Paola Picotti

Chemically induced USP21-KLHL12 association recruits USP21 to COPII assembly

The paper shows that BAY-805 induces USP21-KLHL12 association, recruiting USP21 to COPII vesicles and impairing large cargo transport.

Weak interactions drive selective proteome demixing and tune the differential response to environmental perturbations

This study introduces QuPID-MS to measure protein phase separation in cells, showing weak interactions drive proteome demixing and influence environmental response.

The Human Bindome: A Proteome-scale Atlas of Designed Binder Candidates

A parallelized BindCraft pipeline generated 306,146 in silico binder candidates against 8,296 human proteins, each with sequence, predicted complex and confidence metrics, freely accessible online.

Paradoxical non-catalytic kinase functions are driven by inhibitor-induced displacement of autoinhibitory domains

The paper identifies inhibitor-induced structural changes in kinases that drive non-catalytic effects, revealing the ATP-binding site as a key regulator of kinase conformation and interactions.

Deconvolving the structural heterogeneity of alpha-Synuclein in vitro and in situ

This paper develops a method to quantitatively analyze the structural states of alpha-synuclein in vitro and in situ, revealing conformational changes in yeast and human neurons.

Neuronal calcium sensors emerge as novel adenylyl cyclase 8 regulators

This study identifies HPCAL1 as a Ca2+-dependent regulator of AC8, revealing a new mechanism for cAMP signaling regulation.

In-source fragmentation in mass spectrometry-based proteomics: prevalence, impact, and strategies for mitigation

The paper identifies and quantifies in-source fragmentation (ISF) in proteomics data, showing its prevalence and impact, and proposes an open-source method to detect and remove ISF peptides.

Structure-function relationship of alpha-synuclein fibrillar polymorphs derived from distinct synucleinopathies

This study identifies structural and functional differences in alpha-synuclein fibrils from Parkinson's disease, Dementia with Lewy Bodies, and Multiple System Atrophy, linking these differences to disease-specific cellular responses and potential therapeutic targets.

Limited proteolysis-coupled mass spectrometry captures proteome-wide protein structural alterations and biomolecular condensation in living cells

The paper introduces in-cell LiP-MS to study protein structural changes and biomolecular condensates in live human cells, revealing structural alterations under stress and validating them with microscopy.

Systematic structural and functional analysis of metal-binding sites in native proteomes

This study systematically maps metal-binding sites in E. coli using Metal-LiP, identifies 424 candidate metal-binding proteins, and suggests functional roles for metal binding.

The environmental stress response controls the biophysical properties of the cytoplasm and is critical for survival in quiescence

This study shows that respiration-induced gene expression and stress response pathways are critical for maintaining cytoplasmic properties and survival in yeast quiescence.

The Main protease (Mpro) from SARS-CoV-2 triggers plasma clotting in vitro by activating coagulation factors VII and FXII

This study shows that SARS-CoV-2 main protease (Mpro) activates coagulation factors VII and XII, increasing plasma clotting probability by 2.5-fold.

Enhancing the biological insight from limited proteolysis-coupled mass spectrometry

The paper introduces a framework to deconvolve LiP-MS signals and infer protein structural changes using data from three species.

Systematic identification of structure-specific protein-protein interactions

This study systematically identifies structure-specific protein-protein interactions using LiP-MS, demonstrating its application to alpha-synuclein in Parkinson's disease.

An approach to characterize mechanisms of action of anti-amyloidogenic compounds in vitro and in situ

This paper introduces a structural proteomic pipeline to study anti-amyloidogenic compounds' mechanisms in vitro and in situ, revealing off-target effects and structural interactions with α-Synuclein.

Large-scale changes of molecular network states explain complex traits

The paper identifies a central state transition in yeast molecular networks linked to PKA and TOR signaling, showing how genetic variants can cause global or local molecular changes affecting multiple cellular traits.

Systematic detection of functional proteoform groups from bottom-up proteomic datasets

This paper introduces a data-driven method to detect functional proteoform groups from bottom-up proteomic datasets, identifying state-specific proteoform groups linked to molecular mechanisms.

The ASC inflammasome adapter controls the extent of peripheral protein aggregate deposition in inflammation-associated amyloidosis

This paper shows that ASC controls AA amyloidosis by interacting with SAA and that anti-ASC antibodies reduce amyloid loads in mice.

Deciphering the Signaling Network Landscape of Breast Cancer Improves Drug Sensitivity Prediction

The paper uses single-cell proteomics and perturbation experiments to improve drug sensitivity predictions in breast cancer and identify genomic features associated with treatment response.

A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth

The paper identifies a natural variant in fission yeast Pyk1 that reduces glycolytic flux, increases respiration, and enhances oxidative-stress resistance but decreases growth.

LiP-Quant, an automated chemoproteomic approach to identify drug targets in complex proteomes

LiP-Quant identifies drug targets in complex proteomes using limited proteolysis and mass spectrometry, providing EC50 estimates and distinguishing between homologous proteins.