Alfonso De Simone

发表

Toward Understanding the Molecular Bases of Stretch Activation

A. Pastore, A. De Simone, B. Bullard, 2016, The Journal of Biological Chemistry.

The N-terminal Acetylation of α-Synuclein Changes the Affinity for Lipid Membranes but not the Structural Properties of the Bound State

C. Dobson, M. Vendruscolo, A. De Simone, 2020, Scientific Reports.

C-terminal calcium binding of α-synuclein modulates synaptic vesicle interaction

Romain F. Laine, Claire H. Michel, Marcus J. Fantham, 2018, Nature Communications.

Comparative Studies in the A30P and A53T α-Synuclein C. elegans Strains to Investigate the Molecular Origins of Parkinson's Disease

Romain F. Laine, J. B. Kirkegaard, C. Dobson, 2021, Frontiers in Cell and Developmental Biology.

Corrigendum: Structural basis of synaptic vesicle assembly promoted by α-synuclein

C. Dobson, T. Pape, M. Vendruscolo, 2017, Nature Communications.

Direct Observation of the Three Regions in α-Synuclein that Determine its Membrane-Bound Behaviour

Michele Vendruscolo, Christopher M. Dobson, Gianluigi Veglia, 2014, Nature Communications.

The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes

C. Dobson, F. Chiti, F. Bemporad, 2022, Frontiers in Molecular Biosciences.

Structure of a low-population intermediate state in the release of an enzyme product

C. Dobson, M. Vendruscolo, Anne Dhulesia, 2015, eLife.

Characterization of the interdomain motions in hen lysozyme using residual dipolar couplings as replica-averaged structural restraints in molecular dynamics simulations.

Michele Vendruscolo, Christopher M Dobson, C. Dobson, 2013, Biochemistry.

Cavitation energies can outperform dispersion interactions

A. De Simone, T. Heine, W. Nau, 2018, Nature Chemistry.

Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts.

Carlo Camilloni, Michele Vendruscolo, Wim F Vranken, 2012, Biochemistry.

Carbohydrate recognition by RpfB from Mycobacterium tuberculosis unveiled by crystallographic and molecular dynamics analyses.

R. Berisio, L. Vitagliano, A. Ruggiero, 2013, Biophysical journal.

Extent of N-terminus exposure of monomeric alpha-synuclein determines its aggregation propensity

H. Lashuel, F. Sobott, A. De Simone, 2020, Nature Communications.

Structural basis of membrane disruption and cellular toxicity by α-synuclein oligomers

C. Dobson, M. Vendruscolo, F. Chiti, 2017, Science.

Molecular determinants of the interaction of EGCG with ordered and disordered proteins

C. Dobson, M. Vendruscolo, F. Ruggeri, 2018, Biopolymers.

Cucurbit[8]uril and blue-box: high-energy water release overwhelms electrostatic interactions.

M. Vendruscolo, A. De Simone, O. Scherman, 2013, Journal of the American Chemical Society.

Release of high-energy water as an essential driving force for the high-affinity binding of cucurbit[n]urils.

Oren A Scherman, A. De Simone, O. Scherman, 2012, Journal of the American Chemical Society.

Structural Basis for Natural Product Selection and Export by Bacterial ABC Transporters.

M. Marahiel, C. Robinson, A. De Simone, 2018, ACS chemical biology.

Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis.

Son Tung Ngo, Bikash R. Sahoo, R. Nussinov, 2021, Chemical reviews.

Cryptic binding properties of a transient folding intermediate in a PDZ tandem repeat

S. Gianni, C. Nardella, A. De Simone, 2022, Protein science : a publication of the Protein Society.

Amyloid β Protein and Alzheimer's Disease: When Computer Simulations Complement Experimental Studies.

N. Buchete, J. H. Viles, S. Melchionna, 2015, Chemical reviews.

The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments

A. Laio, M. Vendruscolo, C. Camilloni, 2015, Scientific Reports.

The structure of Resuscitation promoting factor B from M. tuberculosis reveals unexpected ubiquitin-like domains.

R. Berisio, L. Vitagliano, A. Ruggiero, 2015, Biochimica et biophysica acta.

Glucokinase Gene Mutations: Structural and Genotype-Phenotype Analyses in MODY Children from South Italy

Lucia Sacchetti, A. Zagari, A. Franzese, 2008, PloS one.

