Kinetic proofreading
Encyclopedia
Kinetic proofreading is a mechanism for error correction in biological processes, proposed independently by John Hopfield (1974) and Jacques Ninio (1975). 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.
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 difference between a wrong codon and a right codon can be as small as a difference in a single base. 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 must rely on the small free energy
difference between binding three matched complementary bases or only two.
A one-shot machine which tests whether the codons match or not by examining 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
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.
Another molecular recognition mechanism, which does not require expenditure of free energy is that of conformational proofreading
.
Although one test will only be able to discriminate between mismatched and matched sequences a fraction
of the time, two tests will both fail only 
of the time, and N tests will fail 
of the time. In terms of free energy, the discrimination power of N successive tests for two states with a free energy 
is the same as one test between two states with a free energy 
.
To achieve an error rate of
requires several comparison steps. 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.
Specificity paradox
In protein synthesis, the error rate is on the order of 1 in 10,000. This means that when a ribosomeRibosome
A ribosome is a component of cells that assembles the twenty specific amino acid molecules to form the particular protein molecule determined by the nucleotide sequence of an RNA molecule....
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 difference between a wrong codon and a right codon can be as small as a difference in a single base. 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 must rely on the small free energy
Thermodynamic free energy
The thermodynamic free energy is the amount of work that a thermodynamic system can perform. The concept is useful in the thermodynamics of chemical or thermal processes in engineering and science. The free energy is the internal energy of a system less the amount of energy that cannot be used to...
difference between binding three matched complementary bases or only two.
A one-shot machine which tests whether the codons match or not by examining 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
unless the free energy difference is at least 10kTKT (energy)
kT is the product of the Boltzmann constant, k, and the temperature, T. This product is used in physics as a scaling factor for energy values in molecular-scale systems , as the rates and frequencies of many processes and phenomena depend not on their energy alone, but on the ratio of that energy...
, 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.
Another molecular recognition mechanism, which does not require expenditure of free energy is that of conformational proofreading
Conformational proofreading
Conformational proofreading is a general mechanism of molecular recognition systems, in which introducing a structural mismatch between a molecular recognizer and its target enhances the recognition specificity and quality....
.
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 sequences a fraction
of the time, two tests will both fail only of the time, and N tests will fail of the time. In terms of free energy, the discrimination power of N successive tests for two states with a free energy is the same as one test between two states with a free energy .To achieve an error rate of
requires several comparison steps. 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.Examples
- Charging tRNAs with their respective amino-acids – the enzyme that charges the tRNA is called aminoacyl tRNA synthetaseAminoacyl tRNA synthetaseAn aminoacyl tRNA synthetase is an enzyme that catalyzes the esterification of a specific amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. This is sometimes called "charging" the tRNA with the amino acid...
. This enzyme utilizes a high energy intermediate state to increase the fidelity of binding the right pair of tRNA and amino-acid.
- T-cell receptor signal transduction – As part of the immune system, T-cells recognize foreign proteins that bind to their receptors. After binding the foreign ligand, the receptor undergoes a series of irreversible modifications that enhance its ability to detect the correct protein.
- Homologous recombination – Homologous recombinationHomologous recombinationHomologous recombination is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks...
facilitates the exchange between homologous or almost homologous DNA strands. During this process, the RecA protein polymerizes along a DNA and this DNA-protein filament searches for a homologous DNA sequence. Both processes of RecA polymerization and homology search utilize the kinetic proofreading mechanism.
- DNA damage recognition and repair – a certain DNA repairDNA repairDNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...
mechanism utilizes kinetic proofreading to discriminate damaged DNA.