Biology subjects

Acosta-Reyes, F.

Publications and source records attributed to Acosta-Reyes, F..

3 recordsLinked to original sources

bioRxiv2025

Structural Studies of Nedicistrovirus IRES-Driven, Initiation Factor-independent Translation Shed Light on Key Steps of Eukaryotic Translation Elongation

We utilized the Nedicistrovirus (NediV) intergenic region (IGR) IRES-mediated, initiation factor-independent translation initiation system and determined high-resolution structures of 80S ribosome complexes with the NediV IRES in various functional states, including binary complexes, aminoacyl-tRNA-bound complexes, and complexes with elongation factor eEF2. In binary complexes, the NediV IRES primarily occupies the ribosomal P site, exhibiting conformational flexibility and engaging the ribosome at multiple interaction sites. Upon translocation, the IRES undergoes structural rearrangements, including destabilization of its PKI domain, facilitating the transition to canonical elongation. Crucially, we captured an eEF2-bound complex, along with an eEF1A-bound post-proofreading complex featuring a mismatched tRNA, the latter representing the first instance of a canonical elongation complex visualized in the presence of a natural, hydrolysable nucleotide and without the addition of any trapping agents. These findings provide a comprehensive structural overview of IGR IRES-mediated translation initiation and its transition to elongation, revealing key mechanistic details of viral translation and proofreading.

biochemistry↗

bioRxiv2019

Simulation of cryo-EM ensembles from atomic models of molecules exhibiting continuous conformations

Molecular machines visit a continuum of conformational states as they go through work cycles required for their metabolic functions. Single-molecule cryo-EM of suitable in vitro systems affords the ability to collect a large ensemble of projections depicting the continuum of structures and assign occupancies, or free energies, to the observed states. Through the use of machine learning and dimension reduction algorithms it is possible to determine a low-dimensional free energy landscape from such data, allowing the basis for molecular function to be elucidated. In the absence of ground truth data, testing and validation of such methods is quite difficult, however. In this work, we propose a workflow for generating simulated cryo-EM data from an atomic model subjected to conformational changes. As an example, an ensemble of structures and their multiple projections was created from heat shock protein Hsp90 with two defined conformational degrees of freedom. All scripts for reproducing this workflow are available online. 1

biophysics↗

bioRxiv2019

The Israeli Acute Paralysis Virus IRES captures host ribosomes by mimicking a ribosomal state with hybrid tRNAs.

The Colony Collapse Disorder or CCD is a multi-faceted syndrome decimating bee populations worldwide[1]. A group of viruses of the widely distributed Dicistroviridae family have been identified as a causing agent of CCD[2]. This family of viruses employ non-coding RNA sequences, called Internal Ribosomal Entry Site (IRES), to precisely exploit the host machinery for protein production. Using single-particle cryo-electron microscopy (cryo-EM) we have characterized at high resolution how the IRES of the intergenic region of the Israeli Acute Paralysis Virus (IAPV) captures and redirects translating ribosomes towards viral messengers. Through a series of six structures at nominal resolutions close to 3[A], we could reconstruct the trajectory of IAPV-IRES from an early small subunit recruitment to a final post-translocated state in the ribosome. An early commitment of IRES/ribosome complexes for global pre-translocation mimicry explains the high efficiency observed for this IRES. The presented structures will help guide on-going efforts directed towards fighting CCD through RNA-interference technology [3].

biophysics↗