Imperial College London

ProfessorAlfonsoDe Simone

Faculty of Natural SciencesDepartment of Life Sciences

Visiting Professor
 
 
 
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Contact

 

+44 (0)20 7594 3052a.de-simon Website

 
 
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Location

 

603Sir Ernst Chain BuildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

129 results found

Mansueto S, Fusco G, De Simone A, 2023, α-Synuclein and biological membranes: the danger of loving too much., Chem Commun (Camb), Vol: 59, Pages: 8769-8778

The aberrant aggregation of α-Synuclein (αS), a disordered protein primarily localised at the neuronal synapses, is associated with a number of neurodegenerative disorders including Parkinson's disease (PD). The biological properties of αS are strictly connected with its ability to bind synaptic membranes under both physiological and pathological conditions. Here we overview the recent studies on the structural and biological properties of the membrane interaction by αS. The characterisation of this state is particularly challenging as the membrane binding of αS is weak, transient and features a considerable degree of conformational disorder. Advancements in this area have been achieved through combinations of nuclear magnetic resonance (NMR), super-resolution microscopy, cryo-EM and cellular biophysics. Current data clarified the central role of the equilibrium between ordered and disordered states of αS at the membrane surface, which regulates the membrane affinity, the aggregation into amyloid fibrils and the promotion of vesicle clustering. Recent results on toxic oligomeric species of αS also revealed common features in the membrane interaction of functional and aberrant forms of this protein. These findings therefore evidence the challenging nature of identifying suitable therapeutics to target the aberrant aggregation of αS in PD while leaving its normal physiological form unperturbed.

Journal article

Gonzalez-Garcia M, Fusco G, De Simone A, 2023, Metal interactions of α-synuclein probed by NMR amide-proton exchange., Front Chem, Vol: 11, ISSN: 2296-2646

The aberrant aggregation of α-synuclein (αS), a disordered protein primarily expressed in neuronal cells, is strongly associated with the underlying mechanisms of Parkinson's disease. It is now established that αS has a weak affinity for metal ions and that these interactions alter its conformational properties by generally promoting self-assembly into amyloids. Here, we characterised the nature of the conformational changes associated with metal binding by αS using nuclear magnetic resonance (NMR) to measure the exchange of the backbone amide protons at a residue specific resolution. We complemented these experiments with 15N relaxation and chemical shift perturbations to obtain a comprehensive map of the interaction between αS and divalent (Ca2+, Cu2+, Mn2+, and Zn2+) and monovalent (Cu+) metal ions. The data identified specific effects that the individual cations exert on the conformational properties of αS. In particular, binding to calcium and zinc generated a reduction of the protection factors in the C-terminal region of the protein, whereas both Cu(II) and Cu(I) did not alter the amide proton exchange along the αS sequence. Changes in the R2/R1 ratios from 15N relaxation experiments were, however, detected as a result of the interaction between αS and Cu+ or Zn2+, indicating that binding to these metals induces conformational perturbations in distinctive regions of the protein. Collectively our data suggest that multiple mechanisms of enhanced αS aggregation are associated with the binding of the analysed metals.

Journal article

Vassallo N, Ongeri S, De Simone A, 2023, Editorial: Oligomers in amyloid-associated diseases-structural properties and toxicity., Front Mol Biosci, Vol: 10, ISSN: 2296-889X

Journal article

Fusco G, Biancaniello C, Vrettas MD, De Simone Aet al., 2022, Thermal tuning of protein hydration in a hyperthermophilic enzyme, FRONTIERS IN MOLECULAR BIOSCIENCES, Vol: 9

Journal article

Qi G, Vrettas MD, Biancaniello C, Sanz-Hernandez M, Cafolla CT, Morgan JWR, Wang Y, De Simone A, Wales DJet al., 2022, Enhancing Biomolecular Simulations with Hybrid Potentials Incorporating NMR Data, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, Vol: 18, Pages: 7733-7750, ISSN: 1549-9618

Journal article

Fusco G, Bemporad F, Chiti F, Dobson CMM, De Simone Aet al., 2022, The role of structural dynamics in the thermal adaptation of hyperthermophilic enzymes, FRONTIERS IN MOLECULAR BIOSCIENCES, Vol: 9

