Mechanisms of Ribosomal Translation studied by Molecular Dynamics Simulations

by Sara Gabrielli
Cumulative thesis
Date of Examination:2024-06-21
Date of issue:2024-12-17
Advisor:Prof. Dr. Helmut Grubmüller
Referee:Prof. Dr. Marina Bennati
Referee:Prof. Dr. Holger Stark
Persistent Address: http://dx.doi.org/10.53846/goediss-10909

 

 

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Abstract

English

During translation, the ribosome moves along the mRNA and decodes the genetic information to synthesize proteins. This process proceeds in a step-wise iterative manner during which the ribosome undergoes conformational rearrangements, together with mRNA, tRNAs and interacting protein factors. In bacteria, mechanisms have evolved that regulate gene expression by slowing down or arresting protein synthesis. I used molecular dynamics (MD) simulations to elucidate the atomistic bases of these mechanisms. In the first part of this thesis (Chapter 3), I investigated how single-point mutations in elongation factor G (EF-G), a GTPase that accelerates the translocation of the ribosome and tRNAs along the mRNA, might cause a slowdown in protein synthesis. In the second part (Chapters 4 and 5) I studied mechanisms of programmed translational stalling, i.e., the arrest of the ribosome during translation of specific peptides. In Chapter 4, I elucidated how stalling during translation of peptides containing the Arg-Ala-Pro-Pro (RAPP) motif takes place. I observed that the RAPP arrest motif rewires the hydrogen bond network required for the peptide bond formation and thereby inhibits elongation of the nascent peptide chain. In Chapter 5, I studied how the stalling in the arrest peptide SecM, which displays a similar arrest motif (RAGP) is released by a mechanical force acting on the nascent chain. By elucidating functionally relevant details of the conformational dynamics of unbound and ribosome-bound EF-G, of the peptide containing the RAPP motif, and of the SecM arrest peptide, the results of my MD simulations helped to connect structural information and biochemical data to obtain a detailed picture of atomistic mechanisms underlying ribosome regulation.
Keywords: Elongation Factor-G; ribosome; ribosome simulation; RAPP stallers; SecM; molecular dynamics; computational biophysics