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.     

In silico based virtual screening and mixed mode QM/MM calculation identifies caffeine scaffold for designing potential inhibitors for tyrosyl tRNA synthetase of Mycobacterium tuberculosis

Aminoacyl tRNA synthetases are novel antibacterial drug target because of their important role in protein synthesis. In this study, we performed high throughput virtual screening of 205883 compounds from Asinex ligand database to identify potential specific inhibitors for Tyrosyl tRNA synthetase of Mycobacterium tuberculosis (MtbTyrRS). Compounds are ranked based on the glide extra precision docking score. It is noted that the top ranked compounds have caffeine scaffold. The top five caffeine analogs are further evaluated for other drug‐like properties. The binding energies of caffeine analogs are estimated using mixed mode quantum mechanics/molecular mechanics calculation. The results show that these caffeine analogs have good absorption, distribution, metabolism, and excretion properties and high binding affinity to the MtbTyrRS. This suggests that caffeine could be a new scaffold for designing inhibitors against Tyrosyl tRNA synthetase of M. tuberculosis. The top five caffeine analogs are also subjected to docking calculations with human cytosolic and mitochondrial Tyrosyl tRNA synthetases to ascertain their specificities toward MtbTyrRS. The comparative docking studies indicate that the top five caffeine analogs are specific for MtbTyrRS. © 2014 Wiley Periodicals, Inc.     

Conformational flipping of the N(6) substituent in diprotonated N6‐(N‐glycylcarbonyl)adenines: The role of N(6)H in purine‐ring‐protonated ureido adenines

Conformational transitions of the N(6) substituent, in hypermodified nucleic acid base N⁶‐(N‐glycylcarbonyl)adenine, gc⁶Ade, on diprotonation of the adenine ring at any two of N(1), N(3), and N(7) sites, are studied using the quantum chemical perturbative configuration interaction with localized orbitals (PCILO) method. The N(6) substituent retains the usual “distal” orientation (α=0°) in (N(1),N(3)) diprotonated gc⁶Ade, but the “proximal” orientation (α=180°) is preferred instead, for (N(3),N(7)) and (N(7),N(1)) diprotonated gc⁶Ade. The proximal orientation may alter the reading frame during translation. Intramolecular N(6)HO(13b) hydrogen bonding is the key common feature, present in the preferred structure, for each of these variously diprotonated gc⁶Ade. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 398–405, 2000     

Absolute Quantification of Noncoding RNA by Microscale Thermophoresis

Accurate quantification of the copy numbers of noncoding RNA has recently emerged as an urgent problem, with impact on fields such as RNA modification research, tissue differentiation, and others. Herein, we present a hybridization‐based approach that uses microscale thermophoresis (MST) as a very fast and highly precise readout to quantify, for example, single tRNA species with a turnaround time of about one hour. We developed MST to quantify the effect of tRNA toxins and of heat stress and RNA modification on single tRNA species. A comparative analysis also revealed significant differences to RNA‐Seq‐based quantification approaches, strongly suggesting a bias due to tRNA modifications in the latter. Further applications include the quantification of rRNA as well as of polyA levels in cellular RNA.     

Modular and Versatile Trans-Encoded Genetic Switches

Current bacterial RNA switches suffer from lack of versatile inputs and are difficult to engineer. We present versatile and modular RNA switches that are trans-encoded and based on tRNA-mimicking structures (TMSs). These switches provide a high degree of freedom for reengineering and can thus be designed to accept a wide range of inputs, including RNA, small molecules, and proteins. This powerful approach enables control of the translation of protein expression from plasmid and genome DNA.     

Chemical Synthesis of Oligoribonucleotide (ASL of tRNALys T. brucei) Containing a Recently Discovered Cyclic Form of 2-Methylthio-N6-threonylcarbamoyladenosine (ms2ct6A)

The synthesis of the protected form of 2-methylthio-N⁶-threonylcarbamoyl adenosine ( ms²t⁶A) was developed starting from adenosine or guanosine by using the optimized carbamate method and, for the first time, an isocyanate route. The hypermodified nucleoside was subsequently transformed into the protected ms²t⁶A -phosphoramidite monomer and used in a large-scale synthesis of the precursor 17nt ms²t⁶A -oligonucleotide (the anticodon stem and loop fragment of tRNA^Lys from T. brucei). Finally, stereochemically secure ms²t⁶A → ms²ct⁶A cyclization at the oligonucleotide level efficiently afforded a tRNA fragment bearing the ms²ct⁶A unit. The applied post-synthetic approach provides two sequentially homologous ms²t⁶A - and ms²ct⁶A -oligonucleotides that are suitable for further comparative structure–activity relationship studies.     

Selection of Amino Acids and the Biomimetic Synthesis of Amido Bond in the Presence of β-CD

A new method was developed to construct a special amido bond in the presence of β-cyclodextrin. This process is similar to peptide synthesis in organisms. NMR experiments were performed to investigate the possible mechanism. This work has potential application in biomimetic peptide synthesis.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

A Covalent Approach for Site‐Specific RNA Labeling in Mammalian Cells

Advances in RNA research and RNA nanotechnology depend on the ability to manipulate and probe RNA with high precision through chemical approaches, both in vitro and in mammalian cells. However, covalent RNA labeling methods with scope and versatility comparable to those of current protein labeling strategies are underdeveloped. A method is reported for the site‐ and sequence‐specific covalent labeling of RNAs in mammalian cells by using tRNA^Ile2‐agmatidine synthetase (Tias) and click chemistry. The crystal structure of Tias in complex with an azide‐bearing agmatine analogue was solved to unravel the structural basis for Tias/substrate recognition. The unique RNA sequence specificity and plastic Tias/substrate recognition enable the site‐specific transfer of azide/alkyne groups to an RNA molecule of interest in vitro and in mammalian cells. Subsequent click chemistry reactions facilitate the versatile labeling, functionalization, and visualization of target RNA.