Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis

It is generally accepted that the translation rate depends on the availability of cognate aa-tRNAs. In this study it is shown that the key factor that determines translation rate is the competition between near-cognate and cognate aa-tRNAs. The transport mechanism in the cytoplasm is diffusion, thus the competition between cognate, near-cognate and non-cognate aa-tRNAs to bind to the ribosome is a stochastic process. Two competition measures are introduced; C(i) and R(i) (i = 1, 64) are quotients of the arrival frequencies of near-cognates vs. cognates and non-cognates vs. cognates, respectively. Furthermore, the reaction rates of bound cognates differ from those of bound near-cognates. If a near-cognate aa-tRNA binds to the A site of the ribosome, it may be rejected at the anti-codon recognition step or proofreading step or it may be accepted. Regardless of its fate, the near-cognates and non-cognates have caused delays of varying duration to the observed rate of translation. Rate constants have been measured at a temperature of 20 °C by (Gromadski, K.B., Rodnina, M.V., 2004. Kinetic determinants of high-fidelity tRNA discrimination on the ribosome. Mol. Cell 13, 191–200). These rate constants have been re-evaluated at 37 °C, using experimental data at 24.5 °C and 37 °C (Varenne, S., et al., 1984. Translation in a non-uniform process: effect of tRNA availability on the rate of elongation of nascent polypeptide chains. J. Mol. Biol. 180, 549–576). The key results of the study are: (i) the average time (at 37 °C) to add an amino acid, as defined by the ith codon, to the nascent peptide chain is: τ(i) = 9.06 + 1.445 × [10.48C(i) + 0.5R(i)] (in ms); (ii) the misreading frequency is directly proportional to the near-cognate competition, E(i) = 0.0009C(i); (iii) the competition from near-cognates, and not the availability of cognate aa-tRNAs, is the most important factor that determines the translation rate – the four codons with highest near-cognate competition (in the case of E. coli) are [GCC] > [CGG] > [AGG] > [GGA], which overlap only partially with the rarest codons: [AGG] < [CCA] < [GCC] < [CAC]; (iv) based on the kinetic rates at 37 °C, the average time to insert a cognate amino acid is 9.06 ms and the average delay to process a near-cognate aa-tRNA is 10.45 ms and (vii) the model also provides estimates of the vacancy times of the A site of the ribosome – an important factor in frameshifting.     

A macroscopic kinetic model for DNA polymerase elongation and high-fidelity nucleotide selection

The enzymatically catalyzed template-directed extension of ssDNA/primer complex is an important reaction of extraordinary complexity. The DNA polymerase does not merely facilitate the insertion of dNMP, but it also performs rapid screening of substrates to ensure a high degree of fidelity. Several kinetic studies have determined rate constants and equilibrium constants for the elementary steps that make up the overall pathway. The information is used to develop a macroscopic kinetic model, using an approach described by Ninio [Ninio J., 1987. Alternative to the steady-state method: derivation of reaction rates from first-passage times and pathway probabilities. Proc. Natl. Acad. Sci. U.S.A. 84, 663-667]. The principle idea of the Ninio approach is to track a single template/primer complex over time and to identify the expected behavior. The average time to insert a single nucleotide is a weighted sum of several terms, including the actual time to insert a nucleotide plus delays due to polymerase detachment from either the ternary (template-primer-polymerase) or quaternary (+nucleotide) complexes and time delays associated with the identification and ultimate rejection of an incorrect nucleotide from the binding site. The passage times of all events and their probability of occurrence are expressed in terms of the rate constants of the elementary steps of the reaction pathway. The model accounts for variations in the average insertion time with different nucleotides as well as the influence of G + C content of the sequence in the vicinity of the insertion site. Furthermore the model provides estimates of error frequencies. If nucleotide extension is recognized as a competition between successful insertions and time delaying events, it can be described as a binomial process with a probability distribution. The distribution gives the probability to extend a primer/template complex with a certain number of base pairs and in general it maps annealed complexes into extension products.     

Trace analysis of complex organic mixtures using capillary gas-liquid chromatography and the dynamic solvent effect

A sampling system for high resolution gas-liquid chromatography, based on the dynamic solvent effect, is described. Volatiles are accumulated off-line in a concentrator/injector and delivered to the column using an on-line inlet. Volatiles may be accumulated from gaseous or liquid matrices; they may be transferred to these by gas sparging or solvent extraction of any type of sample. The sampling technique is quantitatively precise; e.g. coefficients of variation of peak percentage areas better than 5% for a range of solutes at a concentration of 2:10⁷. Examples of the application of the sampling system are presented.     

Interconvertions between delta-lactam and delta-lactone derivatives initiated by unique transannular interactions of the rigid cyclohexane boat structure in pentacycloundecane

The pentacycloundecane (PCU) cage structure resembles a perfect boat conformation, and for the first time unique lactam/lactone interconversions on the flagpole carbons of a cyclohexane boat structure are reported. The syntheses of a novel dihydroxy-PCU-delta-lactone and two novel N-substituted PCU-delta-lactams are reported. Hydrolysis of some of the PCU-delta-lactam compounds produced delta-lactones, and reaction of the lactones with ammonia or primary amines again produced delta-lactams. Reaction mechanisms to account for the unusual interconversion reactions induced by transannular interactions are proposed.