RNA structural dynamics as captured by molecular simulations: a comprehensive overview

J Sponer, G Bussi, M Krepl, P Banáš, S Bottaro… - Chemical …, 2018 - ACS Publications
With both catalytic and genetic functions, ribonucleic acid (RNA) is perhaps the most
pluripotent chemical species in molecular biology, and its functions are intimately linked to …

Root of the tree: the significance, evolution, and origins of the ribosome

JC Bowman, AS Petrov, M Frenkel-Pinter… - Chemical …, 2020 - ACS Publications
The ribosome is an ancient molecular fossil that provides a telescope to the origins of life.
Made from RNA and protein, the ribosome translates mRNA to coded protein in all living …

Multiple roles of the coding sequence 5′ end in gene expression regulation

T Tuller, H Zur - Nucleic acids research, 2015 - academic.oup.com
The codon composition of the coding sequence's (ORF) 5′ end first few dozen codons is
known to be distinct to that of the rest of the ORF. Various explanations for the unusual …

Selective protein synthesis by ribosomes with a drug-obstructed exit tunnel

K Kannan, N Vázquez-Laslop, AS Mankin - Cell, 2012 - cell.com
The polypeptide exit tunnel is an important functional compartment of the ribosome where
the newly synthesized proteins are surveyed. The tunnel is the target of clinically important …

SecM-stalled ribosomes adopt an altered geometry at the peptidyl transferase center

S Bhushan, T Hoffmann, B Seidelt, J Frauenfeld… - PLoS …, 2011 - journals.plos.org
As nascent polypeptide chains are synthesized, they pass through a tunnel in the large
ribosomal subunit. Interaction between specific nascent chains and the ribosomal tunnel is …

Computational approaches to RNA structure prediction, analysis, and design

C Laing, T Schlick - Current opinion in structural biology, 2011 - Elsevier
RNA molecules are important cellular components involved in many fundamental biological
processes. Understanding the mechanisms behind their functions requires RNA tertiary …

The key function of a conserved and modified rRNA residue in the ribosomal response to the nascent peptide

N Vázquez‐Laslop, H Ramu, D Klepacki… - The EMBO …, 2010 - embopress.org
The ribosome is able to monitor the structure of the nascent peptide and can stall in
response to specific peptide sequences. Such programmed stalling is used for the …

Amphiphilic small molecule antimicrobials: From cationic antimicrobial peptides (CAMPs) to mechanism-related, structurally-diverse antimicrobials

J Yuan, J Wang, X Li, Y Zhang, J Xian, C Wang… - European Journal of …, 2023 - Elsevier
Bacterial infections are characterized by their rapid and widespread proliferation, leading to
significant morbidity. Despite the availability of a variety of antimicrobial drugs, the …

Protein folding on the ribosome

LD Cabrita, CM Dobson, J Christodoulou - Current opinion in structural …, 2010 - Elsevier
In living systems, polypeptide chains are synthesised on ribosomes, molecular machines
composed of over 50 protein and nucleic acid molecules. As nascent chains emerge from …

Nascent peptide in the ribosome exit tunnel affects functional properties of the A-site of the peptidyl transferase center

H Ramu, N Vázquez-Laslop, D Klepacki, Q Dai… - Molecular cell, 2011 - cell.com
The ability to monitor the nascent peptide structure and to respond functionally to specific
nascent peptide sequences is a fundamental property of the ribosome. An extreme …