Molecular dynamics simulation approach to study UV-induced DNA damage Lo studio strutturale di sequenze di DNA, sensibili al danneggiamento fotochimico, mediante simulazioni di dinamica molecolare (MD)
Contact person Contatto: Luciana Esposito, luciana.esposito
cnr.it
Actors Attori: Luciana Esposito, luciana.espositocnr.it, Roberto Improta, robimpunina.it,
Research areas Aree di ricerca: Structural and electronic properties of nucleic acids Proprietà strutturali ed elettroniche degli acidi nucleici,
Contact person Contatto: Luciana Esposito, luciana.esposito
cnr.itActors Attori: Luciana Esposito, luciana.esposito
cnr.it, Roberto Improta, robimpunina.it, Description Descrizione:
The study of the interaction of nucleic acids with light is of paramountimportance not only for the general understanding of life functioning andevolution, but also for the implications in diseases such as skin cancer andfor the development of biomarkers and therapeutic tools. The absorption ofultraviolet (UV) radiation can cause different types of damage to nucleicacids. The most frequently induced mutagenic DNA lesions involve the formationof chemical bonds between neighboring pyrimidines, leading mainly to twofamilies of dimers: cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4)pyrimidone adducts (64PPs) [1]. Not only DNA sequences in single and doublestranded structures can be sensitive to UV radiation, but also G-quadruplex(G4) structures, which have been proven to undergo photoinduced reactions via production of highly reactiveGuanine radical species [2].
The study of the interaction of nucleic acids with light is of paramountimportance not only for the general understanding of life functioning andevolution, but also for the implications in diseases such as skin cancer andfor the development of biomarkers and therapeutic tools. The absorption ofultraviolet (UV) radiation can cause different types of damage to nucleicacids. The most frequently induced mutagenic DNA lesions involve the formationof chemical bonds between neighboring pyrimidines, leading mainly to twofamilies of dimers: cyclobutane pyrimidine dimers (CPD) and pyrimidine (6-4)pyrimidone adducts (64PPs) [1]. Not only DNA sequences in single and doublestranded structures can be sensitive to UV radiation, but also G-quadruplex(G4) structures, which have been proven to undergo photoinduced reactions via production of highly reactiveGuanine radical species [2].
A full understanding of the molecular basis of oxidative lesionsrequires the combination of experimental and theoretical techniques, which caninvestigate both ground- and excited-state conformations. In this context, classicalMD simulations have been used to study ground-states of DNA photoreactivesequences, in order to get insights into the population of conformers presentat the instant when a molecule absorbs UV photons.
We have studied DNA sequences particularly prone to photodimerization,also including C5-methylated cytosines (5mC): C5-methylation is an importantmodification playing a role in epigenetic regulation of gene expression andbeing correlated to about 40% of melanomas. MD simulations have allowed to findthe
Structural factors that favour photodimerization in DNA sequences ofdifferent lengths, containing TCG, T5mCG, and TT, within different moleculararchitectures (single and double stranded DNA) [3-5]. We have recently extendedour study to the analysis of the structural effects of Guanine radical cationson G-quadruplex structures formed by tracts of the human telomeric sequences.
In quest’ambito di ricerca abbiamo studiato sequenzedi DNA, particolarmente suscettibili alla fotodimerizzazione, che includonoanche basi di citosina metilate al C5: la metilazione è un’importante modificache gioca un ruolo nella regolazione epigenetica dell’espressione genica e cheè stata riconosciuta come associata a circa il 40% dei melanomi. La dinamicamolecolare ci ha permesso di evidenziare i fattori strutturali che favorisconola fotodimerizzazione in sequenze di DNA diversa lunghezza, contenenti TCG,T5mCG, TT e presenti in diverse architetture (duplex, singolo filamento) [3-5].Lo studio si è esteso recentemente all’analisi degli effetti strutturali dellaformazione di cationi radicali Guanina su architetture G-quadruplex formate datratti di sequenze G-rich del telomero umano.
Figures Figure:
Selected papers Lavori selezionati:
[1] Martinez-Fernandez,L., Banyasz, A., Esposito, L., Markovitsi, D., Improta, R. (2017).
UV-induced damage to DNA: effect of cytosine methylation on pyrimidinedimerization. Signal Transduct Target Ther. Jun 9;2:17021.
[2] Martinez-Fernandez,L., Esposito, L., Improta, R. (2020).
Studyingthe excited electronic states of guanine rich DNA quadruplexes by quantummechanical methods: main achievements and perspectives. Photochem. Photobiol.Sci 19(4):436-444.
[3] Banyasz, A., Esposito, L., Douki, T., Perron, M., Lepori, C.,Improta, R., Markovitsi, D. (2016) Effect of C5-Methylation of Cytosine on theUV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors. JPhys Chem B 120, 4232-42.
[4] Esposito,L., Banyasz, A., Douki, T., Perron, M., Markovitsi, D., Improta, R. (2014).
