A. MONARI

Molecular bases and specificity behind the activation of the immune system OAS/RNAse L pathway by viral RNA.

This study uses molecular dynamics simulations to investigate how viral RNA activates the OAS/RNase L immune pathway by altering OAS conformation and free energy profiles.

Interaction Between Yersinia pestis Ail Outer Membrane Protein and the C-Terminal Domain of Human Vitronectin

The paper shows that Yersinia pestis Ail protein interacts with vitronectin's C-terminal domain, forming a stable complex that helps the bacteria evade the immune system.

Interaction of the Immune System TIM-3 Protein with a Model Cellular Membrane Containing Phosphatidyl-Serine Lipids.

This study uses molecular dynamics simulations to investigate the interaction of TIM-3 with phosphatidylserine lipids in a membrane, revealing molecular mechanisms and thermodynamics relevant to immune regulation and cancer.

Molecular Photoswitches Regulating the Activity of the Human Serotonin Transporter

The paper uses molecular dynamics simulations to study how cis- and trans-isomers of a photoswitch affect the activity of the human serotonin transporter.

Efficient Drug Delivering of a Photodynamic Therapy Agent into Cellular Membranes Rationalized by Molecular Dynamics

This study uses molecular dynamics simulations to analyze the behavior of a PDT drug complex in lipid bilayers, showing its internalization and dissociation, supporting its efficacy.

Mechanism of the Covalent Inhibition of Human Transmembrane Protease Serine 2 as an Original Antiviral Strategy

This study uses multiscale molecular modeling to investigate the mechanism of TMPRSS2 inhibition by Nafamostat, revealing its free-energy profile and structural dynamics.

Resolving a Guanine-Quadruplex Structure in the SARS-CoV-2 Genome through Circular Dichroism and Multiscale Molecular Modeling.

The paper determines the structure of a guanine-quadruplex in SARS-CoV-2 RNA using molecular modeling and experimental validation, showing pyridostatin stabilizes it more than another G4 sequence.

Predicting the Three-dimensional Structure of the c-KIT Oncogene Promoter and the Dynamics of Strongly Coupled Guanine-Quadruplexes

The paper predicts the 3D structure of the c-KIT promoter's G4s and shows how their coupling affects structure formation and drug discovery potential.

How SARS-CoV-2 alters the regulation of gene expression in infected cells.

This study uses molecular dynamics simulations to show how SARS-CoV-2 ORF8 protein interacts with DNA via a histone-like motif, affecting epigenetic regulation and potentially informing antiviral strategies.

Molecular basis of the pH-controlled maturation of the tick-borne encephalitis flavivirus

The paper investigates the pH-dependent maturation of the tick-borne encephalitis flavivirus's E protein, revealing how pH affects dimer stabilization and the role of the pr protomer.

Perturbation of Lipid Bilayers by Biomimetic Photoswitches Based on Cyclocurcumin

This paper uses molecular dynamics simulations to study how two isomers of a photoswitch interact with lipid bilayers and affect their structure.

G-quadruplex recognition by DARPIns through epitope/paratope analogy

This study investigates how DARPIns recognize G-quadruplexes through structural complementarity rather than sequence similarity, revealing a charged hollow region in DARPIns that hosts G4 structures.

Hijacking of Cellular Functions by Severe Acute Respiratory Syndrome Coronavirus-2. Permeabilization and Polarization of the Host Lipid Membrane by Viroporins.

The paper uses molecular dynamics simulations to show how SARS-CoV-2 ORF3a permeabilizes the host lipid membrane by forming a water channel, facilitating ion transport and contributing to inflammation.

Unraveling the Enzymatic Mechanism of the SARS-CoV-2 RNA-Dependent-RNA-Polymerase. An Unusual Active Site Leading to High Replication Rates.

This study determines the enzymatic mechanism of SARS-CoV-2 RNA-dependent-RNA polymerase using quantum mechanics/molecular mechanics simulations, revealing a unique active site structure and high replication efficiency.