Journal article

Balasco N, Esposito L, De Simone A, Vitagliano Let al., 2022, Local Backbone Geometry Plays a Critical Role in Determining Conformational Preferences of Amino Acid Residues in Proteins, BIOMOLECULES, Vol: 12

Journal article

Palmas MF, Etzi M, Pisanu A, Camoglio C, Sagheddu C, Santoni M, Manchinu MF, Pala M, Fusco G, De Simone A, Picci L, Mulas G, Spiga S, Scherma M, Fadda P, Pistis M, Simola N, Carboni E, Carta ARet al., 2022, 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, CELLS, Vol: 11

Journal article

Malagrino F, Fusco G, Pennacchietti V, Toto A, Nardella C, Pagano L, de Simone A, Gianni Set al., 2022, Cryptic binding properties of a transient folding intermediate in a PDZ tandem repeat, PROTEIN SCIENCE, Vol: 31, ISSN: 0961-8368

Journal article

Olivieri C, Li GC, Wang Y, Manu VS, Walker C, Kim J, Camilloni C, De Simone A, Vendruscolo M, Bernlohr DA, Taylor SS, Veglia Get al., 2022, ATP-competitive inhibitors modulate the substrate binding cooperativity of a kinase by altering its conformational entropy, SCIENCE ADVANCES, Vol: 8, ISSN: 2375-2548

Journal article

Navarro-Paya C, Sanz-Hernandez M, De Simone A, 2022, Plasticity of Membrane Binding by the Central Region of alpha-Synuclein, FRONTIERS IN MOLECULAR BIOSCIENCES, Vol: 9

Journal article

Reddy UV, Weber DK, Wang S, Larsen EK, Gopinath T, De Simone A, Robia S, Veglia Get al., 2022, A kink in DWORF helical structure controls the activation of the sarcoplasmic reticulum Ca2+-ATPase, STRUCTURE, Vol: 30, Pages: 360-+, ISSN: 0969-2126

Journal article

Palmas MF, Ena A, Burgaletto C, Casu MA, Cantarella G, Carboni E, Etzi M, De Simone A, Fusco G, Cardia MC, Lai F, Picci L, Tweedie D, Scerba MT, Coroneo V, Bernardini R, Greig NH, Pisanu A, Carta ARet al., 2022, Repurposing Pomalidomide as a Neuroprotective Drug: Efficacy in an Alpha-Synuclein-Based Model of Parkinson's Disease, NEUROTHERAPEUTICS, Vol: 19, Pages: 305-324, ISSN: 1933-7213

Journal article

Weber DK, Reddy UV, Wang S, Larsen EK, Gopinath T, Gustavsson MB, Cornea RL, Thomas DD, De Simone A, Veglia Get al., 2021, Structural basis for allosteric control of the SERCA-Phospholamban membrane complex by Ca2+ and phosphorylation, ELIFE, Vol: 10, ISSN: 2050-084X

Journal article

Sanz-Hernandez M, Barritt JD, Sobek J, Hornemann S, Aguzzi A, De Simone Aet al., 2021, Mechanism of misfolding of the human prion protein revealed by a pathological mutation, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 118, ISSN: 0027-8424

Journal article

Perni M, van der Goot A, Limbocker R, van Ham TJ, Aprile FA, Xu CK, Flagmeier P, Thijssen K, Sormanni P, Fusco G, Chen SW, Challa PK, Kirkegaard JB, Laine RF, Ma KY, Muller MBD, Sinnige T, Kumita JR, Cohen SIA, Seinstra R, Kaminski Schierle GS, Kaminski CF, Barbut D, De Simone A, Knowles TPJ, Zasloff M, Nollen EAA, Vendruscolo M, Dobson CMet al., 2021, Comparative studies in the A30P and A53T alpha-Synuclein C. elegans strains to investigate the molecular origins of Parkinson's Disease, Frontiers in Cell and Developmental Biology, Vol: 9, Pages: 1-10, ISSN: 2296-634X