Effect of C5-Methylation of Cytosine on the Photoreactivity of DNA: AJoint Experimental and Computational Study of TCG Trinucleotides.
J. Am.Chem. Soc. 136, 10838-41.
Molecular dynamics simulation approach to study UV-induced DNA damage Lo studio strutturale di sequenze di DNA, sensibili al danneggiamento fotochimico, mediante simulazioni di dinamica molecolare (MD)
Molecular dynamics simulation approach to study UV-induced DNA damage Lo studio strutturale di sequenze di DNA, sensibili al danneggiamento fotochimico, mediante simulazioni di dinamica molecolare (MD)
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Milardi D, Sciacca MFM, Pappalardo M, Grasso DM, La Rosa C
* The Role Of Aromatic Side-Chains In Amyloid Growth And Membrane Interaction Of The Islet Amyloid Polypeptide Fragment Lanflvh (403 visite)
Eur Biophys J, 2011 Jan; 40(1): 1-12.
Impact Factor: 3.832
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Varriale S, Merlino A, Coscia MR, Mazzarella L, Oreste U
* An evolutionary conserved motif is responsible for Immunoglobulin heavy chain packing in the B cell membrane (312 visite)
Molecular Phylogenetics And Evolution (ISSN: 1055-7903), 2010 Dec; 57(3): 1238-1244.
Impact Factor: 3.889
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D'Auria G, Esposito C, Falcigno L, Calvanese L, Iaccarino E, Ruggiero A, Pedone C, Pedone E, Berisio R
* Dynamical properties of cold shock protein A from Mycobacterium tuberculosis (285 visite)
Biochem Biophys Res Commun (ISSN: 0006-291x, 1090-2104, 1090-2104electronic), 2010 Nov 26; 402(4): 693-698.
Impact Factor: 2.595
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Merlino A, Vergara A, Sica F, Aschi M, Amadei A, Di Nola A, Mazzarella L
* Free-Energy Profile for CO Binding to Separated Chains of Human and Trematomus newnesi Hemoglobin: Insights from Molecular Dynamics Simulations and Perturbed Matrix Method (278 visite)
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2010 May 27; 114(20): 7002-7008.
Impact Factor: 3.603
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Diana D, Ziaco B, Scarabelli G, Pedone C, Colombo G, D'Andrea LD, Fattorusso R
* Structural analysis of a helical peptide unfolding pathway (404 visite)
Chemistry (ISSN: 1521-3765, 0947-6539, 1521-3765electronic), 2010 May 10; 16(18): 5400-5407.
Impact Factor: 5.476
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Vitagliano L, Stanzione F, De Simone A, Esposito L
* Dynamics and Stability of Amyloid-Like Steric Zipper Assemblies with Hydrophobic Dry Interfaces (379 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2009 Dec; 91(12): 1161-1171.
Impact Factor: 2.605
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Pietropaolo A, Muccioli L, Zannoni C, Rizzarelli E
* Conformational preferences of the full chicken prion protein in solution and its differences with respect to mammals (319 visite)
Chemphyschem (ISSN: 1439-7641, 1439-4235, 1439-7641electronic), 2009 Jul 13; 10(9-10): 1500-1510.
Impact Factor: 3.453
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Vitagliano L, Esposito L, Pedone C, De Simone A
* Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association (539 visite)
Biochem Biophys Res Commun (ISSN: 1090-2104, 0006-291x, 1090-2104electronic), 2008 Dec 26; 377(4): 1036-1041.
Impact Factor: 2.648
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De Simone A, Vitagliano L, Berisio R
* Role of hydration in collagen triple helix stabilization (348 visite)
Biochem Biophys Res Commun (ISSN: 0006-291x), 2008 Jul 18; 372(1): 121-125.
Impact Factor: 2.648
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Esposito L, Paladino A, Pedone C, Vitagliano L
* Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations (372 visite)
Biophysical Journal (ISSN: 1542-0086, 0006-3495), 2008 May 15; 94(10): 4031-4040.
Impact Factor: 4.683
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Improta R, Berisio R, Vitagliano L
* Contribution of dipole-dipole interactions to the stability of the collagen triple helix (370 visite)
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2008 May; 17(5): 955-961.
Impact Factor: 3.115
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Vergara A, Merlino A, Pizzo E, D'Alessio G, Mazzarella L
* A novel method for detection of selenomethionine incorporation in protein crystals via Raman microscopy (286 visite)
Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking), 2008 Feb; 64: 167-171.
Impact Factor: 2.943
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Staiano M, Saviano M, Herman P, Grycznyski Z, Fini C, Varriale A, Parracino A, Kold AB, Rossi M, D'Auria S
* Time-resolved fluorescence spectroscopy and molecular dynamics simulations point out the effects of pressure on the stability and dynamics of the porcine odorant-binding protein (480 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2008; 89(4): 284-291.
