Kinetic proofreading

Kinetic Proofreading is a mechanism for error correction in biological processes, first proposed by John Hopfield in 1974. Kinetic proofreading allows molecules to discriminate between two possibilities which have nearly the same free energy with an error less than the naive thermodynamic bound ^[1].

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Specificity Paradox

In protein synthesis, the error rate is on the order of 1 in 10,000. This means that when a ribosome is matching anticodons of tRNA to the codons of mRNA, it matches complementary sequences correctly nearly all the time. Hopfield noted that an error rate that small is unachievable with a one-step comparison.

The reason is that the only difference between a wrong codon and a right codon is a short sequence. Both wrong and right tRNA can bind to the ribosome, and the only way the ribosome can discriminate between them is by comparing the anticodon to the mRNA codon. If the comparison is by complementary matching, it can only make use of the small free energy difference between three matched complementary bases and three mismatched ones.

A one-shot machine which tests whether the codons match or not by looking whether the codon and anticodon are bound will not be able to tell the difference between wrong and right codon with an error rate less than e ^{− 10} unless the free energy difference is at least 10kT, which is much larger than the free energy difference for single codon binding. This is a thermodynamic bound, so it cannot be evaded by building a different machine. The only way to evade it is to expend energy.

Multistep Ratchet

Hopfield suggested a simple way to achieve smaller error rates using a molecular ratchet which takes many irreversible steps. At each step, energy is expended, and each step tests to see if the sequences match.

Although one test will only be able to discriminate between mismatched and matched a fraction p = e ^{− ΔF / kT} of the time, two tests will both fail only p² of the time, and N tests will fail p^N of the time. In terms of free energy, the discrimination power of N successive tests for two states with a free energy ΔF is the same as one test between two states with a free energy NΔF.

To achieve an error rate of e ^{− 10} requires several comparison steps. Hopfield predicted based on 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.

References

1. ^ J.J. Hopfield (1974). ""Kinetic Proofreading: A New Mechanism for Reducing Errors in Biosynthetic Processes Requiring High Specificity"". Proceedings of the National Academy of Sciences USA 71: 4135-4139.