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Invisible Catcher: How can dynamic amplification make mistakes disappear?
In biochemical reactions, dynamic school is a mechanism of error correction, and the concept proposed by John Hopfield and Jacques Nigno.Their study points out that during the enzyme reaction, the selectivity between the correct and the wrong products is much higher than what is expected to be inferred based on the difference in activation energy.This discovery not only allowed us to rethink the accuracy of biomolecular synthesis, but also challenged our understanding of biochemical error rates.
Dynamic schooling is introducing irreversible steps, making it easier for reaction intermediates of the wrong products to exit the reaction pathway in advance.Simply put, if an irreversible exit step is rapid relative to the next step in the reaction pathway, then the specificity of the correct product can be significantly improved.This process can be repeated many times to further enhance specificity, but at the same time it will reduce production rates.
For example, if a production line that produces drugs sometimes produces empty boxes and we cannot upgrade the line, we can make the empty boxes more easily blown off by placing a giant fan at the end of the line (with a higher exit rate) , thereby increasing the ratio of the complete box.
However, there is a so-called paradox of specificity in protein synthesis.When the ribosome matches the anti-anti-codon of the tRNA to the codon of the mRNA, the error rate is as high as 10^-4, which means that the ribosomes can almost always match complementary sequences correctly.Hopfield notes that this is because the difference between the right and wrong matrix is very subtle and therefore can only be determined by energy differences.
This error rate is not possible in a one-step mechanism; if the ribosome can only rely on complementary matches to distinguish, it cannot achieve a response less than that error rate without additional energy support without additional energy .
The solution is dynamic correction, which introduces irreversible steps by applying energy, thereby changing the dynamics of the reaction.For example, during the amino acid charging of tRNA, amino acid tRNA synthetase uses high-energy intermediate states to improve the accuracy of the reaction.
In addition, in other biochemical processes such as homologous recombination, RecA proteins will aggregate along the DNA to search for homologous DNA sequences, and dynamic correction is also applied in this process.This suggests that dynamic schooling is not an isolated process, but a set of interrelated biochemical networks.
In some DNA repair mechanisms, DNA polymerases are able to recognize and immediately hydrolyze the wrong nucleotides. This immediate correction process is a typical example of dynamic correction.
In theory, this behavior can be achieved through many different biochemical networks, and at large scale, dynamic schools are showing a close to universal, exponential shape completion time.In addition, the topological structure of this process is closely related to the improvement of specificity. The more closed loops there is, the more specificity increases exponentially.
The discovery of dynamic correction not only deepens our understanding of life processes, but also leads to a series of research on how to optimize these processes.The development of science and technology may allow us to explore these biochemical mechanisms more deeply in the future, and even find opportunities for practical applications in the fields of medical care and biotechnology.
Think further, how can we use these principles of biochemical processes to improve the quality of human life and reduce the error rate in the ever-expanding world of bioengineering?
