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1. Foldamers wave to the ribosome

   https://doi.org/10.1038/s41557-018-0036-5  

   Schepartz, Alanna (April 2018, Nature Chemistry)
2. The energy landscape of the ribosome

   https://doi.org/10.1002/bip.23570  

   Byju, Sandra; Hassan, Asem; Whitford, Paul C. (December 2023, Biopolymers)

   Abstract The ribosome is a prototypical assembly that can be used to establish general principles and techniques for the study of biological molecular machines. Motivated by the fact that the dynamics of every biomolecule is governed by an underlying energy landscape, there has been great interest to understand and quantify ribosome energetics. In the present review, we will focus on theoretical and computational strategies for probing the interactions that shape the energy landscape of the ribosome, with an emphasis on more recent studies of the elongation cycle. These efforts include the application of quantum mechanical methods for describing chemical kinetics, as well as classical descriptions to characterize slower (microsecond to millisecond) large‐scale (10–100 Å) rearrangements, where motion is described in terms of diffusion across an energy landscape. Together, these studies provide broad insights into the factors that control a diverse range of dynamical processes in this assembly. 

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3. RiboProP: a probabilistic ribosome positioning algorithm for ribosome profiling

   https://doi.org/10.1093/bioinformatics/bty854  

   Zhao, Dengke; Baez, William D; Fredrick, Kurt; Bundschuh, Ralf; Berger, Bonnie (October 2018, Bioinformatics)
4. In vitro ribosome synthesis and evolution through ribosome display

   https://doi.org/10.1038/s41467-020-14705-2  

   Hammerling, Michael J.; Fritz, Brian R.; Yoesep, Danielle J.; Kim, Do Soon; Carlson, Erik D.; Jewett, Michael C. (February 2020, Nature Communications)

   Abstract Directed evolution of the ribosome for expanded substrate incorporation and novel functions is challenging because the requirement of cell viability limits the mutations that can be made. Here we address this challenge by combining cell-free synthesis and assembly of translationally competent ribosomes with ribosome display to develop a fully in vitro methodology for ribosome synthesis and evolution (called RISE). We validate the RISE method by selecting active genotypes from a ~1.7 × 10⁷member library of ribosomal RNA (rRNA) variants, as well as identifying mutant ribosomes resistant to the antibiotic clindamycin from a library of ~4 × 10³rRNA variants. We further demonstrate the prevalence of positive epistasis in resistant genotypes, highlighting the importance of such interactions in selecting for new function. We anticipate that RISE will facilitate understanding of molecular translation and enable selection of ribosomes with altered properties. 

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5. The energetics of subunit rotation in the ribosome

   https://doi.org/10.1007/s12551-021-00877-8  

   Hassan, Asem; Byju, Sandra; Whitford, Paul C. (December 2021, Biophysical Reviews)