Publications by Matteo Dal Peraro

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Ribonuclease H (RNase H) belongs to the nucleotidyl-transferase (NT) superfamily and hydrolyzes the phosphodiester linkages that form the backbone of the RNA strand in RNA x DNA hybrids. This enzyme is implicated in replication initiation and DNA topology ...

MolecularWebXR is a new web-based platform for education, science communication and scientific peer discussion in chemistry and biology, based on modern web-based Virtual Reality (VR) and Augmented Reality (AR). With no installs as it is all web-served, Mo ...

Fatty acid metabolism is an important feature of the pathogenicity of Mycobacterium tuberculosis during infection. Consumption of fatty acids requires regulation of carbon flux bifurcation between the oxidative TCA cycle and the glyoxylate shunt. In Escher ...

Bruton's tyrosine kinase (Btk) is critical for B-cell maturation and activation. Btk loss-of-function mutations cause human X-linked agammaglobulinemia (XLA). In contrast, Btk signaling sustains growth of several B-cell neoplasms which may be treated with ...

KAP1 (KRAB domain-associated protein 1) plays a fundamental role in regulating gene expression in mammalian cells by recruiting different transcription factors and altering the chromatin state. In doing so, KAP1 acts both as a platform for macromolecular i ...

The M2 protein of influenza A virus performs the crucial function of transporting protons to the interior of virions enclosed in the endosome. Adamantane drugs, amantadine (AMN) and rimantidine (RMN), block the proton conduction in some strains, and have b ...

Injectisomes are multi-protein transmembrane machines allowing pathogenic bacteria to inject effector proteins into eukaryotic host cells, a process called type III secretion. Here we present the first three-dimensional structure of Yersinia enterocolitica ...

Provided herein are aerolysin polypeptides and/or mutant aerolysin monomers comprising modified amino acid sequences that could have improved substrate analyte, such as (poly)nucleotide and peptide, improved reading properties such as enhanced substrate an ...

We present a new method to incorporate electrostatic interactions in coarse-grained representations of proteins. The model is based on a topologically reconstructed multipolar expansion of the all-atom centers of charge, specifically of the backbone dipole ...

Transcription Activator-Like (TAL) effectors are DNA-binding proteins secreted by phytopathogenic bacteria that interfere with native cellular functions by binding to plant DNA promoters. The key element of their architecture is a domain of tandem-repeats ...

Mycobacterium tuberculosis possesses a thick and highly hydrophobic cell wall principally composed of a mycolyl-arabinogalactan-peptidoglycan complex, which is critical for survival and virulence. DprE1 is a well-characterized component of decaprenyl-phosp ...

The thermosensor histidine kinase DesK from Bacillus subtilis senses changes in membrane fluidity initiating an adaptive response. Structural changes in DesK have been implicated in transmembrane signaling, but direct evidence is still lacking. On the basi ...

It is well-known that crowded environments affect the stability of proteins, with strong biological and biotechnological implications; however, beyond this, crowding is also expected to affect the dynamic properties of proteins, an idea that is hard to pro ...

Capillary morphogenesis gene 2 (CMG2/ANTXR2) is a cell surface receptor for both collagen VI and anthrax toxin. Biallelic loss-of-function mutations in CMG2 lead to a severe condition, hyaline fibromatosis syndrome (HFS). We have here dissected a network o ...

Because of high mutation rates, viruses constantly adapt to new environments. When propagated in cell lines, certain viruses acquire positively charged amino acids on their surface proteins, enabling them to utilize negatively charged heparan sulfate (HS) ...

Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the first wwPDB Hybrid/Integrative Meth ...

The physical chemical principles underlying,enzymatic thermostability are keys to understand the way evolution has shaped proteins,to adapt to a broad range of temperatures. Understanding the molecular determinants at the basis of protein thermostability i ...

Type II topoisomerase (topoII) is a metalloenzyme targeted by clinical antibiotics and anticancer agents. Here, we integrate existing structural data with molecular simulation and propose a model for the yet uncharacterized structure of the reactant state ...

Matteo Dal Peraro

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Phosphodiester Cleavage in Ribonuclease H Occurs via an Associative Two-Metal-Aided Catalytic Mechanism

MolecularWebXR: Multiuser discussions in chemistry and biology through immersive and inclusive augmented and virtual reality

A rheostat mechanism governs the bifurcation of carbon flux in mycobacteria

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

KAP1 is an antiparallel dimer with a functional asymmetry

Computational study of drug binding to the membrane-bound tetrameric M2 peptide bundle from influenza A virus

In situ structural analysis of the Yersinia enterocolitica injectisome

Overcoming the hydrophobic barrier of the membrane: The role of COQ9 in promoting coenzyme Q biosynthesis

Mutant aerolysin and uses thereof

Topologically based multipolar reconstruction of electrostatic interactions in multiscale simulations of proteins

TAL Effectors Specificity Stems from Negative Discrimination

GtrA Protein Rv3789 Is Required for Arabinosylation of Arabinogalactan in Mycobacterium tuberculosis

A coiled coil switch mediates cold sensing by the thermosensory protein DesK

All-atom simulations of crowding effects on ubiquitin dynamics

Ligand Binding to the Collagen VI Receptor Triggers a Talin-to-RhoA Switch that Regulates Receptor Endocytosis

Virus adaptation to heparan sulfate comes with capsid stability tradeoff

Outcome of the First wwPDB Hybrid/Integrative Methods Task Force Workshop

The role of PTM crosstalks in Httex1 structure, aggregation and membrane interaction

Understanding and Engineering Thermostability in DNA Ligase from Thermococcus sp 1519

Molecular Simulations Highlight the Role of Metals in Catalysis and Inhibition of Type II Topoisomerase