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Author Luca Maragliano

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Thermodynamics and Kinetics of Ion Permeation in Wild-Type and Mutated Open Active Conformation of the Human α7 Nicotinic Receptor.

Grazia Cottone, Letizia Chiodo, Luca Maragliano,

Molecular studies of human pentameric ligand-gated ion channels (LGICs) expressed in neurons and at neuromuscular junctions are of utmost importance in the development of therapeutic strategies for neurological disorders. We focus here on the nicotinic acetylcholine receptor nAChR-α7, a homopentameric channel widely expressed in the human brain, with a proven ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2020, :]

Cited: 0 times

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Engineering REST-Specific Synthetic PUF Proteins to Control Neuronal Gene Expression: A Combined Experimental and Computational Study.

Stefania Criscuolo, Mahad Gatti Iou, Assunta Merolla, Luca Maragliano, Fabrizia Cesca, Fabio Benfenati,

Regulation of gene transcription is an essential mechanism for differentiation and adaptation of organisms. A key actor in this regulation process is the repressor element 1 (RE1)-silencing transcription factor (REST), a transcriptional repressor that controls more than 2000 putative target genes, most of which are neuron-specific. With the purpose of ... Read more >>

ACS Synth Biol (ACS synthetic biology)
[2020, 9(8):2039-2054]

Cited: 0 times

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Neuronal firing modulation by a membrane-targeted photoswitch.

Mattia Lorenzo DiFrancesco, Francesco Lodola, Elisabetta Colombo, Luca Maragliano, Mattia Bramini, Giuseppe Maria Paternò, Pietro Baldelli, Mauro Dalla Serra, Lorenzo Lunelli, Marta Marchioretto, Giorgio Grasselli, Simone Cimò, Letizia Colella, Daniele Fazzi, Fausto Ortica, Vito Vurro, Cyril Giles Eleftheriou, Dmytro Shmal, José Fernando Maya-Vetencourt, Chiara Bertarelli, Guglielmo Lanzani, Fabio Benfenati,

Optical technologies allowing modulation of neuronal activity at high spatio-temporal resolution are becoming paramount in neuroscience. In this respect, azobenzene-based photoswitches are promising nanoscale tools for neuronal photostimulation. Here we engineered a light-sensitive azobenzene compound (Ziapin2) that stably partitions into the plasma membrane and causes its thinning through trans-dimerization in ... Read more >>

Nat Nanotechnol (Nature nanotechnology)
[2020, 15(4):296-306]

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Synapsins are expressed at neuronal and non-neuronal locations in Octopus vulgaris.

Federica Maiole, Giulia Tedeschi, Simona Candiani, Luca Maragliano, Fabio Benfenati, Letizia Zullo,

Synapsins are a family of phosphoproteins fundamental to the regulation of neurotransmitter release. They are typically neuron-specific, although recent evidence pointed to their expression in non-neuronal cells where they play a role in exocytosis and vesicle trafficking. In this work, we characterized synapsin transcripts in the invertebrate mollusk Octopus vulgaris ... Read more >>

Sci Rep (Scientific reports)
[2019, 9(1):15430]

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A Membrane-Targeted Photoswitch Potently Modulates Neuronal Firing

Mattia DiFrancesco, Francesco Lodola, Elisabetta Colombo, Luca Maragliano, Giuseppe Paternò, Mattia Bramini, Simone Cimò, Letizia Colella, Daniele Fazzi, Cyril Eleftheriou, José Fernando Maya-Vetencourt, Chiara Bertarelli, Guglielmo Lanzani, Fabio Benfenati,

ABSTRACT Optical technologies allowing modulation of neuronal activity at high spatio-temporal resolution are becoming paramount in neuroscience. We engineered novel light-sensitive molecules by adding polar groups to a hydrophobic backbone containing azobenzene and azepane moieties. We demonstrate that the probes stably partition into the plasma membrane, with affinity for lipid ... Read more >>

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Molecular Dynamics Simulations of Ion Selectivity in a Claudin-15 Paracellular Channel.

Giulio Alberini, Fabio Benfenati, Luca Maragliano,

Claudins are tissue-specific transmembrane proteins able to form junctions between two cells and regulate the flow of physiological solutes parallel to the cell walls, that is, the paracellular transport. Claudin-15 is highly expressed in the intestine where it forms efficient Na+ channels and Cl- barriers. However, the molecular details of ... Read more >>

J Phys Chem B (The journal of physical chemistry. B)
[2018, 122(48):10783-10792]

Cited: 4 times

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Closed-Locked and Apo-Resting State Structures of the Human α7 Nicotinic Receptor: A Computational Study.

