Renaturation

Most plasmids are topologically closed circles of DNA. They can be separated from the bulk of the chromosomal DNA by virtue of their resistance to alkaline solution. The double-stranded stmcture of DNA is denatured at high pH, but because the two strands of the plasmid are topologically joined they are more readily renatured. This property is exploited in rapid procedures for the isolation of plasmid DNA from recombinant microorganisms (5,6). 

The renaturation rate of DNA is an excellent indicator of the sequence complexity of DNA. For example, bacteriophage T4 DNA contains about 2 X 10 nucleotide pairs, whereas Escherichia coli DNA possesses 4.64 X 10 . E. coli DNA is considerably more complex in that it encodes more information. Expressed another way, for any given amount of DNA (in grams), the sequences represented in an E. coli sample are more heterogeneous, that is, more dissimilar from one another, than those in an equal weight of phage T4 DNA. Therefore, it will take the E. coli DNA strands longer to find their complementary partners and reanneal. This situation can be analyzed quantitatively. 

FIGURE 12.19 Steps in the thermal denaturation and renaturation ofDNA. The nucle-ation phase of the reaction is a second-order process depending on sequence alignment of the two strands. This process takes place slowly because it takes time for complementary sequences to encounter one another in solution and then align themselves in register. Once the sequences are aligned, the strands zipper up quickly. 

Denaturation is accompanied by changes in both physical and biological properties. Solubility is drastically decreased, as occurs when egg white is cooked and the albumins unfold and coagulate. Most enzymes also lose all catalytic activity when denatured, since a precisely defined tertiary structure is required for their action. Although most denaturation is irreversible, some cases are known where spontaneous renaturation of an unfolded protein to its stable tertiary structure occurs. Renaturation is accompanied by a full recovery of biological activity. 

Bokman, S. H., and Ward, W. W. (1981). Renaturation of Aequorea green-fluorescent protein. Biochem. Biophys. Res. Commun. 101 1372-1380. 

Fig, 27. The possible pathways of collagen renaturation proposed by Harrington et al.135)... 

To answer the question whether the ds-transisomerization of the bridged polypeptides with a Ala-Gly-Pro sequence represents the rate-determining step, the following experiment was carried out The polypeptide with a chain length n = 8 was denaturated in a rapid reaction with a temperature jump from 9.2 to 30 °C and subjected to renatura-tion at 9.2 °C after an incubation time of 25 s. In a second and a third experiment, the incubation in the coiled state was prolonged respectively to 75 and 125 s. It could be observed that the amplitude of the rapid phase depends on the time that lapses between the denaturation and renaturation (Fig. 32). 

One may conclude that the rate-determining step of the renaturation is at least partly influenced by the cis-trans isomerization of the peptide bond the secondary nitrogen atom of which arises from proline. Otherwise, only the entropy-controlled slow nuclea-tion should be observed kinetically. The covalent bridging through Lys-Lys, therefore, gives rise not only to thermodynamic stabilization of the triple helix but also to kinetic properties which have hitherto been observed in the case of type III procollagen146) and its aminoterminal fragment Col 1-3144). 

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. 

Muller, C. and Rinas, U., Renaturation of heterodimeric platelet-derived growth factor from inclusion bodies of recombinant Escherichia coli using size-exclusion chromatography, /. Chromatogr. A, 855, 203, 1999. 

Stem, B. D., Wilson, M., and Jagus, R. (1993). Use of nonreducing SDS-PAGE for monitoring renaturation of recombinant protein synthesis initiation factor, eIF-4 alpha. Protein Expr. Purif. 4, 320-327. 

Kumar, C.V. and Chaudhari A. (2001) Efficient renaturation of immobilized met-hemoglobin at the galleries of alpha-zirconium phosphonate. Chemistry of Materials, 13, 238-240. 

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