The aggregation of α-synuclein is a hallmark of Parkinson's disease (PD) and a variety of related neurological disorders. A number of mutations in this protein, including A30P and A53T, are associated with familial forms of the disease. Patients carrying the A30P mutation typically exhibit a similar age of onset and symptoms as sporadic PD, while those carrying the A53T mutation generally have an earlier age of onset and an accelerated progression. We report two C. elegans models of PD (PDA30P and PDA53T), which express these mutational variants in the muscle cells, and probed their behavior relative to animals expressing the wild-type protein (PDWT). PDA30P worms showed a reduced speed of movement and an increased paralysis rate, control worms, but no change in the frequency of body bends. By contrast, in PDA53T worms both speed and frequency of body bends were significantly decreased, and paralysis rate was increased. α-Synuclein was also observed to be less well localized into aggregates in PDA30P worms compared to PDA53T and PDWT worms, and amyloid-like features were evident later in the life of the animals, despite comparable levels of expression of α-synuclein. Furthermore, squalamine, a natural product currently in clinical trials for treating symptomatic aspects of PD, was found to reduce significantly the aggregation of α-synuclein and its associated toxicity in PDA53T and PDWT worms, but had less marked effects in PDA30P. In addition, using an antibody that targets the N-terminal region of α-synuclein, we observed a suppression of toxicity in PDA30P, PDA53T and PDWT worms. These results illustrate the use of these two C. elegans models in fundamental and applied PD research.

Journal article

Gonzalez-Garcia M, Fusco G, De Simone A, 2021, Membrane interactions and toxicity by misfolded protein oligomers, Frontiers in Cell and Developmental Biology, Vol: 9, Pages: 1-12, ISSN: 2296-634X

The conversion of otherwise soluble proteins into insoluble amyloid aggregates is associated with a range of neurodegenerative disorders, including Alzheimer’s and Parkinson’s diseases, as well as non-neuropathic conditions such as type II diabetes and systemic amyloidoses. It is increasingly evident that the most pernicious species among those forming during protein aggregation are small prefibrillar oligomers. In this review, we describe the recent progress in the characterization of the cellular and molecular interactions by toxic misfolded protein oligomers. A fundamental interaction by these aggregates involves biological membranes, resulting in two major model mechanisms at the onset of the cellular toxicity. These include the membrane disruption model, resulting in calcium imbalance, mitochondrial dysfunction and intracellular reactive oxygen species, and the direct interaction with membrane proteins, leading to the alteration of their native function. A key challenge remains in the characterization of transient interactions involving heterogeneous protein aggregates. Solving this task is crucial in the quest of identifying suitable therapeutic approaches to suppress the cellular toxicity in protein misfolding diseases.

Journal article

Sanz-Hernandez M, De Simone A, 2021, Backbone NMR assignments of the C-terminal domain of the human prion protein and its disease-associated T183A variant, BIOMOLECULAR NMR ASSIGNMENTS, Vol: 15, Pages: 193-196, ISSN: 1874-2718

Journal article

Man W, Tahirbegi B, Vrettas M, Ying L, Vendruscolo M, De Simone A, Fusco Get al., 2021, The docking of synaptic vesicles on the presynaptic membrane induced by α-synuclein is modulated by lipid composition, Nature Communications, Vol: 12, ISSN: 2041-1723

α-Synuclein (αS) is a presynaptic disordered protein whose aberrant aggregation is associated with Parkinson’s disease. The functional role of αS is still debated, although it has been involved in the regulation of neurotransmitter release via the interaction with synaptic vesicles (SVs). We report here a detailed characterisation of the conformational properties of αS bound to the inner and outer leaflets of the presynaptic plasma membrane (PM), using small unilamellar vesicles. Our results suggest that αS preferentially binds the inner PM leaflet. On the basis of these studies we characterise in vitro a mechanism by which αS stabilises, in a concentration-dependent manner, the docking of SVs on the PM by establishing a dynamic link between the two membranes. The study then provides evidence that changes in the lipid composition of the PM, typically associated with neurodegenerative diseases, alter the modes of binding of αS, specifically in a segment of the sequence overlapping with the non-amyloid component region. Taken together, these results reveal how lipid composition modulates the interaction of αS with the PM and underlie its functional and pathological behaviours in vitro.

