Translation error rate

We started out this section by emphasizing the importance of getting the amino acid sequence right. After all, the sequence determines the three-dimensional structure of proteins and that, in turn, is critical for function. Through multiple mechanisms, several of which we have mentioned, translation of the genetic code is remarkably accurate. The error rate is about 1 out of 10,000. Of course, many of the errors which... 

The reverse transcriptase enzyme (RT) is the primary enzyme responsible for the conversion of the viral single-strand RNA to the double-strand DNA. The reverse transcriptase enzyme is a component of the virion and is encoded by the pol gene. The RT is manufactured in the HIV-infected cells as a gag-pol fusion polyprotein. The RT is not the only enzyme necessary for the translation of RNA to DNA. The other enzymes for this conversion include RNA-dependent DNA polymerase, DNA-dependent DNA polymerase, and RNase H (Gilboa and Mitra, 1978 Prasad and Gogg, 1990). The reverse transcriptase enzyme has a high error rate (1 in 2000 bases), which produces higher incidents of mutation. Some of these mutations make the virus resistant to NNRTI treatment. 

The two trial rule, for example in a placebo controlled setting, effectively translates into a very stringent requirement for statistical significance. In a single trial the conventional two-sided type I error rate is 0.05. It follows that in order... 

The zinc site is less well suited to discrimination against serine because this amino acid does have a hydroxyl group that can bind to the zinc. Indeed, with only this mechanism available, threonyl-tRNA synthetase does mistakenly couple serine to threonyl-tRNA at a rate 10 2 to 10 3 times that for threonine. As noted in Section 29. LL this error rate is likely to lead to many translation errors. How is a higher level of specificity achieved ... 

Because some amino acids are so similar structurally, aminoacyl-tRNA synthetases sometimes make mistakes. These are corrected, however, by the enzymes themselves, which have a proofreading activity that checks the fit In their amino acid-binding pocket. If the wrong amino acid becomes attached to a tRNA, the bound synthetase catalyzes removal of the amino acid from the tRNA. This crucial function helps guarantee that a tRNA delivers the correct amino acid to the protein-synthesizing machinery. The overall error rate for translation In E. coli Is very low, approximately 1 per... 

Errors made during protein translation can result in misfolded proteins, which represent a burden to the cell. Mutations that make a protein more susceptible to error-induced misfolding will result in a loss of fitness. If the mutation occurs in a highly expressed protein, then translational errors (and misfolding events) will be more common, resulting in a larger fitness loss. Hence, protein expression will scale directly with selective constraint, and inversely with evolutionary rate [11]. 

Coordination of the threonine hydroxyl by an active site Zn in the threonyl-tRNA synthetase allows discrimination between threonine and the isosteric valine (Sankaranarayanan et al., Nat. Struct. Biol. 7[2000] 461-465). Given the similarity of serine and threonine (Ser lacks only the methyl group of Thr), if this is the only mechanism for amino acid discrimination available, threonyl-tRNA synthetase mistakenly couples Ser to threonyl-tRNA at a rate several-fold higher than it does threonine. Since this would lead to unacceptably high error rates in translation, how it is it avoided ... 

The databases listed in Table 8.2 are maintained by independent research groups and can be accessed through the Internet. Some of these databases are nucleotide databases, and some protein databases that have been translated from the nucleotide databases. They are updated frequently and contain comprehensive lists of protein and nucleotide sequences. The choice of a particular database is dictated by the extensiveness of sequence entries, low redundancy rate, low error rate, and a high degree of annotation. A custom-made database can be assembled into a composite nonredundant database by including entries from all protein databases and translated-nucleotide databases (into protein sequences) and removing any duplicate entries. 

Given the complexity of protein synthesis, there are many steps at which mistakes can occur, and it is remarkable that the error rate is as low as it is. The two principal categories of translational mistakes are missense errors, in which one amino acid is substituted for another or a stop codon is not recognized, and errors of processivity, in which frameshifting or premature termination occur. 

The small subunit 16S rRNA also contains regions that appear to be involved in translational accuracy. In particular, substitutions at nucleotides in the so-called 530 loop lead to changes in the error rate of protein synthesis. This rRNA loop is known to be spatially near the proteins S4, S5, and SI2, and effects of nucleotide changes in the 530 loop parallel those observed for the proteins. Thus, the rRNA and proteins in this part of the small subunit together act as a proofreading domain. Substitutions at some of these nucleotides increase the rate of missense or frameshift errors, while others are detrimental because they prevent binding of the EF-Tu GTP AA-tRNA ternary complex. Still other mutations actually increase the accuracy of translation, in that they make the ribosomes resistant to error-inducing antibiotics. 

This question was addressed by use of classical trajectory techniques with an ion-quadrupole plus anisotropic polarizability potential to determine the collision rate constant (k ). Over one million trajectories with initial conditions covering a range of translational temperature, neutral rotor state, and isotopic composition were calculated. The results for the thermally average 300 K values for are listed in the last column of Table 3 and indicate that reaction (11) for H2/H2, D2/D2, and HD /HD proceeds at essentially the classical collision rate, whereas the reported experimental rates for H2/D2 and D2/H2 reactions seem to be in error as they are significantly larger than k. This conclusion raises two questions (1) If the symmetry restrictions outlined in Table 2 apply, how are they essentially completely overcome at 300 K (2) Do conditions exist where the restriction would give rise to observable kinetic effects ... 

The surface distribution for mean annual h results from two properties of atmospheric flow conservation of h following the large-scale flow and the maintenance of the vertical profile of h by convective processes. These features of the climate system allow one to quantify the expected errors for assuming that mean annual h is invariant with longitude and altitude for the present-day distribution. Forest et al. (1999) examined the distribution and calculated the expected error from assuming zonal invariance to be 4.5 kJ/kg for the mean annual climate. This error translates to an altitude error of 460 m and is compared with an equivalent error of 540 m from the mean annual temperature approach. Moreover, the uncertainty of the terrestrial lapse rate, y(, increases the expected error in elevation as elevations increase, particularly when small lapse rates are assumed. 

The determination of a complete Arrhenius relation is a long procedure. Even for quite unstable materials, degradation rates are low as room temperatures are approached, yet room temperature must be approached to minimize the errors of extrapolation. Once the slope of the line is established for a given material, the regression data from one oven-aging experiment can be translated to life at room temperature for other samples. Unfortunately, much of the Arrhenius data at hand for paper does not separate hydrolytic from oxidative degradation. The method will make more reliable predictions when such a separation is made. 

---