University of Stuttgart

Computational Chemistry Group
(Kästner Group)

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Ribosome

The ribosome translates between the main alphabets in biology: the DNA sequence and the amino acid sequence in proteins. In doing so it connects amino acids to a peptide chain. The bond which is formed between these amino acids is called a peptide bond. The ribosome is an evolutionary ancient enzyme. RNA probably catalyzed reactions even before nature "invented" proteins. The structure of the ribosome has been solved many years ago – a significant achievement for which the Nobel price in chemistry was awarded in 2009.

A striking fact about the ribosome is that its active center, the peptidyl transferase center, consists exclusively of chemically inert moieties: RNA, water, and most certainly some cations like sodium or magnesium. The same holds true for other ribozymes which also consist of RNA. Yet the ribosome is able to accelerate the formation of peptide bonds by more than 6 orders of magnitude.

We investigated [17] the reaction catalyzed by the ribosome by means of QM/MM simulations. This allowed us to describe those atoms involved in the reaction with high accuracy, while still including enough of the environment to have a realistic model. The beauty of theory is, that we can artificially switch on and off various compounds and effects and use that to understand how chemical systems work.

In order to find out how those inert compounds are able to perform some chemistry, we investigated entropic effects by using umbrella sampling simulations with umbrella integration analysis. However, the entropy is not responsible for the catalytic effect.

Some enzymes work by mainly spatially aligning the reactants in a favorable way, so basically making sure that they reside close to each other. However, these steric effects alone lead to a strong increase in the barrier and counteract the catalytic activity. So the structural influence of the RNA environment can also not be responsible for the catalytic activity.

Finally, we calculated the electrostatic influence of individual parts of the system, each RNA unit, each water molecule and each sodium ion. This lead to striking evidence [17] that the sodium ions, counter-ions to the negatively charged RNA, have a strong effect in lowering the barrier and, thus, accelerating the reaction. Hardly any of these ions are seen in the crystal structure, which means that they are mobile and not well-ordered. They must be there, however, because the phosphate group of each RNA unit is negatively charged. Overall the space within the ribosome must be approximately neutral. Otherwise the structure would decompose. To obtain charge neutrality, the concentration of cations must be about 25 times higher than the physiological concentration. This estimate holds true for all species made up of RNA (and DNA), and, thus, also for other ribozymes.

While this study [17] may still need some additional validation calculations, it shows that the ability of theory to modify chemical systems and investigate different effects separately from each other is a promising tool to solve puzzling questions like that.

Ribosome overview
The total structure of the ribosome. The active center, the peptidyl transferase center is in the center of the red circle. Some parts have been removed for clarity withn the blue rectangle. This makes the tips of the tRNA visible. The amino acids to be linked are located on these tips. The picture has been created using Chimera.




4-membered transition state and transition mode of the
           peptide-bond formation catalysed by the ribosome
One possible transition state of the reaction catalyzed by the ribosome. The carbon (gray) - oxygen (red) bond is broken, the carbon - nitrogen (blue) bond is formed. One hydrogen atom (white) is transferred from nitrogen to oxygen. The picture has been created using VMD




 
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