Letizia Chiodo, Thérèse E Malliavin, Sergio Giuffrida, Luca Maragliano, Grazia Cottone,

Nicotinic acetylcholine receptors, belonging to the Cys-loop superfamily of ligand-gated ion channels (LGICs), are membrane proteins present in neurons and at neuromuscular junctions. They are responsible for signal transmission, and their function is regulated by neurotransmitters, agonists, and antagonists drugs. A detailed knowledge of their conformational transition in response to ... Read more >>

J Chem Inf Model (Journal of chemical information and modeling)
[2018, 58(11):2278-2293]

Cited: 1 time

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De novo mutations of the ATP6V1A gene cause developmental encephalopathy with epilepsy.

Anna Fassio, Alessandro Esposito, Mitsuhiro Kato, Hirotomo Saitsu, Davide Mei, Carla Marini, Valerio Conti, Mitsuko Nakashima, Nobuhiko Okamoto, Akgun Olmez Turker, Burcu Albuz, C Nur Semerci Gündüz, Keiko Yanagihara, Elisa Belmonte, Luca Maragliano, Keri Ramsey, Chris Balak, Ashley Siniard, Vinodh Narayanan, , Chihiro Ohba, Masaaki Shiina, Kazuhiro Ogata, Naomichi Matsumoto, Fabio Benfenati, Renzo Guerrini,

V-type proton (H+) ATPase (v-ATPase) is a multi-subunit proton pump that regulates pH homeostasis in all eukaryotic cells; in neurons, v-ATPase plays additional and unique roles in synapse function. Through whole exome sequencing, we identified de novo heterozygous mutations (p.Pro27Arg, p.Asp100Tyr, p.Asp349Asn, p.Asp371Gly) in ATP6V1A, encoding the A subunit of ... Read more >>

Brain (Brain : a journal of neurology)
[2018, 141(6):1703-1718]

Cited: 6 times

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Effect of Intercalated Water on Potassium Ion Transport through Kv1.2 Channels Studied via On-the-Fly Free-Energy Parametrization.

S Alexis Paz, Luca Maragliano, Cameron F Abrams,

We introduce a two-dimensional version of the method called on-the-fly free energy parametrization (OTFP) to reconstruct free-energy surfaces using Molecular Dynamics simulations, which we name OTFP-2D. We first test the new method by reconstructing the well-known dihedral angles free energy surface of solvated alanine dipeptide. Then, we use it to ... Read more >>

J Chem Theory Comput (Journal of chemical theory and computation)
[2018, 14(5):2743-2750]

Cited: 0 times

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Correction: A refined model of claudin-15 tight junction paracellular architecture by molecular dynamics simulations.

Giulio Alberini, Fabio Benfenati, Luca Maragliano,

[This corrects the article DOI: 10.1371/journal.pone.0184190.]. ... Read more >>

PLoS One (PloS one)
[2018, 13(2):e0193383]

Cited: 0 times

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A novel topology of proline-rich transmembrane protein 2 (PRRT2): Hints for an intracellular function at the synapse.

Pia Rossi, Bruno Sterlini, Enrico Castroflorio, Antonella Marte, Franco Onofri, Flavia Valtorta, Luca Maragliano, Anna Corradi, Fabio Benfenati,

J. Biol. Chem. (The Journal of biological chemistry)
[2018, 293(12):4581]

Cited: 1 time

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Optogenetic Modulation of Intracellular Signalling and Transcription: Focus on Neuronal Plasticity.

Cyril Eleftheriou, Fabrizia Cesca, Luca Maragliano, Fabio Benfenati, Jose Fernando Maya-Vetencourt,

Several fields in neuroscience have been revolutionized by the advent of optogenetics, a technique that offers the possibility to modulate neuronal physiology in response to light stimulation. This innovative and far-reaching tool provided unprecedented spatial and temporal resolution to explore the activity of neural circuits underlying cognition and behaviour. With ... Read more >>

(Journal of experimental neuroscience)
[2017, 11:1179069517703354]

Cited: 5 times

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Extended Phase-Space Methods for Enhanced Sampling in Molecular Simulations: A Review.

Hiroshi Fujisaki, Kei Moritsugu, Yasuhiro Matsunaga, Tetsuya Morishita, Luca Maragliano,

Molecular Dynamics simulations are a powerful approach to study biomolecular conformational changes or protein-ligand, protein-protein, and protein-DNA/RNA interactions. Straightforward applications, however, are often hampered by incomplete sampling, since in a typical simulated trajectory the system will spend most of its time trapped by high energy barriers in restricted regions of ... Read more >>

(Frontiers in bioengineering and biotechnology)
[2015, 3:125]

Cited: 9 times

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Temperature Accelerated Molecular Dynamics with Soft-Ratcheting Criterion Orients Enhanced Sampling by Low-Resolution Information.

