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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. 相似文献
63.
HJ. Mellin 《Acta Mathematica》1887,9(1):137-166
Ohne Zusammenfassung 相似文献
64.
To determine if ilmenites are stoichiometric, the ratio of ferric to ferrous ions is measured by Mössbauer spectroscopy and the oxygen content by nuclear bombardment. This latter measurement implies also the determination of the nitrogen content, if any. It was surprisingly found that the five ilmenite crystals analyzed contain nitrogen from 0.51% to 2%. These exceed the values for most other minerals. Heating experiments suggest that the nitrogen is not located in fluid inclusions. These results suggest that ilmenite could be a major reservoir for nitrogen inside the earth. 相似文献
65.
Toman Rudolf Garidel Patrick Andrä Jörg Slaba Katarina Hussein Ahmed Koch Michel HJ Brandenburg Klaus 《BMC biochemistry》2004,5(1):1-14
Background
Coxiella burnetiiis the etiological agent of Q fever found worldwide. The microorganism has like other Gram-negative bacteria a lipopolysaccharide (LPS, endotoxin) in its outer membrane, which is important for the pathogenicity of the bacteria. In order to understand the biological activity of LPS, a detailed physico-chemical analysis of LPS is of utmost importace. 相似文献66.
67.
van Steen E Claeys M Dry ME van de Loosdrecht J Viljoen EL Visagie JL 《The journal of physical chemistry. B》2005,109(8):3575-3577
The stability of nanosized materials differs significantly from the stability of bulk materials. In this study a thermodynamic analysis on the simultaneous oxidation and re-reduction of small metallic cobalt crystallites in the presence of water and hydrogen as a function of the crystallite diameter was performed as a model for catalyst deactivation in the Fischer-Tropsch synthesis. It is shown that spherical cobalt crystallites with a diameter less than 4.4 nm are likely to be oxidized under realistic Fischer-Tropsch synthesis conditions (p(H)(2)(O)/p(H)(2) < 1.5, T = 493 K). 相似文献
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