Stochastic mechano-chemical kinetics of molecular motors: a multidisciplinary enterprise from a physicist's perspective

D Chowdhury - Physics Reports, 2013 - Elsevier
A molecular motor is made of either a single macromolecule or a macromolecular complex.
Just like their macroscopic counterparts, molecular motors “transduce” input energy into …

The ribosome,(slow) beating heart of cancer (stem) cell

A Bastide, A David - Oncogenesis, 2018 - nature.com
The ribosome has long been considered as a consistent molecular factory, with a rather
passive role in the translation process. Recent findings have shifted this obsolete view …

A model for competition for ribosomes in the cell

A Raveh, M Margaliot… - Journal of The Royal …, 2016 - royalsocietypublishing.org
A single mammalian cell includes an order of 104–105 mRNA molecules and as many as
105–106 ribosomes. Large-scale simultaneous mRNA translation induces correlations …

Ribosome traffic on mRNAs maps to gene ontology: genome-wide quantification of translation initiation rates and polysome size regulation

L Ciandrini, I Stansfield… - PLoS computational …, 2013 - journals.plos.org
To understand the complex relationship governing transcript abundance and the level of the
encoded protein, we integrate genome-wide experimental data of ribosomal density on …

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

H Zur, T Tuller - Nucleic acids research, 2016 - academic.oup.com
Abstract mRNA translation is the fundamental process of decoding the information encoded
in mRNA molecules by the ribosome for the synthesis of proteins. The centrality of this …

Ribosome-directed therapies in cancer

G Temaj, S Chichiarelli, M Eufemi, F Altieri… - Biomedicines, 2022 - mdpi.com
The human ribosomes are the cellular machines that participate in protein synthesis, which
is deeply affected during cancer transformation by different oncoproteins and is shown to …

The extent of ribosome queuing in budding yeast

A Diament, A Feldman, E Schochet… - PLoS computational …, 2018 - journals.plos.org
Ribosome queuing is a fundamental phenomenon suggested to be related to topics such as
genome evolution, synthetic biology, gene expression regulation, intracellular biophysics …

Inverted translational control of eukaryotic gene expression by ribosome collisions

H Park, AR Subramaniam - PLoS biology, 2019 - journals.plos.org
The canonical model of eukaryotic translation posits that efficient translation initiation
increases protein expression and mRNA stability. Contrary to this model, we find that …

Optimizing the dynamics of protein expression

JH Trösemeier, S Rudorf, H Loessner, B Hofner… - Scientific reports, 2019 - nature.com
Heterologously expressed genes require adaptation to the host organism to ensure
adequate levels of protein synthesis, which is typically approached by replacing codons by …

Large-scale mRNA translation and the intricate effects of competition for the finite pool of ribosomes

A Jain, M Margaliot, AK Gupta - Journal of The Royal …, 2022 - royalsocietypublishing.org
We present a new theoretical framework for large-scale mRNA translation using a network of
models called the ribosome flow model with Langmuir kinetics (RFMLK), interconnected via …