Kinetic proofreading
Kinetic proofreading allows enzymes to discriminate between two possible reaction pathways leading to correct or incorrect products with an accuracy higher than what one would predict based on the difference in the activation energy between these two pathways.
[1][2] Increased specificity is obtained by introducing an irreversible step exiting the pathway, with reaction intermediates leading to incorrect products more likely to prematurely exit the pathway than reaction intermediates leading to the correct product.
By lengthening the final section and adding more giant fans (multistep proofreading), the specificity can be increased arbitrarily, at the cost of decreasing production rate.
Hopfield noted that because of how similar the substrates are (the difference between a wrong codon and a right codon can be as small as a difference in a single base), an error rate that small is unachievable with a one-step mechanism.
Both wrong and right tRNA can bind to the ribosome, and if the ribosome can only discriminate between them by complementary matching of the anticodon, it must rely on the small free energy difference between binding three matched complementary bases or only two.
However, this can be overcome by kinetic proofreading, which introduces an irreversible step through the input of energy.
[3] Another molecular recognition mechanism, which does not require expenditure of free energy is that of conformational proofreading.
Hopfield suggested a simple way to achieve smaller error rates using a molecular ratchet which takes many irreversible steps, each testing to see if the sequences match.
The requirement for energy in each step of the ratchet is due to the need for the steps to be irreversible; for specificity to increase, entry of substrate and analogue must occur largely through the entry pathway, and exit largely through the exit pathway.
Hopfield predicted on the basis of this theory that there is a multistage ratchet in the ribosome which tests the match several times before incorporating the next amino acid into the protein.
Nonetheless, many such networks result in the times to completion of the molecular assembly and the proofreading steps (also known as the first passage time) that approach a near-universal, exponential shape for high proofreading rates and large network sizes.
[10] Since exponential completion times are characteristic of a two-state Markov process, this observation makes kinetic proofreading one of only a few examples of biochemical processes where structural complexity results in a much simpler large-scale, phenomenological dynamics.
[11][12] An example is homologous recombination in which the number of loops scales like the square of DNA length.
[5][6] The universal completion time emerges precisely in this regime of large number of loops and high amplification.