Isidro Cortes-Ciriano, Guillaume Bouvier, Michael Nilges, Luca Maragliano, Thérèse E Malliavin,

Many proteins exhibit an equilibrium between multiple conformations, some of them being characterized only by low-resolution information. Visiting all conformations is a demanding task for computational techniques performing enhanced but unfocused exploration of collective variable (CV) space. Otherwise, pulling a structure toward a target condition biases the exploration in a ... Read more >>

J Chem Theory Comput (Journal of chemical theory and computation)
[2015, 11(7):3446-3454]

Cited: 6 times

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Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

Zeynab Mohammad Hosseini Naveh, Therese E Malliavin, Luca Maragliano, Grazia Cottone, Giovanni Ciccotti,

Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of ... Read more >>

PLoS ONE (PloS one)
[2014, 9(2):e88555]

Cited: 6 times

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Temperature-accelerated molecular dynamics gives insights into globular conformations sampled in the free state of the AC catalytic domain.

Edithe Selwa, Tru Huynh, Giovanni Ciccotti, Luca Maragliano, Thérèse E Malliavin,

The catalytic domain of the adenyl cyclase (AC) toxin from Bordetella pertussis is activated by interaction with calmodulin (CaM), resulting in cAMP overproduction in the infected cell. In the X-ray crystallographic structure of the complex between AC and the C terminal lobe of CaM, the toxin displays a markedly elongated ... Read more >>

Proteins (Proteins)
[2014, 82(10):2483-2496]

Cited: 9 times

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Identification and Expression of Acetylcholinesterase in Octopus vulgaris Arm Development and Regeneration: a Conserved Role for ACHE?

Sara Maria Fossati, Simona Candiani, Marie-Therese Nödl, Luca Maragliano, Maria Pennuto, Pedro Domingues, Fabio Benfenati, Mario Pestarino, Letizia Zullo,

Acetylcholinesterase (ACHE) is a glycoprotein with a key role in terminating synaptic transmission in cholinergic neurons of both vertebrates and invertebrates. ACHE is also involved in the regulation of cell growth and morphogenesis during embryogenesis and regeneration acting through its non-cholinergic sites. The mollusk Octopus vulgaris provides a powerful model ... Read more >>

Mol. Neurobiol. (Molecular neurobiology)
[2015, 52(1):45-56]

Cited: 9 times

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Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer.

Wei Jiang, Yun Luo, Luca Maragliano, Benoît Roux,

An extremely scalable computational strategy is described for calculations of the potential of mean force (PMF) in multidimensions on massively distributed supercomputers. The approach involves coupling thousands of umbrella sampling (US) simulation windows distributed to cover the space of order parameters with a Hamiltonian molecular dynamics replica-exchange (H-REMD) algorithm to ... Read more >>

J Chem Theory Comput (Journal of chemical theory and computation)
[2012, 8(11):4672-4680]

Cited: 29 times

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Direct imaging of DNA fibers: the visage of double helix.

Francesco Gentile, Manola Moretti, Tania Limongi, Andrea Falqui, Giovanni Bertoni, Alice Scarpellini, Stefania Santoriello, Luca Maragliano, Remo Proietti Zaccaria, Enzo di Fabrizio,

Direct imaging becomes important when the knowledge at few/single molecule level is requested and where the diffraction does not allow to get structural and functional information. Here we report on the direct imaging of double stranded (ds) λ-DNA in the A conformation, obtained by combining a novel sample preparation method ... Read more >>

Nano Lett. (Nano letters)
[2012, 12(12):6453-6458]

Cited: 16 times

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Mapping the network of pathways of CO diffusion in myoglobin.

Luca Maragliano, Grazia Cottone, Giovanni Ciccotti, Eric Vanden-Eijnden,

The pathways of diffusion of a CO molecule inside a myoglobin protein and toward the solvent are investigated. Specifically, the three-dimensional potential of mean force (PMF or free energy) of the CO molecule position inside the protein is calculated by using the single-sweep method in concert with fully resolved atomistic ... Read more >>

J. Am. Chem. Soc. (Journal of the American Chemical Society)
[2010, 132(3):1010-1017]

Cited: 53 times

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Single-sweep methods for free energy calculations.

Luca Maragliano, Eric Vanden-Eijnden,

A simple, efficient, and accurate method is proposed to map multidimensional free energy landscapes. The method combines the temperature-accelerated molecular dynamics (TAMD) proposed in [L. Maragliano and E. Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006)] with a variational reconstruction method using radial-basis functions for the representation of the free energy. ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2008, 128(18):184110]

Cited: 45 times

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String method in collective variables: minimum free energy paths and isocommittor surfaces.

Luca Maragliano, Alexander Fischer, Eric Vanden-Eijnden, Giovanni Ciccotti,

A computational technique is proposed which combines the string method with a sampling technique to determine minimum free energy paths. The technique only requires to compute the mean force and another conditional expectation locally along the string, and therefore can be applied even if the number of collective variables kept ... Read more >>

J Chem Phys (The Journal of chemical physics)
[2006, 125(2):24106]

Cited: 181 times

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