Mikhail M. Savitski

Post-assembly proteostasis of the respiratory chain is independent of respirasome organization

This study shows that respirasomes are not essential for maintaining respiratory-chain complexes after their assembly, even under mitochondrial stress or impaired OXPHOS biogenesis.

In-cell discovery and characterization of a non-canonical bacterial protein translocation-folding complex

The paper identifies and characterizes a non-canonical bacterial protein translocation-folding complex using cryo-electron tomography, proteomics, and structure prediction in Mycoplasma pneumoniae.

Pervasive phosphorylation by phage T7 kinase disarms bacterial defenses

This study reveals that phage T7 kinase broadly phosphorylates host and phage proteins, disabling bacterial defense systems through widespread phosphorylation.

Systematic differences in protein stability underlie species-specific developmental tempo

The paper identifies slower protein degradation in human cells compared to mice, linking protein stability differences to interspecies variations in developmental tempo.

Intrinsic flexibility of Type VII secretion central pore is required for substrate translocation

This study shows that the flexibility of the central pore in the ESX-5 type VII secretion system is essential for efficient substrate translocation, as rigidification of key residues impairs secretion.

Snapshot of in-cell protein contact sites reveals new host factors and hijacking of paraspeckles during influenza A virus infection

The paper maps virus-host protein contact sites during influenza A virus infection, revealing new interactions and paraspeckle disassembly as a novel infection mechanism.

Bacterial metabolism of synthetic steroids across ecosystems reveals diverse biotransformation products, reactions, and enzymes

This study maps bacterial metabolism of synthetic steroids across ecosystems, identifying transformation products, reactions, and enzymes, and reveals cooperative microbial interactions in steroid metabolism.

Ubiquitin selective ribosome profiling reveals systematic principles of co-translational quality control

The paper introduces UbSeRP to map co-translational ubiquitination across the translatome, revealing RQC substrates, biophysical features predicting RQC, and aging-related changes in CTU.

Personalized microbiotas (counter-)select for antibiotic resistant pathogens

This study identifies how personalized gut microbiotas influence the competitiveness of antibiotic-resistant pathogens through carbohydrate competition and specific genetic mutations.

NLRP3 activators disrupt the endocytic AP2 complex and plasma membrane signaling

The paper shows NLRP3 activators disrupt the AP2 complex and impair plasma membrane signaling, leading to inflammation and cell death.

Multi-omics and biophysical phosphoproteomics upon BRAF inhibition uncover functional networks of BRAFV600E-driven signaling

This study uses multi-omics and biophysical phosphoproteomics to analyze BRAFV600E signaling, identifying ETV3 as a new downstream regulator and revealing mechanisms of drug resistance.

High-throughput peptide-centric local stability assay extends protein-ligand identification to membrane proteins, tissues, and bacteria

This paper introduces HT-PELSA, a high-throughput adaptation of a peptide-centric local stability assay, enabling sensitive protein-ligand profiling in diverse biological samples.

Extensive PFAS accumulation by human gut bacteria

This study shows human gut bacteria can accumulate PFAS, with some species like Bacteroides uniformis accumulating them to high concentrations, and identifies mechanisms involving transmembrane transport and efflux pumps.

Dynamic multi-omics and mechanistic modeling approach uncovers novel mechanisms of kidney fibrosis progression

This paper uses time-resolved multi-omics analysis of kidney fibrosis to identify novel mechanisms and validate transcription factors involved in collagen deposition.

Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria

This study identifies nitroxoline's broad antibacterial activity against Gram-negative bacteria, its mode of action involving metal homeostasis and outer membrane disruption, and resistance mechanisms across multiple species.

Evaluating signaling pathway inference from kinase-substrate interactions and phosphoproteomics data

The paper evaluates methods for inferring kinase-driven signaling pathways using phosphoproteomics data and kinase-substrate networks, finding that literature-curated networks with network propagation best recover ground truth interactions.

Essentiality of LD-Transpeptidation in Agrobacterium tumefaciens

This study identifies the essential role of LD-transpeptidation in Agrobacterium tumefaciens cell wall integrity and growth by analyzing LDTs and their genetic interactions.

RNA-binding proteins identified by R-DeeP/TripepSVM are involved in heterocyst differentiation

The paper identifies RNA-binding proteins involved in heterocyst differentiation in cyanobacteria using mass spectrometry and bioinformatics, revealing a new master regulator.

Subcellular thermal profiling enables the deep functional exploration of the mitochondrial proteome

The paper introduces mito-TPP, a thermal proteome profiling workflow for studying mitochondrial protein interactions and proteoforms, detecting over 180 proteins with multiple proteoform groups.

Molecular profiling of sponge deflation reveals an ancient relaxant-inflammatory response

The paper identifies an ancient relaxant-inflammatory response in sponges during deflation, driven by actomyosin relaxation and associated with inflammation-like states.

Hierarchical Gaussian process models explore the dark meltome of thermal proteome profiling experiments.

The paper introduces GPMelt, a hierarchical Gaussian process model for analyzing TPP-TR datasets, enabling unbiased analysis of unconventional melting curves and improving the detection of protein interactions.

Deep quantitative glycoproteomics reveals gut microbiome induced remodeling of the brain glycoproteome

The paper introduces a high-throughput glycoproteomics method to quantify brain glycoproteome changes induced by gut microbiome composition.

Structure and dynamics of the quaternary hunchback mRNA translation repression complex

The paper characterizes the quaternary hunchback mRNA repression complex formed by Brat, Pum, and Nanos, revealing its flexibility and independent binding of RNA components.

Impact of phosphorylation on thermal stability of proteins

The paper assesses the impact of phosphorylation on protein thermal stability using phospho-TPP in HeLa cells, finding that phosphorylation affects stability less than previously reported.

Comparative chromatin accessibility upon BDNF-induced neuronal activity delineates neuronal regulatory elements

The paper identifies BDNF-specific chromatin accessibility changes in neurons and links them to gene regulation and neurodevelopmental traits.

Computational analysis of ligand dose range thermal proteome profiles

The paper develops a statistical method to analyze thermal proteome profiles and identifies off-target drug interactions in epigenetic drugs.

Aggregation and Disaggregation Features of the Human Proteome

The paper characterizes aggregation and disaggregation of proteins in human cells after heat shock, identifying factors influencing these processes and their implications for protein quality control.

Long-term synaptic depression triggers local biogenesis of autophagic vesicles in dendrites and requires autophagic degradation

This study shows that long-term synaptic depression triggers local autophagic vesicle biogenesis in dendrites, which is essential for synaptic remodeling and cognitive flexibility.

Towards a systematic map of the functional role of protein phosphorylation

The paper systematically maps the functional role of phosphorylation by analyzing phospho-deficient mutants in yeast and linking yeast phenotypes to human functional relevance.

The functional landscape of the human phosphoproteome

The paper creates a comprehensive human phosphoproteome by integrating 6,801 phospho-enriched mass spectrometry experiments and prioritizes functional phosphosites using machine learning.