Dynamics and Energetics of Ribosomal Translation
The ribosome is a large biomolecular complex composed of ribonucleic acids and proteins. Ribosomes translate the genetic code (mRNA) into proteins and are therefore essential in all kingdoms of life. The aim of this project is to understand functional mechanisms of the ribosome at an atomic level using MD simulations.
Individual DNA bases are known to be able to flip out of the helical stack, providing enzymes with access to the genetic information otherwise hidden inside the helix. Consequently, base flipping is a necessary first step to many more complex biological processes such as DNA transcription or replication.
The binding affinity of DNA-binding proteins, e.g. transcription factors such as ZIF268, is essential for their function. It is one fundamental goal in modern biochemistry to find out, why, and more importantly, how these proteins bind selectively to specific DNA sequences.
The kink-turn (k-turn), a RNA structural motif found in the spliceosome and the ribosome, serves as a specific protein recognition element and as a structural building block. To elucidate whether the k-turn also exists in this folded conformation in the free U4 snRNA t, we investigated the formation by single-molecule FRET measurements
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