Giulia Palermo

Publications

• Two-Metal Ion Mechanism of DNA Cleavage in CRISPR-Cas9
• Factor H-Inspired Design of Peptide Biomarkers of the Complement C3d Protein
• Unveiling the RNA-mediated allosteric activation discloses functional hotspots in CRISPR-Cas13a
• Structural Basis for Reduced Dynamics of Three Engineered HNH Endonuclease Lys-to-Ala Mutants for the Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Associated 9 (CRISPR/Cas9) Enzyme
• GPU-Enhanced DFTB Metadynamics for Efficiently Predicting Free Energies of Biochemical Systems
• The electronic structure of genome editors from the first principles
• Establishing the allosteric mechanism in CRISPR‐Cas9
• Machines on Genes through the Computational Microscope
• Celebrating Women of Color in Computational Chemistry
• Unveiling Cas8 Dynamics and Regulation within a transposon-encoded Cascade-TniQ Complex
• Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes
• Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods
• Controlled Trafficking of Multiple and Diverse Cations Prompts Nucleic Acid Hydrolysis
• Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes
• Celebrating the Next Generation of Women in Computational Chemistry to Increase Diversity, Equity, Inclusion, and Respect
• An Alpha-helical Lid Guides the Target DNA toward Catalysis in CRISPR-Cas12a
• Mapping the Structural and Dynamic Determinants of pH-Sensitive Heparin Binding to Granulocyte Macrophage Colony Stimulating Factor
• Enhanced Specificity Mutations Perturb Allosteric Signaling in CRISPR-Cas9
• Establishing the fundamental rules for genetic code expansion
• Disruption of electrostatic contacts in the HNH nuclease from a thermophilic Cas9 rewires allosteric motions and enhances high-temperature DNA cleavage
• RNA-mediated Allosteric Activation in CRISPR-Cas13a
• New design strategies for ultra-specific CRISPR-Cas13a-based RNA-diagnostic tools with single-nucleotide mismatch sensitivity
• Flexibility in PAM Recognition Expands DNA Targeting in xCas9
• The Future of Chemistry is through Computations
• The synchronized catalytic dance of CRISPR-Cas9
• Editorial: Editing DNA and RNA through Computations
• Structure and Dynamics of the CRISPR–Cas9 Catalytic Complex
• Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations
• Allosteric Motions of the CRISPR-Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics
• Frontiers in CryoEM Modeling
• Structure and Dynamics of the Acyl Chains in the Membrane Trafficking and Enzymatic Processing of Lipids
• Women Make COMP: Mentoring the Next Generation of Women in Computational Chemistry
• NMR and computational methods for molecular resolution of allosteric pathways in enzyme complexes
• Allosteric Motions of the CRISPR–Cas9 HNH Nuclease Probed by NMR and Molecular Dynamics
• Faces of Contemporary CryoEM Information and Modeling
• Fighting COVID-19 Using Molecular Dynamics Simulations
• Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a
• Catalytic Mechanism of Non-Target DNA Cleavage in CRISPR-Cas9 Revealed by Ab Initio Molecular Dynamics
• Gaussian accelerated molecular dynamics: Principles and applications
• Cover Image, Volume 11, Issue 3
• An alpha-helical lid guides the target DNA toward catalysis in CRISPR-Cas12a
• High-fidelity, hyper-accurate, and evolved mutants rewire atomic-level communication in CRISPR-Cas9
• RNA targeting and cleavage by the type III-Dv CRISPR effector complex
• Graph theory approaches for molecular dynamics simulations
• Dimerization of the deaminase domain and locking interactions with Cas9 boost base editing efficiency in ABE8e
• Mechanism of expanded DNA recognition in xCas9
• Flexibility in PAM Recognition Expands DNA Targeting in xCas9
• Flexibility in PAM recognition expands DNA targeting in xCas9
• Flexibility in PAM recognition expands DNA targeting in xCas9
• Embolización gástrica percutánea en pacientes con obesidad: un estudio prospectivo de resultados a medio plazo
• The invisible dance of CRISPR-Cas9
• Dissecting Structure and Function of DNA·RNA Hybrids
• An Organometallic Compound which Exhibits a DNA Topology‐Dependent One‐Stranded Intercalation Mode
• An optimized polyamine moiety boosts the potency of human type II topoisomerase poisons as quantified by comparative analysis centered on the clinical candidate F14512
• Anandamide hydrolysis in FAAH reveals a dual strategy for efficient enzyme-assisted amide bond cleavage via nitrogen inversion
• Molecular simulations highlight the role of metals in catalysis and inhibition of type II topoisomerase
• Computational insights into function and inhibition of fatty acid amide hydrolase
• Covalent inhibitors of fatty acid amide hydrolase: A rationale for the activity of piperidine and piperazine aryl ureas
• Computational characterization of the dependence of halide perovskite effective masses on chemical composition and structure
• Fighting Cancer with Transition Metal Complexes: From Naked DNA to Protein and Chromatin Targeting Strategies
• Keys to Lipid Selection in Fatty Acid Amide Hydrolase Catalysis: Structural Flexibility, Gating Residues and Multiple Binding Pockets
• Wagging the tail: Essential role of substrate flexibility in FAAH catalysis
• Who Activates the Nucleophile in Ribozyme Catalysis? An Answer from the Splicing Mechanism of Group II Introns
• The Molecular Basis for Dual Fatty Acid Amide Hydrolase (FAAH)/Cyclooxygenase (COX) Inhibition
• Allosteric cross-talk in chromatin can mediate drug-drug synergy
• Effect of electronegative substituents and angular dependence on the heteronuclear spin-spin coupling constant3JC-H an empirical prediction equation derived by density functional theory calculations
• Catalytic metal ions and enzymatic processing of DNA and RNA
• Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain
• Valence and conduction band tuning in halide perovskites for solar cell applications
• Disclosing the impact of carcinogenic SF3b mutations on pre-mRNA recognition via all-atom simulations
• Striking plasticity of CRISPR-Cas9 and key role of non-target DNA, as revealed by molecular simulations
• Allostery in Its Many Disguises: From Theory to Applications
• Pushing the frontiers of first-principles based computer simulations of chemical and biological systems
• Development of Site-Specific Mg2+–RNA Force Field Parameters: A Dream or Reality? Guidelines from Combined Molecular Dynamics and Quantum Mechanics Simulations
• An Organometallic Compound which Exhibits a DNA Topology‐Dependent One‐Stranded Intercalation Mode
• CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations
• Protospacer Adjacent Motif-Induced Allostery Activates CRISPR-Cas9
• All-atom simulations disentangle the functional dynamics underlying gene maturation in the intron lariat spliceosome
• Molecular mechanism of off-target effects in CRISPR-Cas9
• Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics
• CRISPR–Cas12a REC2 – NUC interactions drive target-strand cleavage and constrain trans cleavage.
• Unveiling Cas8 dynamics and regulation within a transposon-encoded Cascade–TniQ complex