Mechanisms of protein mutation

See also Mechanisms of Protein Mutation, Antibody Structure, Clonal Selection Theory, Gene Rearrangements (from Chapter 25), Generating Antibody Diversity (from Chapter 25)... 

See also Globin Gene Expression in Development, Mechanisms of Protein Mutation, Hemoglobin Variants... 

Work with the carcinogen acetylaminofluorene found that residues of the compound in ribosomal RNA may correlate more closely with liver tumor formation than residues in DNA. Direct interactions with the mechanisms of protein synthesis, or with DNA and RNA polymerase enzymes, can also be seen as possible mechanisms. For instance, a modification of the polymerase enzymes by a carcinogen, either directly or indirectly, could lead to the erroneous replication of DNA or RNA and hence the permanent incorporation of a mutation. 

Undoubtedly there are often questions about the mechanism of protein evolution that can be addressed by making ancestral proteins and testing their properties, especially the origin of new functions. Lysozyme provides an example for that type of investigation because on two occasions in mammalian evolution it has been recruited for functioning in the harsh conditions of the stomach fluid.41-42 The sequences of the common ancestor have been inferred by tree analysis, and at least four of the new selection pressures faced by this enzyme are known. Irwin et a/.43 have reviewed this subject and the speculations regarding the possibility that double or triple mutations were required to achieve new functions. 

Detailed information on the mechanism of biochemical reactions may be of crucial importance in designing new molecules having a pharmacological activity. For example, the detailed mechanism of protein hydrolysis by thermolysin has been studied at the QM/MM semiempirical level [25]. The various steps of the reaction and their transition states have been characterized. Fig. 3 (see color plate) shows the structure of the transition state of the rate-determining step. The important consequence of this approach is the fact that it is possible to evaluate the influence of the whole macro-molecular surroundings on the energetics of the process. It then becomes possible, for instance, to predict the influence of a mutation on the reaction kinetics. 

When taking into account the fact that the admitted mechanism of protein synthesis allows for the direct incorporation of only twenty amino acids, it becomes manifest that the natural hormones possess almost optimal active structures arrived at by natural mutation and selection. 

A general mechanism of resistance is reducing the affinity of the antiretroviral compound for its mutant target protein. Resistance mutations associated with reduced affinity are observed during treatment failure with a fusion inhibitor, nonnucleoside reverse transcriptase inhibitors (NNRTl), integrase inhibitor, and protease inhibitors as reviewed in Chaps. 3,4, 6, and 7 (Hazuda et al. 2007 Hsiou et al. 2001 King et al. 2002 Mink et al. 2005). 

Another important protein of the Clp family is ClpB which possesses ATPase activity. In a clpB mutation, 45% of the denatured and aggregated protein arising transiently after the transfer of an E. coli culture from 30 to 45 °C is stabilized [14]. ClpB seems to play an important role in the renaturation or proteolysis of the aggregated proteins, but the mechanism of action of ClpB is not yet known. One can suppose that it might participate in the resolubilization of aggregated proteins. 

The mechanism of acquired resistance in Pseudomonas aeruginosa is different. Chromosomal mutations result in the increase of a specific outer membrane protein with a concomitant reduction in divalent cations. Polymyxins bind to the outer membrane at sites normally occupied by divalent cations, and therefore it is thought that a reduction in these sites will lead to decreased binding of the antibiotic with a consequent decreased susceptibility of the cell. 

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