylation is a posttranslational chemical modification that is used by prokaryotic and eukaryotic cells to define the properties of a large... 

Allelic polymorphism in a specific gene can produce nearly identical proteins with primary sequences that differ by one or more amino acids. Primary sequence isoforms can be readily separated by CIEF on the basis of their pi if the amino acid substitution changes the surface charge of the protein. Similarly, enzymatic or nonenzymatic posttranslational chemical modification of ionizable protein functional groups can produce chemically distinct isoforms of the same protein with detectably different surface charge and pi. Analysis of hemoglobin by CIEF is an excellent example of how this technique can be applied for the identification and quantification of a family of related proteins that represent a concise subset of the human proteome. Members of this family include many primary... 

Chemical modifications of proteins have been carried out for a long time prior to any interest in the understanding of the chemical basis of the process. Early studies were motivated by the interest in quantitative determination of proteins and amino acids that conform its structure [104]. Intramolecular reactions occur naturally in posttranslational modifications such as disulfide bonding, glycosylation, or terminal residue cyclization. These modifications are relevant in structure-function relationships. They can produce conformational changes in order to switch between... 

The proteins produced by recombinant DNA technology are frequently accompanied by structural variants resulting from expression errors, in vivo modifications, posttranslational errors, improper folding, aggregation, and chemical modifications that occur during purification. The presence of vari-... 

Even when the purpose of a given posttranslational modification is understood, an examination of how and where it occurs is also likely to yield only limited information. The cell biological sites and processes involved in the reactions, the specificity by which certain amino acid residues or specific peptide bonds are selected for chemical modification and the mechanism by which the transformations are carried out remain obscure for a large number of these reactions. 

Following translation into the polypeptidyl chain, proteins undergo not only specific chemical modifications but also many nonspecific modifications. Some modifications are the result of continual exposure of the proteins to the potential action of proteolytic enzymes. The level of a specific protein in vivo is the result of a balance achieved between the rate of biosynthesis of that protein and its rate of degradation by proteolytic enzymes. In part, the rate of degradation of a protein is a function of the relative levels of native (N) and reversibly (R) denatured protein (N R) under a given set of conditions. Nutritional state and health of the organism, the extent of posttranslational modification, and environ-... 

In the analysis of proteins in forensic applications, the chemical modifications that occur to proteins, posttranslationally and nonenzymatically, are of primary importance. These chemical changes are a result of chemical reactions between side chains of the protein and reactive groups of metabolites and/or exogenous toxicants, including drugs present in extracellular fluid such as serum. The analytical accessibility of these modified proteins depends on their rate of turnover. For example, those with a slow turnover rate will be long-lived, and such problems will be much more easy to identify than those with faster turnover rates. 

Although the total synthesis of a protein allows complete control over the structure, including posttranslational modifications and introduction of labels at desired sites in the sequence, it is still a major undertaking for which most laboratories whose main interest is in the biology of their target proteins are not equipped. In certain cases, for example when the site of introduction of a specific chemical modification is near the C-terminus, a combination of molecular biological and chemical methods has proved to be very powerful. 

In addition to the twenty standard amino acids, many nonstandard amino acids are also found in almost all proteins. Generally, these amino acids arise as a consequence of various chemical modifications after they have been incorporated into protein. Posttranslational modification of amino acids is one basis of the regulation of protein activity, specificity, and stability. 

Posttranslational modification (Section 28.6) A chemical modification of a protein that occurs after translation from DNA. 

The results for bacterial whole-cell analysis described here establish the utility of MALDI-FTMS for mass spectral analysis of whole-cell bacteria and (potentially) more complex single-celled organisms. The use of MALDI-measured accurate mass values combined with mass defect plots is rapid, accurate, and simpler in sample preparation then conventional liquid chromatographic methods for bacterial lipid analysis. Intact cell MALDI-FTMS bacterial lipid characterization complements the use of proteomics profiling by mass spectrometry because it relies on accurate mass measurements of chemical species that are not subject to posttranslational modification or proteolytic degradation. 

Biosynthesis of the polypeptide chain is realised by a complicated process called translation. The basic polypeptide chain is subsequently chemically modified by the so-called posttranslational modifications. During this sequence of events the peptide chain can be cleaved by directed proteolysis, some of the amino acids can be covalently modified (hydroxylated, dehydrogenated, amidated, etc.) or different so-called prosthetic groups such as haem (haemoproteins), phosphate residues (phosphoproteins), metal ions (metal-loproteins) or (oligo)saccharide chains (glycoproteins) can be attached to the molecule by covalent bonds. Naturally, one protein molecule can be modified by more means. 

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