Enzymes are really useful organic molecules, speeding up chemical reactions without being consumed. They are essential components of cells, and widely used in industrial processes. Getting the enzyme to work in the precise conditions required by many industrial applications has engaged the attention of many researchers: "there is a strong interest in developing experimental and theoretical methods for changing the pH-dependent characteristics of enzymes."
The authors of the paper abstracted below review these problems and explain that specific mutations in the active site can change the pH-activity profiles, but these mutations are actually very difficult to engineer. "The conclusion from two decade's work is that very specific point mutations in the active sites can change the pH dependence of enzymatic activity, but unless such specific active site point mutations are known (e.g., from comparative studies), there is not much hope of achieving a dramatic pH-activity profile shift with rational engineering methods. This somewhat disheartening conclusion is reached because mutations that give large pH-activity profile shifts normally are close to the active site and therefore likely to give mutant enzymes that are inactive or have dramatically reduced activity."
In ID circles, this would be described as "fine tuning", as a pointer to intelligent design, and an example of why random mutations and natural selection is an inappropriate mechanism to achieve the exquisite properties of the enzymes found in living things.
Redesigning protein pKa values
Barbara Mary Tynan-Connolly and Jens Erik Nielsen
Protein Science (2007), 16:239-249
The ability to re-engineer enzymatic pH-activity profiles is of importance for industrial applications of enzymes. We theoretically explore the feasibility of re-engineering enzymatic pH-activity profiles by changing active site pKa values using point mutations. We calculate the maximum achievable delta pKa values for 141 target titratable groups in seven enzymes by introducing conservative net-charge altering point mutations. We examine the importance of the number of mutations introduced, their distance from the target titratable group, and the characteristics of the target group itself. The results show that multiple mutations at 10Ãƒâ€¦ can change pKa values up to two units, but that the introduction of a requirement to keep other pKa values constant reduces the magnitude of the achievable delta pKa. The algorithm presented shows a good correlation with existing experimental data and is available for download and via a web server at http://enzyme.ucd.ie/pKD.
This is from the introduction:
[snip] ... there is a strong interest in developing experimental and theoretical methods for changing the pH-dependent characteristics of enzymes. Advances have been made in the fields of protein engineering and directed evolution, and it is presently possible to routinely optimize the performance of enzymes for a range of conditions using either rational engineering or screening/selection-based approaches (Cherry et al. 1999; Farinas et al. 2001). Unfortunately, not all characteristics of enzymes are equally easy to optimize and successes in rational re-engineering of enzymatic pH-activity profiles remain few despite decades of studies on enzyme structure-function relationships.
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