Autophagy and evasion of immune system by SARS-CoV-2. Structural features of the Non-structural protein 6 from Wild Type and Omicron viral strains interacting with a model lipid bilayer.

This study investigates structural changes in SARS-CoV-2 Nsp6 protein between wild-type and Omicron variants using molecular dynamics and machine learning to analyze interactions with lipid bilayers.

Structure of the 5' untranslated region in SARS-CoV-2 genome and its specific recognition by innate immune system via the human oligoadenylate synthase 1

The paper reports the structure of SARS-CoV-2 5-UTR RNA complexed with OAS1, revealing how the SL1 region enhances specific interactions with the enzyme.

Never cared for what they do. High structural stability of Guanine-quadruplexes in presence of strand-break damages

The paper shows that guanine-quadruplexes remain structurally stable even with two strand breaks, unlike B-DNA, suggesting an evolutionary mechanism to mitigate ionizing radiation damage.

Structural and functional characterization of DdrC, a novel DNA damage-induced nucleoid associated protein involved in DNA compaction

This study characterizes DdrC, a DNA damage-induced protein in D. radiodurans, showing it compacts DNA and modulates its topology to aid in DNA repair.

Molecular mechanisms associated with clustered lesion-induced impairment of 8-oxoG recognition by the human glycosylase OGG1

This study investigates how clustered 8-oxoG lesions affect hOGG1 recognition using molecular dynamics and machine learning, finding that mismatches reduce repair efficiency by altering 8-oxoG structure.

The iron maiden. Cytosolic aconitase/IRP1 conformational transition in the regulation of ferritin translation and iron hemostasis

This study uses molecular dynamics simulations to analyze how the iron-sulfur cluster influences the conformational transition of aconitase/IRP1 and its interaction with mRNA, impacting ferritin translation and iron homeostasis.

How fragile we are. Influence of STimulator of INterferon Genes, STING, variants on pathogen recognition and immune response efficiency

The paper uses molecular simulations and machine learning to analyze STING variants and explains how structural changes affect immune response efficiency.

Staring at the naked Goddess. Unraveling structure and reactivity of Artemis endonuclease interacting with a DNA double strand.

This study uses molecular dynamics simulations to investigate Artemis endonuclease's interaction with DNA and its catalytic mechanism.

Structure and dynamics of RNA guanine quadruplexes in SARS-CoV-2 genome. Original strategies against emerging viruses

The paper calculates the first G4 structure of the RG-1 RNA sequence in SARS-CoV-2 genome using multiscale modeling and validates it with circular dichroism spectra, showing its stability and potential interaction with inhibitory ligands.

Recognition of a Tandem Lesion by DNA Glycosylases Explored Combining Molecular Dynamics and Machine Learning

This study uses molecular dynamics and machine learning to analyze how DNA glycosylase MutM recognizes tandem lesions versus single lesions in DNA.

Forever Young: Structural Stability of Telomeric Guanine-Quadruplexes in Presence of Oxidative DNA Lesions.

The paper investigates the structural stability of telomeric G-quadruplexes in the presence of oxidative DNA lesions using experimental and computational methods.

Photoinduced DNA Lesions in Dormant Bacteria. The Peculiar Route Leading to Spore Photoproduct Unraveled by Multiscale Molecular Dynamics

This paper uses molecular dynamics simulations to explain why spores form spore photoproducts instead of cyclobutane pyrimidine dimers under UV radiation.

Impact of the nucleosome histone core on the structure and dynamics of DNA containing pyrimidine-pyrimidone (6-4) photoproduct

The paper uses molecular dynamics simulations to study how the nucleosome histone core affects DNA structure and dynamics with 64-PP lesions, showing increased local flexibility and potential repair recognition signals.

Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses

This study investigates how RNA guanine quadruplexes interact with the SARS Unique Domain using molecular dynamics simulations to understand their role in viral infection and potential therapeutic targeting.