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Author Grazia Cottone

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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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Hepatitis B protein HBx binds the DLEU2 lncRNA to sustain cccDNA and host cancer-related gene transcription.

Debora Salerno, Letizia Chiodo, Vincenzo Alfano, Oceane Floriot, Grazia Cottone, Alexia Paturel, Matteo Pallocca, Marie-Laure Plissonnier, Safaa Jeddari, Laura Belloni, Mirjam Zeisel, Massimo Levrero, Francesca Guerrieri,

OBJECTIVE:The HBV HBx regulatory protein is required for transcription from the covalently closed circular DNA (cccDNA) minichromosome and affects the epigenetic control of both viral and host cellular chromatin. DESIGN:We explored, in relevant cellular models of HBV replication, the functional consequences of HBx interaction with DLEU2, a long non-coding RNA ... Read more >>

Gut (Gut)
[2020, :]

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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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Bioprotection Can Be Tuned with a Proper Protein/Saccharide Ratio: The Case of Solid Amorphous Matrices.

Sergio Giuffrida, Lorenzo Cordone, Grazia Cottone,

Saccharides, and in particular trehalose, are well known for their high efficiency in protecting biostructures against adverse environmental conditions. The protein dynamics is known to be highly inhibited in a low-water trehalose host medium, the inhibition being markedly dependent on the amount of residual water. Besides hydration, the protein/sugar ratio ... Read more >>

J Phys Chem B (The journal of physical chemistry. B)
[2018, 122(37):8642-8653]

Cited: 1 time

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Biopreservation of Myoglobin in Crowded Environment: A Comparison between Gelatin and Trehalose Matrixes.

Enrico F Semeraro, Sergio Giuffrida, Grazia Cottone, Antonio Cupane,

Biopreservation by sugar and/or polymeric matrixes is a thoroughly studied research topic with wide technological relevance. Ternary amorphous systems containing both saccharides and proteins are extensively exploited to model the in vivo biopreservation process. With the aim of disentangling the effect of saccharides and polypeptidic crowders (such as gelatin) on ... Read more >>

J Phys Chem B (The journal of physical chemistry. B)
[2017, 121(37):8731-8741]

Cited: 1 time

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The water association band as a marker of hydrogen bonds in trehalose amorphous matrices.

Sergio Giuffrida, Grazia Cottone, Lorenzo Cordone,

The relevant role played by residual water in modulating the dynamics and structure of a protein, a matrix and their coupling has been thoroughly studied in bioprotective amorphous saccharide matrices via experiments and simulations. In order to better characterize this residual water and the hydrogen bond structures in which it ... Read more >>

Phys Chem Chem Phys (Physical chemistry chemical physics : PCCP)
[2017, 19(6):4251-4265]

Cited: 0 times

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Ultrafast myoglobin structural dynamics observed with an X-ray free-electron laser.

Matteo Levantino, Giorgio Schirò, Henrik Till Lemke, Grazia Cottone, James Michael Glownia, Diling Zhu, Mathieu Chollet, Hyotcherl Ihee, Antonio Cupane, Marco Cammarata,

Light absorption can trigger biologically relevant protein conformational changes. The light-induced structural rearrangement at the level of a photoexcited chromophore is known to occur in the femtosecond timescale and is expected to propagate through the protein as a quake-like intramolecular motion. Here we report direct experimental evidence of such 'proteinquake' ... Read more >>

Nat Commun (Nature communications)
[2015, 6:6772]

Cited: 46 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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Protein thermal denaturation and matrix glass transition in different protein-trehalose-water systems.

Giuseppe Bellavia, Sergio Giuffrida, Grazia Cottone, Antonio Cupane, Lorenzo Cordone,

Biopreservation by saccharides is a widely studied issue due to its scientific and technological importance; in particular, ternary amorphous protein-saccharide-water systems are extensively exploited to model the characteristics of the in vivo biopreservation process. We present here a differential scanning calorimetry (DSC) study on amorphous trehalose-water systems with embedded different ... Read more >>

J Phys Chem B (The journal of physical chemistry. B)
[2011, 115(19):6340-6346]

Cited: 16 times

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Myoglobin embedded in saccharide amorphous matrices: water-dependent domains evidenced by small angle X-ray scattering.

