M. Dal Peraro

Context-aware geometric deep learning for protein sequence design

This paper introduces a geometric transformer model that predicts protein sequences from backbone scaffolds while considering molecular environment restraints.

Exploring new nanopore sensors from the aerolysin family

The paper explores new nanopore sensors from the aerolysin family by analyzing structure and sensing capabilities of three family members, finding ETX can translocate ssDNA with higher sensitivity than aerolysin.

Dissecting the membrane association mechanism of aerolysin pore at femtomolar concentrations using water as a probe

This study uses AR-SHS and current measurements to analyze aerolysin's membrane association and pore formation at femtomolar concentrations, revealing binding affinities and structural changes during the process.

MolecularWebXR: Multiuser discussions about chemistry and biology in immersive and inclusive VR

MolecularWebXR enables multiuser VR/AR discussions about chemistry and biology in immersive environments accessible via web browsers and consumer devices.

Deep learning-assisted single-molecule detection of protein post-translational modifications with a biological nanopore

This study uses a biological nanopore and deep learning to detect and distinguish single and multiple PTMs on -synuclein peptides at picomolar concentrations.

A humoral stress response protects Drosophila tissues from antimicrobial peptides

This study identifies Turandot stress proteins that protect Drosophila tissues from antimicrobial peptide-induced damage by binding phosphatidylserine and inhibiting AMP pore formation.

Structure and functionality of a multimeric human COQ7:COQ9 complex

The paper presents the structure and functional analysis of a multimeric COQ7:COQ9 complex involved in CoQ biosynthesis, revealing its mechanism for accessing hydrophobic precursors and coordinating CoQ synthesis.

S-acylation controls SARS-Cov-2 membrane lipid organization and enhances infectivity

The paper shows that S-acylation by ZDHHC20 modifies SARS-CoV-2 membrane proteins, promoting lipid domain formation and enhancing viral infectivity.

Investigating crosstalk among PTMs provides novel insight into the structural basis underlying the differential effects of Nt17 PTMs on mutant Httex1 aggregation

This study investigates how PTMs in Nt17 of mutant Httex1 affect aggregation, showing that oxM8 delays aggregation and that combinations with AcK6 inhibit fibrillization, with structural insights from spectroscopy and simulations.

Molecular mode of action of an Acyl Protein thioesterase

The paper investigates the molecular mechanism of APT2, showing it interacts with membranes via a hydrophobic loop and S-acylation, deforms lipid bilayers to extract acyl chains, and is subject to ubiquitination and degradation.

Molecular Bases of the Membrane Association Mechanism Potentiating Antibiotic Resistance by New Delhi Metallo--Lactamase 1

This study identifies key residues in NDM-1 that mediate its membrane association, providing targets for combating antibiotic resistance.

Btk SH2-kinase interface is critical for allosteric kinase activation and its targeting inhibits B-cell neoplasms

This study identifies the Btk SH2-kinase interface as critical for activation and shows that targeting it with a repebody inhibits B-cell neoplasms.

KAP1 is an antiparallel dimer with a natively functional asymmetry

This paper shows KAP1 forms an antiparallel dimer with a native asymmetry, which affects its SUMOylation and interaction with HP1.

Conserved lipid and small molecule modulation of COQ8 reveals regulation of the ancient UbiB family

This study identifies lipid and small molecule modulators of COQ8, an ancient UbiB family protein, and establishes a chemical genetic system to study its role in CoQ biosynthesis.