Molecular simulations of the ribosome and associated translation factors

• Published in: Current opinion in structural biology 2018-04, Vol.49, p.27-35
• Main Authors: Bock, Lars V, Kolář, Michal H, Grubmüller, Helmut
• Format: Article
• Language: English
• Subjects: Animals; Cryoelectron Microscopy - methods; Crystallography, X-Ray - methods; Humans; Molecular Dynamics Simulation; Protein Biosynthesis; Protein Conformation; Protein Folding; Ribosomal Proteins - chemistry; Ribosomal Proteins - metabolism; Ribosomes - chemistry; Ribosomes - metabolism; RNA, Transfer - chemistry; RNA, Transfer - metabolism; Thermodynamics
• ISSN: 0959-440X; 1879-033X
• DOI: 10.1016/j.sbi.2017.11.003

[Display omitted] •Advances in methodology have enhanced the predictive power of molecular simulations.•Molecular simulations complement structures with energetics and dynamics.•In silico experiments provide information on processes not accessible by experiment.•Free-energy calculations test putative mechanisms and allow comparison to experiments.•Computer experiments establish cause–effect chains beyond mere correlation. The ribosome is a macromolecular complex which is responsible for protein synthesis in all living cells according to their transcribed genetic information. Using X-ray crystallography and, more recently, cryo-electron microscopy (cryo-EM), the structure of the ribosome was resolved at atomic resolution in many functional and conformational states. Molecular dynamics simulations have added information on dynamics and energetics to the available structural information, thereby have bridged the gap to the kinetics obtained from single-molecule and bulk experiments. Here, we review recent computational studies that brought notable insights into ribosomal structure and function.