Biology subjects

Palo, M. Z.

Publications and source records attributed to Palo, M. Z..

3 recordsLinked to original sources

bioRxiv2025

RNA regulates repeat-associated non-AUG (RAN) translation initiation in C9orf72 FTD/ALS

Repeat-associated non-AUG (RAN) translation synthesizes protein in the absence of a cognate AUG start codon 1,2In frontotemporal dementia and amyotrophic lateral sclerosis, a GGGGCC (G4C2) repeat expansion in an intron of C9orf72 leads to synthesis of neurotoxic dipeptide-repeat proteins, underscoring the need to understand the mechanism of C9orf72 RAN translation1-5. RNA sequence and structure have been implicated, but how they direct C9orf72 RAN translation, particularly the rate-limiting, multi-step initiation phase, remains unclear6-10. We applied single-molecule biophysics to a reconstituted human translation initiation system and tracked fluorescently labeled ribosomes and initiation factors in real time. We show that RNA G4C2 repeats and sequence context alter initiation factor dynamics after ribosomal scanning, generating a kinetic bottleneck in the commitment to initiate at a near-cognate CUG start codon. Our model of C9orf72 RAN translation provides a mechanistic framework for how repeat expansions change underlying translation dynamics and may be broadly relevant to other disorders that involve RAN translation.

biophysics↗

bioRxiv2025

Complex Water Networks Visualized through 2.2-2.3 Angstrom Cryogenic Electron Microscopy of RNA

The stability and function of biomolecules are directly influenced by their myriad interactions with water. In this study, we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule, the Tetrahymena ribozyme, determined at 2.2 and 2.3 [A] resolutions. By employing segmentation-guided water and ion modeling (SWIM), an approach combining resolvability and chemical parameters, we automatically modeled and cross-validated water molecules and Mg2+ ions in the ribozyme core, revealing the extensive involvement of water in mediating RNA non-canonical interactions. Unexpectedly, in regions where SWIM does not model ordered water, we observed highly similar densities in both cryo-EM maps. In many of these regions, the cryo-EM densities superimpose with complex water networks predicted by molecular dynamics (MD), supporting their assignment as water and suggesting a biophysical explanation for their elusiveness to conventional atomic coordinate modeling. Our study demonstrates an approach to unveil both rigid and flexible waters that surround biomolecules through cryo-EM map densities, statistical and chemical metrics, and MD simulations.

biophysics↗

bioRxiv2023

Minimization of the E. coli ribosome, aided and optimized by community science

The ribosome is a ribonucleoprotein complex found in all domains of life. Its role is to catalyze protein synthesis, the messenger RNA (mRNA)-templated formation of amide bonds between -amino acid monomers. Amide bond formation occurs within a highly conserved region of the large ribosomal subunit known as the peptidyl transferase center (PTC). Here we describe the stepwise design and characterization of mini-PTC 1.1, a 284-nucleotide RNA that recapitulates many essential features of the Escherichia coli PTC. Mini-PTC 1.1 folds into a PTC-like structure under physiological conditions, even in the absence of r-proteins, and engages small molecule analogs of A- and P-site tRNAs. The sequence of mini-PTC 1.1 differs from the wild type E. coli ribosome at 12 nucleotides that were installed by a cohort of citizen scientists using the on-line video game Eterna. These base changes improve both the secondary structure and tertiary folding of mini-PTC 1.1 as well as its ability to bind small molecule substrate analogs. Here, the combined input from Eterna citizen-scientists and RNA structural analysis provides a robust workflow for the design of a minimal PTC that recapitulates many features of an intact ribosome.

synthetic biology↗