Journal article

Nguyen PH, Ramamoorthy A, Sahoo BR, Zheng J, Faller P, Straub JE, Dominguez L, Shea J-E, Dokholyan N, De Simone A, Ma B, Nussinov R, Najafi S, Ngo ST, Loquet A, Chiricotto M, Ganguly P, McCarty J, Li MS, Hall C, Wang Y, Miller Y, Melchionna S, Habenstein B, Timr S, Chen J, Hnath B, Strodel B, Kayed R, Lesne S, Wei G, Sterpone F, Doig AJ, Derreumaux Pet al., 2021, Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer's Disease, Parkinson's Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis, CHEMICAL REVIEWS, Vol: 121, Pages: 2545-2647, ISSN: 0009-2665

Journal article

O'Brien HER, Zhang XF, Sanz-Hernandez M, Chion A, Shapiro S, Mobayen G, Xu Y, De Simone A, Laffan MA, McKinnon TAJet al., 2021, Blocking von Willebrand factor free thiols inhibits binding to collagen under high and pathological shear stress, Journal of Thrombosis and Haemostasis, Vol: 19, Pages: 358-369, ISSN: 1538-7836

BackgroundVon Willebrand factor (VWF) contains a number of free thiols, the majority of which are located in its C‐domains, and these have been shown to alter VWF function, However, the impact of free thiols on function following acute exposure of VWF to collagen under high and pathological shear stress has not been determined.MethodsVWF free thiols were blocked with N‐ethylmaleimide and flow assays performed under high and pathological shear rates to determine the impact on platelet capture and collagen binding function. Atomic force microscopy (AFM) was used to probe the interaction of VWF with collagen and molecular simulations conducted to determine the effect of free thiols on the flexibility of the VWF‐C4 domain.ResultsBlockade of VWF free thiols reduced VWF‐mediated platelet capture to collagen in a shear‐dependent manner, with platelet capture virtually abolished above 5000 s−1 and in regions of stenosis in microfluidic channels. Direct visualization of VWF fibers formed under extreme pathological shear rates and analysis of collagen‐bound VWF attributed the effect to altered binding of VWF to collagen. AFM measurements showed that thiol‐blockade reduced the lifetime and strength of the VWF‐collagen bond. Pulling simulations of the VWF‐C4 domain demonstrated that with one or two reduced disulphide bonds the C4 domain has increased flexibility and the propensity to undergo free‐thiol exchange.ConclusionsWe conclude that free thiols in the C‐domains of VWF enhance the flexibility of the molecule and enable it to withstand high shear forces following collagen binding, demonstrating a previously unrecognized role for VWF free thiols.

Journal article

Boi L, Pisanu A, Fusco G, Carboni E, Casu MA, Satta V, Scherma M, Janda E, Palmas MF, Mocci I, Ena A, Mulas G, Spiga S, Fadda P, De Simone A, Carta Aet al., 2020, Modeling Parkinson’s disease neuropathology and symptoms by intranigral inoculation of preformed human α-synuclein oligomers, International Journal of Molecular Sciences, Vol: 21, ISSN: 1422-0067

The accumulation of aggregated α-synuclein (αSyn) is a hallmark of Parkinson’s disease (PD). Current evidence indicates that small soluble αSyn oligomers (αSynOs) are the most toxic species among the forms of αSyn aggregates, and that size and topological structural properties are crucial factors for αSynOs-mediated toxicity, involving the interaction with either neurons or glial cells. We previously characterized a human αSynO (H-αSynO) with specific structural properties promoting toxicity against neuronal membranes. Here, we tested the neurotoxic potential of these H-αSynOs in vivo, in relation to the neuropathological and symptomatic features of PD. The H-αSynOs were unilaterally infused into the rat substantia nigra pars compacta (SNpc). Phosphorylated αSyn (p129-αSyn), reactive microglia, and cytokine levels were measured at progressive time points. Additionally, a phagocytosis assay in vitro was performed after microglia pre-exposure to αsynOs. Dopaminergic loss, motor, and cognitive performances were assessed. H-αSynOs triggered p129-αSyn deposition in SNpc neurons and microglia and spread to the striatum. Early and persistent neuroinflammatory responses were induced in the SNpc. In vitro, H-αSynOs inhibited the phagocytic function of microglia. H-αsynOs-infused rats displayed early mitochondrial loss and abnormalities in SNpc neurons, followed by a gradual nigrostriatal dopaminergic loss, associated with motor and cognitive impairment. The intracerebral inoculation of structurally characterized H-αSynOs provides a model of progressive PD neuropathology in rats, which will be helpful for testing neuroprotective therapies.

