Biology subjects

Corsepius, N. C.

Publications and source records attributed to Corsepius, N. C..

3 recordsLinked to original sources

bioRxiv2025

PDBCleanV2: A Python Library for Generating Consistent Structure Datasets

The number of structures in the Protein Data Bank has grown rapidly in recent years. Nonetheless, comparing structures of a specific system often proves challenging due to variant nomenclature, origins from different species, presence of various ligands, and missing atoms or chains. To address these issues, we have developed PDBCleanV2, a Python package that enables users to create consistent datasets of structures, simplifying comparison among structures. This library generates individual files for each molecule in a structure file, corrects labeling errors, and standardizes chain names and numbering. Our aim is to provide researchers with consistent datasets that streamline their analysis. The source code, installation instructions, and tutorials can be found in PDBCleanV2s GitHub repository and Zenodo accessible at https://github.com/fatipardo/PDBClean-0.0.2/ and https://doi.org/10.5281/zenodo.14014241, respectively.

bioinformatics↗

bioRxiv2021

Mechanisms that ensure speed and fidelity in eukaryotic translation termination

Translation termination, which liberates a nascent polypeptide from the ribosome specifically at stop codons, must occur accurately and rapidly. We established single-molecule fluorescence assays to track the dynamics of ribosomes and two requisite release factors (eRF1 and eRF3) throughout termination using an in vitro-reconstituted yeast translation system. We found that the two eukaryotic release factors bind together to recognize stop codons rapidly and elicit termination via a tightly regulated, multi-step process that resembles tRNA selection during translation elongation. Because the release factors are conserved from yeast to humans, the molecular events that underlie yeast translation termination are likely broadly fundamental to eukaryotic protein synthesis. One Sentence SummaryDirect visualization of eukaryotic translation reveals the dynamics of termination at stop codons.

biochemistry↗

bioRxiv2019

RACK1 on and off the ribosome

Receptor for activated C kinase 1 (RACK1) is a eukaryote-specific ribosomal protein implicated in diverse biological functions. To engineer ribosomes for specific fluorescent labeling, we selected RACK1 as an target given its location on the small ribosomal subunit and other properties. However, prior results suggested that RACK1 has roles both on and off the ribosome, and such an exchange might be related to its various cellular functions and hinder our ability to use RACK1 as a stable fluorescent tag for the ribosome. In addition, the kinetics of spontaneous exchange of RACK1 or any ribosomal protein from a mature ribosome in vitro remain unclear. To address these issues, we engineered fluorescently-labeled human ribosomes via RACK1, and applied bulk and single-molecule biochemical analyses to track RACK1 on and off the human ribosome. Our results demonstrate that, despite its cellular non-essentiality from yeast to humans, RACK1 readily re-associates with the ribosome, displays limited conformational dynamics, and remains stably bound to the ribosome for hours in vitro. This work sheds insight onto the biochemical basis of ribosomal protein exchange on and off a mature ribosome and provides tools for single-molecule analysis of human translation.

biochemistry↗