The superpowers of molecular shredders - by evolution, or design?
The enzymes created in the body and supplied by, say fruit, are the chainsaws and industrial shredders of the body. One molecule of bromelain, the enzyme found in pineapples, particularly in the core, can locate, secure, chop, and expel 30,000 proteins in a single second. This is why it’s so effective in digestion and reducing inflammation.
Papain from papaya fruit works at a similar rate, targeting fibrin – the tough material around cancer cells. Natural chemo? Draw your own conclusions! The fastest enzymes that chemists have been able to create work at a rate of 2 per second.
Despite the fast-growing body of knowledge, there is an ongoing debate as to how enzymes such as ornithine decarboxylase achieve rate accelerations as high as 10 power 17 (that’s 100 thousand trillion) thus performing within milliseconds a reaction that in their absence takes millions of years (Table 1). Furthermore, fundamental questions regarding the evolution of enzymes also remain open; for example, how their function is related to their fold and whether, in the formation of enzyme active sites, substrate binding precedes the catalytic chemistry or vice versa.
The dismal failure is explained by the need for chemists to work in a truly Darwinian way, by trial and error combining pieces from a library of genetic strips. No useful protein is made of less than about 40 amino acids, and the real action only begins at around 50. The largest libraries created are nucleic acid repertoires containing about 10 power 15 molecules.
To give you an idea of the difficulty, remember these proteins are only measurable in angstroms. The mass of a fully randomized 50 nucleotide library with 10 power 30 variants is over 25,000 tonnes.
Thus, in practice, the in vitro evolution of an active molecule relies on the sampling of a negligible fraction of the potential consequences
http://www.weizmann.ac.il/Biological_Chemistry/scientist/Tawfik/papers/Article5.pdf
https://web.archive.org/web/20130503211721/http://iaincarstairs.wordpress.com/2013/03/25/as-smart-as-molecules/
The enzymes created in the body and supplied by, say fruit, are the chainsaws and industrial shredders of the body. One molecule of bromelain, the enzyme found in pineapples, particularly in the core, can locate, secure, chop, and expel 30,000 proteins in a single second. This is why it’s so effective in digestion and reducing inflammation.
Papain from papaya fruit works at a similar rate, targeting fibrin – the tough material around cancer cells. Natural chemo? Draw your own conclusions! The fastest enzymes that chemists have been able to create work at a rate of 2 per second.
Despite the fast-growing body of knowledge, there is an ongoing debate as to how enzymes such as ornithine decarboxylase achieve rate accelerations as high as 10 power 17 (that’s 100 thousand trillion) thus performing within milliseconds a reaction that in their absence takes millions of years (Table 1). Furthermore, fundamental questions regarding the evolution of enzymes also remain open; for example, how their function is related to their fold and whether, in the formation of enzyme active sites, substrate binding precedes the catalytic chemistry or vice versa.
The dismal failure is explained by the need for chemists to work in a truly Darwinian way, by trial and error combining pieces from a library of genetic strips. No useful protein is made of less than about 40 amino acids, and the real action only begins at around 50. The largest libraries created are nucleic acid repertoires containing about 10 power 15 molecules.
To give you an idea of the difficulty, remember these proteins are only measurable in angstroms. The mass of a fully randomized 50 nucleotide library with 10 power 30 variants is over 25,000 tonnes.
Thus, in practice, the in vitro evolution of an active molecule relies on the sampling of a negligible fraction of the potential consequences
http://www.weizmann.ac.il/Biological_Chemistry/scientist/Tawfik/papers/Article5.pdf
https://web.archive.org/web/20130503211721/http://iaincarstairs.wordpress.com/2013/03/25/as-smart-as-molecules/