Characterizing protein crystal contacts and their role in crystallization: rubredoxin as a case study.

P. Charbonneau, D. Fusco, J. Headd, 2012, Soft matter.

Sequence Specificity in the Entropy-Driven Binding of a Small Molecule and a Disordered Peptide.

Massimiliano Bonomi, Carlo Camilloni, Michele Vendruscolo, 2017, Journal of molecular biology.

Structure-Free Validation of Residual Dipolar Coupling and Paramagnetic Relaxation Enhancement Measurements of Disordered Proteins.

Francisco N. Newby, C. Dobson, X. Salvatella, 2015, Biochemistry.

Conformational recognition of an intrinsically disordered protein.

M. Lewitzky, P. Simister, S. Feller, 2014, Biophysical journal.

Order and disorder in the physiological membrane binding of α-synuclein.

A. De Simone, Giuliana Fusco, Máximo Sanz-Hernández, 2018, Current opinion in structural biology.

ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy

Susan S. Taylor, M. Vendruscolo, D. Bernlohr, 2022, Science advances.

Role of side chains in collagen triple helix stabilization and partner recognition

R. Berisio, L. Vitagliano, R. Improta, 2009, Journal of peptide science : an official publication of the European Peptide Society.

Role of hydration in collagen triple helix stabilization.

R. Berisio, L. Vitagliano, A. De Simone, 2008, Biochemical and biophysical research communications.

Structure and Dynamics of the Integrin LFA-1 I-Domain in the Inactive State Underlie its Inside-Out/Outside-In Signaling and Allosteric Mechanisms

Carlo Camilloni, Michele Vendruscolo, Predrag Kukic, 2015, Structure.

Small-molecule sequestration of amyloid-β as a drug discovery strategy for Alzheimer’s disease

C. Dobson, M. Vendruscolo, M. Bonomi, 2019, Science Advances.

Identification of small-molecule binding pockets in the soluble monomeric form of the Aβ42 peptide.

Michele Vendruscolo, Gergely Toth, Christopher M Dobson, 2013, The Journal of chemical physics.

The Intranigral Infusion of Human-Alpha Synuclein Oligomers Induces a Cognitive Impairment in Rats Associated with Changes in Neuronal Firing and Neuroinflammation in the Anterior Cingulate Cortex

M. Pistis, E. Carboni, A. De Simone, 2022, Cells.

Repurposing Pomalidomide as a Neuroprotective Drug: Efficacy in an Alpha-Synuclein-Based Model of Parkinson’s Disease

N. Greig, E. Carboni, M. Casu, 2022, Neurotherapeutics.

The toxicity of misfolded protein oligomers is independent of their secondary structure.

C. Dobson, F. Chiti, M. Vivoli Vega, 2019, ACS chemical biology.

Experimental free energy surfaces reveal the mechanisms of maintenance of protein solubility

Michele Vendruscolo, Fabrizio Chiti, Shang-Te Danny Hsu, 2011, Proceedings of the National Academy of Sciences.

The docking of synaptic vesicles on the presynaptic membrane induced by α-synuclein is modulated by lipid composition

Michail D. Vrettas, M. Vendruscolo, L. Ying, 2021, Nature Communications.

Structural Ensembles of Membrane-bound α-Synuclein Reveal the Molecular Determinants of Synaptic Vesicle Affinity

C. Dobson, M. Vendruscolo, G. Veglia, 2016, Scientific Reports.

Protein kinase R dependent phosphorylation of α-synuclein regulates its membrane binding and aggregation

H. Lashuel, A. De Simone, Min Shi, 2022, PNAS nexus.

Toward the understanding of MNEI sweetness from hydration map surfaces.

F. Fraternali, A. De Simone, P. Temussi, 2006, Biophysical journal.

Prion and water: tight and dynamical hydration sites have a key role in structural stability.

Chandra S Verma, Franca Fraternali, A. Zagari, 2005, Proceedings of the National Academy of Sciences of the United States of America.

