Protein, nonfunctional

Given a large population of individuals, a considerable number of sequence variants can be found for a protein. These variants are a consequence of mutations in a gene (base substitutions in DNA) that have arisen naturally within the population. Gene mutations lead to mutant forms of the protein in which the amino acid sequence is altered at one or more positions. Many of these mutant forms are neutral in that the functional properties of the protein are unaffected by the amino acid substitution. Others may be nonfunctional (if loss of function is not lethal to the individual), and still others may display a range of aberrations between these two extremes. The severity of the effects on function depends on the nature of the amino acid substitution and its role in the protein. These conclusions are exemplified by the more than 300 human... 

Pseudogenes are nonfunctional relatives of known genes that have lost their ability to encode proteins. 

Cadepond, F., Schweizeer, G.G., Segatd, M.I., Jibard, N., Hollenberg, S.M., Giguere, V., Evans, R.M., Baulieu, E. (1991). Heat shock protein 90 as a critical factor in maintaining glucocorticosteroid receptor in a nonfunctional state. J. Biol. Chem. 266, 5834-5841. 

In the case of prothrombin and related clotting factors, interruption of the vitamin K cycle leads to the production of nonfunctional, undercarboxylated proteins, which are duly exported from hepatocytes into blood (Thijssen 1995). They are nonfunctional because there is a requirement for the additional carboxyl residues in the clotting process. Ionized carboxyl groups can establish links with negatively charged sites on neighboring phospholipid molecules of cell surfaces via calcium bridges. 

Warfarin and the second-generation superwarfarins are ARs that have a structural resemblance to dicoumarol and vitamin K. They act as vitamin K antagonists, thereby retarding or stopping the carboxylation of clotting proteins in the hepatic endoplasmic reticulum. The buildup of nonfunctional, undercarboxylated clotting proteins in the blood leads eventually to death by hemorrhaging. 

The cause of Wilson disease was also revealed in 1993, when it was reported that a variety of mutations in a gene encoding a copper-binding P-type ATPase were responsible. The gene is estimated to encode a protein of 1411 amino acids, which is highly homologous to the product of the gene affected in Menkes disease. In a manner not yet fully explained, a nonfunctional ATPase causes defective excretion of copper into the bile, a reduction of incorporation of copper into... 

Upon encountering a stop codon on the mRNA, the ribosome will halt incorporation of further amino acids into the polypeptide as there is no tRNA complementary to a stop codon (UAG, UGA, UAA). In order to liberate the polypeptide, the ester bond between the peptide and the tRNA residing in the P site has to be hydrolyzed — a reaction that is also catalyzed in the peptidyltransferase center. It is critical for protein synthesis that peptide release is tightly coupled to the presence of a stop codon in the decoding center to avoid premature termination resulting in shortened, nonfunctional proteins. Both functions, recognizing the stop codon and triggering... 

Some enzymes are nonfunctional until posttranslationally modified. Examples of these enzymes include the acyl- and carboxyltransferases. While lipoate and phosphopantetheine are necessary for acyl transfer chemistry, tethered biotin is used in carboxyl transfer chemistry. Biotin and lipoate tethering occur under a similar mechanism the natural small molecule is activated with ATP to form biotinyl-AMP or lipoyl-AMP (Scheme 20). A lysine from the target protein then attacks the activated acid and transfers the group to the protein. The phosphopantetheine moiety is transferred using its own enzyme, the phosphopantetheinyltrans-ferase (PPTase). The PPTase uses a nucleophilic hydroxy-containing amino acid, serine, to attach the phosphopantetheinyl (Ppant) arm found in coenzyme A to convert the apo (inactive) carrier protein to its holo (active) form. The reaction is Mg -dependent. 

There are several mutations in the CETR protein that render it nonfunctional. However, one specific mutation underlies about 70% of the cases. 

The diuretic effect of spironolactone develops fully only with continuous administration for several days. Two possible explanations are (1) the conversion of spironolactone into and accumulation of the more slowly eliminated metabolite canrenone (2) an inhibition of aldosterone-stimulated protein synthesis would become noticeable only if existing proteins had become nonfunctional and needed to be replaced by de novo synthesis. A particular adverse effect results from interference with gonadal hormones, as evidenced by the development of gynecomastia (enlargement of male breast). Clinical uses include conditions of increased aldosterone secretion, e.g., liver cirrhosis with ascites. 

That aminoglycoside binding interferes with translation has been known for at least four decades. The mode of action of these antibiotics decreases the fidelity of translation, such that the organism biosynthesizes proteins that are defective. The presence of defective or nonfunctional proteins leads to the demise of bacteria. Consequently, paromomycin s bactericidal mode of action may come from its ability to lock the A-site into a conformation in which discrimination of cognate and near cognate tRNA is significantly diminished. 

A hydrogen bond, involving an acidic hydrogen atom borne by a fluorine-substituted or halogen-substituted carbon, seems to contribute to the activity and selectivity of volatile fluorinated anesthetics (Table 3.2). These molecules, although nonfunctional, can bind stereoselectively with protein targets of the central nervous system. Different biological behaviors have been reported for both enantiomers of isoflurane (cf. Chapter 8). ... 

When ionizing radiation affects just one nucleotide in a sequence, this may produce a point mutation. Most point mutations are of little consequence because the same protein or a functional variation is made anyway. However, some point mutations result in a nonsense message from which a nonfunctional protein is constructed, while other point mutations give a meaningful but changed message leading to a protein with altered properties. 

The intercalating drugs and nucleic acid synthesis inhibitors discussed in the preceding sections interfere indirectly with every phase of nucleic acid action because the DNA is rendered nonfunctional. Other drugs, discussed below, affect the regulation of protein synthesis even when the genome, the DNA structure, is intact. Such activity can be the result of interference either with transcription of messenger RNA or with translation of the mRNA to protein. 

Inside the cell, aminoglycosides bind to specific 30S-subunit ribosomal proteins (S12 in the case of streptomycin). Protein synthesis is inhibited by aminoglycosides in at least three ways (Figure 45-3) (1) interference with the initiation complex of peptide formation (2) misreading of mRNA, which causes incorporation of incorrect amino acids into the peptide and results in a nonfunctional or toxic protein and (3) breakup of polysomes into nonfunctional monosomes. These activities occur more or less simultaneously, and the overall effect is irreversible and lethal for the cell. 

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