Machine learning solutions for predicting protein–protein interactions

R Casadio, PL Martelli… - Wiley Interdisciplinary …, 2022 - Wiley Online Library
Proteins are “social molecules.” Recent experimental evidence supports the notion that
large protein aggregates, known as biomolecular condensates, affect structurally and …

Chemical cross-linking and mass spectrometry enabled systems-level structural biology

L Botticelli, AA Bakhtina, NK Kaiser, A Keller… - Current Opinion in …, 2024 - Elsevier
Structural information on protein–protein interactions (PPIs) is essential for improved
understanding of regulatory interactome networks that confer various physiological and …

Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery

PC Havugimana, RK Goel, S Phanse, A Youssef… - Nature …, 2022 - nature.com
Co-fractionation/mass spectrometry (CF/MS) enables the mapping of endogenous
macromolecular networks on a proteome scale, but current methods are experimentally …

Integrative modeling reveals the molecular architecture of the intraflagellar transport A (IFT-A) complex

CL McCafferty, O Papoulas, MA Jordan… - Elife, 2022 - elifesciences.org
Intraflagellar transport (IFT) is a conserved process of cargo transport in cilia that is essential
for development and homeostasis in organisms ranging from algae to vertebrates. In …

[HTML][HTML] Trends in co-fractionation mass spectrometry: A new gold-standard in global protein interaction network discovery

RK Goel, N Bithi, A Emili - Current Opinion in Structural Biology, 2024 - Elsevier
Co-fractionation mass spectrometry (CF-MS) uses biochemical fractionation to isolate and
characterize macromolecular complexes from cellular lysates without the need for affinity …

[HTML][HTML] An amino acid-resolution interactome for motile cilia illuminates the structure and function of ciliopathy protein complexes

CL McCafferty, O Papoulas, C Lee, KH Bui, DW Taylor… - bioRxiv, 2023 - ncbi.nlm.nih.gov
Motile cilia are ancient, evolutionarily conserved organelles whose dysfunction underlies
motile ciliopathies, a broad class of human diseases. Motile cilia contain myriad different …

Integration of data‐independent acquisition (DIA) with co‐fractionation mass spectrometry (CF‐MS) to enhance interactome mapping capabilities

BN Hay, MO Akinlaja, TC Baker, AA Houfani… - …, 2023 - Wiley Online Library
Proteomics technologies are continually advancing, providing opportunities to develop
stronger and more robust protein interaction networks (PINs). In part, this is due to the ever …

The protein organization of a red blood cell

W Sae-Lee, CL McCafferty, EJ Verbeke… - Cell reports, 2022 - cell.com
Red blood cells (RBCs)(erythrocytes) are the simplest primary human cells, lacking nuclei
and major organelles and instead employing about a thousand proteins to dynamically …

Don't let go: co‐fractionation mass spectrometry for untargeted mapping of protein–metabolite interactomes

D Schlossarek, Y Zhang, EM Sokolowska… - The Plant …, 2023 - Wiley Online Library
The chemical complexity of metabolomes goes hand in hand with their functional diversity.
Small molecules have many essential roles, many of which are executed by binding and …

Co-fractionation–mass spectrometry to characterize native mitochondrial protein assemblies in mammalian neurons and brain

M Zilocchi, M Rahmatbakhsh, MT Moutaoufik… - Nature …, 2023 - nature.com
Human mitochondrial (mt) protein assemblies are vital for neuronal and brain function, and
their alteration contributes to many human disorders, eg, neurodegenerative diseases …