Plasticity of Membrane Binding by the Central Region of α-Synuclein

A. De Simone, Máximo Sanz-Hernández, Carlos Navarro-Paya, 2022, Frontiers in Molecular Biosciences.

Structural basis of synaptic vesicle assembly promoted by α-synuclein

C. Dobson, T. Pape, M. Vendruscolo, 2016, Nature Communications.

Josephin domain of ataxin‐3 contains two distinct ubiquitin‐binding sites

G. Nicastro, A. Pastore, F. Fraternali, 2009, Biopolymers.

Atomic structure and hierarchical assembly of a cross-β amyloid fibril

Michele Vendruscolo, Robert G Griffin, Galia T Debelouchina, 2013, Proceedings of the National Academy of Sciences.

A Role of Cholesterol in Modulating the Binding of α-Synuclein to Synaptic-Like Vesicles

C. Dobson, M. Vendruscolo, A. De Simone, 2020, Frontiers in Neuroscience.

Electrostatically-guided inhibition of Curli amyloid nucleation by the CsgC-like family of chaperones

S. Kazarian, Sebastian Lambert, M. Chapman, 2016, Scientific Reports.

Membrane Interactions and Toxicity by Misfolded Protein Oligomers

A. De Simone, Giuliana Fusco, M. Gonzalez-Garcia, 2021, Frontiers in Cell and Developmental Biology.

A method of determining RNA conformational ensembles using structure-based calculations of residual dipolar couplings.

M. Vendruscolo, A. De Simone, Aditi N. Borkar, 2013, The Journal of chemical physics.

Toward an accurate determination of free energy landscapes in solution states of proteins.

X. Salvatella, M. Vendruscolo, Barbara Richter, 2009, Journal of the American Chemical Society.

Characterization of the Conformational Fluctuations in the Josephin Domain of Ataxin-3

Michele Vendruscolo, Annalisa Pastore, Andrea Cavalli, 2014, Biophysical journal.

Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins

L. Vitagliano, L. Esposito, N. Balasco, 2022, Biomolecules.

α-Synuclein and Mitochondria: Probing the Dynamics of Disordered Membrane-protein Regions Using Solid-State Nuclear Magnetic Resonance

Giuliana Fusco, Angelo Gallo, Silvia Mansueto, 2024, JACS Au.

Metal interactions of α-synuclein probed by NMR amide-proton exchange

A. De Simone, Giuliana Fusco, Mario Gonzalez-Garcia, 2023, Frontiers in Chemistry.

Mechanism of misfolding of the human prion protein revealed by a pathological mutation

S. Hornemann, A. Aguzzi, A. De Simone, 2021, Proceedings of the National Academy of Sciences.

Modeling Parkinson’s Disease Neuropathology and Symptoms by Intranigral Inoculation of Preformed Human α-Synuclein Oligomers

E. Carboni, M. Casu, A. De Simone, 2020, International journal of molecular sciences.

Structural differences between toxic and nontoxic HypF-N oligomers.

C. Dobson, M. Vendruscolo, F. Chiti, 2018, Chemical communications.

Structural dynamics and conformational equilibria of SERCA regulatory proteins in membranes by solid-state NMR restrained simulations.

G. Veglia, A. De Simone, Kaustubh R. Mote, 2014, Biophysical journal.

Determination of Conformational Equilibria in Proteins Using Residual Dipolar Couplings

Michele Vendruscolo, M. Vendruscolo, A. De Simone, 2011, Journal of chemical theory and computation.

Force-field dependence of chignolin folding and misfolding: comparison with experiment and redesign.

R. Best, M. Otyepka, A. De Simone, 2012, Biophysical journal.

α-Synuclein and biological membranes: the danger of loving too much

A. De Simone, Giuliana Fusco, Silvia Mansueto, 2023, Chemical communications.

Probing the Origin of the Toxicity of Oligomeric Aggregates of α-Synuclein with Antibodies

C. Dobson, M. Vendruscolo, F. Chiti, 2019, ACS chemical biology.

Intrinsic disorder modulates protein self-assembly and aggregation

D. Frenkel, C. Dobson, M. Sunde, 2012, Proceedings of the National Academy of Sciences.

Polyproline helices in protein structures: A statistical survey.

R. Berisio, L. Vitagliano, A. Zagari, 2006, Protein and peptide letters.