Journal article

Heller GT, Aprile FA, Michaels TCT, Limbocker R, Perni M, Ruggeri FS, Mannini B, Lohr T, Bonomi M, Camilloni C, De Simone A, Felli IC, Pierattelli R, Knowles TPJ, Dobson CM, Vendruscolo Met al., 2020, Small-molecule sequestration of amyloid-beta as a drug discovery strategy for Alzheimer's disease, SCIENCE ADVANCES, Vol: 6, ISSN: 2375-2548

Journal article

Stephens AD, Zacharopoulou M, Moons R, Fusco G, Seetaloo N, Chiki A, Woodhams PJ, Mela I, Lashuel HA, Phillips JJ, De Simone A, Sobott F, Schierle GSKet al., 2020, Extent of N-terminus exposure of monomeric alpha-synuclein determines its aggregation propensity, NATURE COMMUNICATIONS, Vol: 11, ISSN: 2041-1723

Journal article

Navarro-Paya C, Sanz-Hernandez M, De Simone A, 2020, In Silico Study of the Mechanism of Binding of the N-Terminal Region of alpha Synuclein to Synaptic-Like Membranes, LIFE-BASEL, Vol: 10

Journal article

Carta AR, Boi L, Pisanu A, Palmas MF, Carboni E, De Simone Aet al., 2020, Advances in modelling alpha-synuclein-induced Parkinson's diseases in rodents: Virus-based models versus inoculation of exogenous preformed toxic species, JOURNAL OF NEUROSCIENCE METHODS, Vol: 338, ISSN: 0165-0270

Journal article

Visconti L, Toto A, Jarvis J, Troilo F, Malagrino F, De Simone A, Gianni Set al., 2020, Demonstration of binding induced structural plasticity in a SH2 domain, Frontiers in Molecular Biosciences, Vol: 7, ISSN: 2296-889X

SH2 domains are common protein interaction domains able to recognize short aminoacidic sequences presenting a phosphorylated tyrosine (pY). In spite of their fundamental importance for cell physiology there is a lack of information about the mechanism by which these domains recognize and bind their natural ligands. The N-terminal SH2 (N-SH2) domain of PI3K mediates the interaction with different scaffolding proteins and is known to recognize a specific pY-X-X-M consensus sequence. These interactions are at the cross roads of different molecular pathways and play a key role for cell development and division. By combining mutagenesis, chemical kinetics and NMR, here we provide a complete characterization of the interaction between N-SH2 and a peptide mimicking the scaffolding protein Gab2. Our results highlight that N-SH2 is characterized by a remarkable structural plasticity, with the binding reaction being mediated by a diffused structural region and not solely by the residues located in the binding pocket. Furthermore, the analysis of kinetic data allow us to pinpoint an allosteric network involving residues far from the binding pocket involved in specificity. Results are discussed on the light of previous works on the binding properties of SH2 domains.

Journal article

Man WK, De Simone A, Barritt JD, Vendruscolo M, Dobson CM, Fusco Get al., 2020, A Role of Cholesterol in Modulating the Binding of alpha-Synuclein to Synaptic-Like Vesicles, FRONTIERS IN NEUROSCIENCE, Vol: 14

Journal article

Runfola M, De Simone A, Vendruscolo M, Dobson CM, Fusco Get al., 2020, The N-terminal Acetylation of alpha-Synuclein Changes the Affinity for Lipid Membranes but not the Structural Properties of the Bound State, SCIENTIFIC REPORTS, Vol: 10, ISSN: 2045-2322

Journal article

Baum J, Chiti F, De Simone A, Knowles TPJ, Kumita JR, Radford SE, Robinson CV, Salvatella X, Valelli K, Vendruscolo M, Pastore A, Tartaglia GGet al., 2019, Homage to Chris Dobson, FRONTIERS IN MOLECULAR BIOSCIENCES, Vol: 6

Journal article

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