Biology subjects

Ferro, L. S.

Publications and source records attributed to Ferro, L. S..

5 recordsLinked to original sources

bioRxiv2026

The Molecular Interplay of Tau and Motor Proteins on Microtubules

Tau is a microtubule (MT)-associated protein essential for neuronal cytoskeletal organization and intracellular transport, yet how tau physically regulates motor proteins remains elusive. Here, we integrate single-molecule imaging, cryo-electron microscopy, and molecular dynamics (MD) simulations to investigate the molecular mechanisms underlying tau-mediated inhibition of kinesin-1 and cytoplasmic dynein motility. We show that tau suppresses MT landing and triggers frequent pausing and premature detachment when motors encounter tau-enriched patches. Unexpectedly, tau impairs each motor using different mechanisms. Tau and kinesin-1 compete for the same surface on tubulin, precluding simultaneous binding to the same MT site. On the other hand, while dynein and tau can co-occupy the same tubulin, tau inhibits the transition of dynein into its high-affinity MT-binding state. Thus, tau can act as a physical or a conformational roadblock in a concentration-dependent manner, exerting distinct structural constraints on kinesin and dynein transport. These findings establish a structural framework for tau-mediated regulation of axonal transport.

biophysics↗

bioRxiv2024

A scalable approach to absolute quantitation in metabolomics

Mass spectrometry-based metabolomics allows for the quantitation of metabolite levels in diverse biological samples. The traditional method of converting peak areas to absolute concentrations involves the use of matched heavy isotopologues. However, this approach is laborious and limited to a small number of metabolites. We addressed these limitations by developing PyxisTM, a machine learning-based technology which converts raw mass spectrometry data to absolute concentration measurements without the need for per-analyte standards. Here, we demonstrate Pyxis performance by quantifying metabolome concentration dynamics in murine blood plasma. Pyxis performed equivalently to traditional quantitation workflows used by research institutions, with a fraction of the time needed for analysis. We show that absolute quantitation by Pyxis can be expanded to include concentrations for additional metabolites, without the need to acquire new data. Furthermore, Pyxis allows for absolute quantitation as part of an untargeted metabolomics workflow. By removing the bottleneck of per-analyte standards, Pyxis allows for absolute quantitation in metabolomics that is scalable to large numbers of metabolites. The ability of Pyxis to make concentration-based measurements across the metabolome has the potential to deepen our understanding of diverse metabolic perturbations.

systems biology↗

bioRxiv2020

The mechanism of motor inhibition by microtubule-associated proteins

Microtubule (MT)-associated proteins (MAPs) regulate intracellular transport by selectively recruiting or excluding kinesin and dynein motors from MTs. We used single-molecule and cryo-electron imaging to determine the mechanism of MAP-motor interactions in vitro. Unexpectedly, we found that the regulatory role of a MAP cannot be predicted based on whether it overlaps with the motor binding site or forms liquid condensates on the MT. Although the MT binding domain (MTBD) of MAP7 overlaps with the kinesin-1 binding site, tethering of kinesin-1 by the MAP7 projection domain supersedes this inhibition and results in biphasic regulation of kinesin-1 motility. Conversely, the MTBD of tau inhibits dynein motility without overlapping with the dynein binding site or by forming tau islands on the MT. Our results indicate that MAPs sort intracellular cargos moving in both directions, as neither dynein nor kinesin can walk on a MAP-coated MT without favorably interacting with that MAP. HIGHLIGHTSO_LIMAP7 binds to a novel site and can coexist with tau on the MT. C_LIO_LIKinesin-1 motility is biphasically regulated by MAP7 accumulation on the microtubule. C_LIO_LIMT decoration of MAPs inhibits motors even when they do not block the motor binding site. C_LIO_LIMotors need to interact with a MAP to walk on MAP-decorated MTs C_LI

biophysics↗

bioRxiv2020

SARS CoV-2 nucleocapsid protein forms condensates with viral genomic RNA

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection causes COVID-19, a pandemic that seriously threatens global health. SARS-CoV-2 propagates by packaging its RNA genome into membrane enclosures in host cells. The packaging of the viral genome into the nascent virion is mediated by the nucleocapsid (N) protein, but the underlying mechanism remains unclear. Here, we show that the N protein forms biomolecular condensates with viral genomic RNA both in vitro and in mammalian cells. Phase separation is driven, in part, by hydrophobic and electrostatic interactions. While the N protein forms spherical assemblies with unstructured RNA, it forms asymmetric condensates with viral RNA strands that contain secondary structure elements. Cross-linking mass spectrometry identified a region that forms interactions between N proteins in condensates, and truncation of this region disrupts phase separation. We also identified small molecules that alter the formation of N protein condensates. These results suggest that the N protein may utilize biomolecular condensation to package the SARS-CoV-2 RNA genome into a viral particle.

biophysics↗

bioRxiv2019

Kinesin-1 and dynein use distinct mechanisms to bypass obstacles

Kinesin-1 and cytoplasmic dynein are microtubule (MT) motors that transport intracellular cargos. It remains unclear how these motors move along MTs densely coated with obstacles of various sizes in the cytoplasm. Here, we tested the ability of single and multiple motors to bypass synthetic obstacles on MTs in vitro. Contrary to previous reports, we found that mammalian dynein is highly capable of bypassing obstacles. Unlike dynein, single kinesin motors stall in the presence of obstacles, consistent with their inability to take sideways steps to neighboring protofilaments. Kinesins overcome this limitation when working in teams, bypassing obstacles as effectively as multiple dyneins. Cargos driven by multiple kinesin or dyneins are also capable of rotating around the MT to bypass large obstacles. These results suggest that multiplicity of motors is required not only for transporting cargos over long distances and generating higher forces, but also for maneuvering of the cargos on obstacle-coated MT surfaces.

biophysics↗