Alessandro Longo, Sergio Giuffrida, Grazia Cottone, Lorenzo Cordone,

We report Small Angle X-ray Scattering (SAXS) measurements performed on samples of carboxy-myoglobin (MbCO) embedded in low-water trehalose glasses. Results showed that, in such samples, "low-protein" trehalose-water domains are present, surrounded by a protein-trehalose-water background; such finding is supported by Infrared Spectroscopy (FTIR) measurements. These domains, which do not appear ... Read more >>

Phys Chem Chem Phys (Physical chemistry chemical physics : PCCP)
[2010, 12(25):6852-6858]

Cited: 5 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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Thermal denaturation of myoglobin in water--disaccharide matrixes: relation with the glass transition of the system.

Giuseppe Bellavia, Grazia Cottone, Sergio Giuffrida, Antonio Cupane, Lorenzo Cordone,

Proteins embedded in glassy saccharide systems are protected against adverse environmental conditions [Crowe et al. Annu. Rev. Physiol. 1998, 60, 73-103]. To further characterize this process, we studied the relationship between the glass transition temperature of the protein-containing saccharide system (T(g)) and the temperature of thermal denaturation of the embedded ... Read more >>

J Phys Chem B (The journal of physical chemistry. B)
[2009, 113(33):11543-11549]

Cited: 11 times

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Density functional theory study of the trans-trans-cis (TTC)-->trans-trans-trans (TTT) isomerization of a photochromic spiropyran merocyanine.

Grazia Cottone, Rosina Noto, Gianfranco La Manna,

Density Functional Theory (DFT) calculations have been performed on the TTC-->TTT isomerization reaction of the open forms of the 1',3'-dihydro-8-bromo-6-nitro-1',3',3'-trimethylspiro[2H-1-benzopyran-2,2'-(2H)indole (8-Br-6-nitro-BIPS) system. The calculations were carried out in vacuo and in methylene chloride solution at different temperatures. Results are compared with the available experimental values of free energy difference and ... Read more >>

Molecules (Molecules (Basel, Switzerland))
[2008, 13(6):1246-1252]

Cited: 4 times

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GFP-mut2 proteins in trehalose-water matrixes: spatially heterogeneous protein-water-sugar structures.

Laura D'Alfonso, Maddalena Collini, Fabio Cannone, Giuseppe Chirico, Barbara Campanini, Grazia Cottone, Lorenzo Cordone,

We report investigations on the properties of nanoenvironments around single-GFP-mut2 proteins in trehalose-water matrixes. Single-GFPmut2 molecules embedded in thin trehalose-water films were characterized in terms of their fluorescence brightness, bleaching dynamics, excited state lifetime, and fluorescence polarization. For each property, sets of approximately 100-150 single molecules have been investigated as ... Read more >>

Biophys. J. (Biophysical journal)
[2007, 93(1):284-293]

Cited: 1 time

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Role of solvent on protein-matrix coupling in MbCO embedded in water-saccharide systems: a Fourier transform infrared spectroscopy study.

Sergio Giuffrida, Grazia Cottone, Lorenzo Cordone,

Embedding protein in sugar systems of low water content enables one to investigate the protein dynamic-structure function in matrixes whose rigidity is modulated by varying the content of residual water. Accordingly, studying the dynamics and structure thermal evolution of a protein in sugar systems of different hydration constitutes a tool ... Read more >>

Biophys. J. (Biophysical journal)
[2006, 91(3):968-980]

Cited: 18 times

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A comparative study of carboxy myoglobin in saccharide-water systems by molecular dynamics simulation.

Grazia Cottone,

Results from room-temperature molecular dynamics simulation on a system containing carboxy-myoglobin, water, and maltose molecules are reported. Protein atomic fluctuations, protein-solvent and solvent-solvent hydrogen bonding have been analyzed and compared to the ones in trehalose-water and sucrose-water systems (Proteins 2005, 59, 291-302). Results help in rationalizing, at a molecular level, ... Read more >>

J Phys Chem B (The journal of physical chemistry. B)
[2007, 111(13):3563-3569]

Cited: 13 times

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Internal dynamics and protein-matrix coupling in trehalose-coated proteins.

Lorenzo Cordone, Grazia Cottone, Sergio Giuffrida, Gerardo Palazzo, Giovanni Venturoli, Cristiano Viappiani,

We review recent studies on the role played by non-liquid, water-containing matrices on the dynamics and structure of embedded proteins. Two proteins were studied, in water-trehalose matrices: a water-soluble protein (carboxy derivative of horse heart myoglobin) and a membrane protein (reaction centre from Rhodobacter sphaeroides). Several experimental techniques were used: ... Read more >>

Biochim. Biophys. Acta (Biochimica et biophysica acta)
[2005, 1749(2):252-281]

Cited: 38 times

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