Impact Factor: 2.823
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Vitale RM, Pedone C, Amodeo P, Antel J, Wurl M, Scozzafava A, Supuran CT, De Simone G
* Molecular modeling study for the binding of zonisamide and topiramate to the human mitochondrial carbonic anhydrase isoform VA (314 visite)
Bioorg Med Chem (ISSN: 0968-0896, 1464-3391, 1464-3391electronic), 2007 Jun 15; 15(12): 4152-4158.
Impact Factor: 2.662
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Ronga L, Langella E, Palladino P, Marasco D, Tizzano B, Saviano M, Pedone C, Improta R, Ruvo M
* Does Tetracycline Bind Helix 2 Of Prion? An Integrated Spectroscopical And Computational Study Of The Interaction Between The Antibiotic And Alpha Helix 2 Human Prion Protein Fragments (435 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2007 Feb 15; 66(3): 707-715.
Impact Factor: 3.354
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Pappalardo M, Milardi D, Grasso D, La Rosa C
* Steered molecular dynamics studies reveal different unfolding pathways of prions from mammalian and non-mammalian species (279 visite)
New J Chem (ISSN: 1144-0546), 2007; 31(6): 901-905.
Impact Factor: 2.651
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Esposito L, Pedone C, Vitagliano L
* Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation (568 visite)
P Natl Acad Sci Usa (ISSN: 0027-8424, 1091-6490, 0027-8424print), 2006 Sep 1; 103(31): 11533-11538.
Impact Factor: 9.643
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Langella E, Improta R, Crescenzi O, Barone V
* Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKα calculations and molecular dynamics simulations (457 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jul 1; 64(1): 167-177.
Impact Factor: 3.73
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Merlino A, Esposito L, Vitagliano L
* Polyglutamine Repeats And Beta-Helix Structure: Molecular Dynamics Study (470 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jun 1; 63(4): 918-927.
Impact Factor: 3.73
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* Water molecules as structural determinants among prions of low sequence identity (308 visite)
Febs Lett (ISSN: 0014-5793print, 0014-5793linking, 1873-3468electronic), 2006 May 1; 580(10): 2488-2494.
Impact Factor: 3.372
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De Capua A, Goodman M, Amino Y, Saviano M, Benedetti E
* Conformation analysis of aspartame-based sweeteners by NMR spectroscopy, molecular dynamics simulations, and X-ray diffraction studies (595 visite)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2006 Feb; 7(2): 377-387.
Impact Factor: 4.1
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* Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations (398 visite)
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2005 Mar 8; 44(9): 3358-3368.
Impact Factor: 3.848
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Merlino A, Ceruso MA, Vitagliano L, Mazzarella L
* Open interface and large quaternary structure movements in 3D domain swapped proteins: Insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease (525 visite)
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2005 Mar; 88(3): 2003-2012.
Impact Factor: 4.507
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Vergara A, Lorber B, Sauter C, Giege R, Zagari A
* Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology (299 visite)
Biophys Chem (ISSN: 0301-4622, 0301-4622linking), 2005; 118(2-3): 102-112.
Impact Factor: 1.925
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Langella E, Improta R, Barone V
* Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: Effect of protonation of histidine residues (334 visite)
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2004 Dec; 87(6): 3623-3632.
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* Structural features of the inactive and active states of the melanin-concentrating hormone receptors: Insights from molecular simulations (432 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2004 Sep 15; 56(3): 430-448.
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Merlino A, Vitagliano L, Ceruso MA, Mazzarella L
* Subtle functional collective motions in pancreatic-like ribonucleases: From ribonuclease A to angiogenin (349 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2003 Oct 1; 53(1): 101-110.
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Oliva R, Falcigno L, D'Auria G, Dettin M, Scarinci C, Pasquato A, Di Bello C, Paolillo L
* Structural investigation of the HIV-1 envelope glycoprotein gp160 cleavage site (347 visite)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2003 Sep 4; 4(8): 727-733.
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Pappalardo M, Milardi D, Grasso DM, La Rosa C
* Free energy perturbation and molecular dynamics calculations of copper binding to azurin (361 visite)
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2003 Apr 30; 24(6): 779-785.
Impact Factor: 3.186
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Merlino A, Vitagliano L, Ceruso M, Di Nola A, Mazzarella L
* Global and local motions in ribonuclease A: A molecular dynamics study (390 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2002 Nov 15; 65(4): 274-283.
Impact Factor: 2.372
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Oliva R, Leone M, Falcigno L, D'Auria G, Dettin M, Scarinci C, Di Bello C, Paolillo L
* Structural investigation of the HIV-1 envelope glycoprotein gp160 cleavage site (363 visite)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2002 Mar 15; 8(6): 1467-1473.
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Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
* Molecular interactions between nuclear factor κB (NF-κB) transcription factors and a PNA-DNA chimera mimicking NF-κB binding sites (393 visite)
Eur J Biochem (ISSN: 0014-2956, 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.
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Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
* Molecular interactions with nuclear factor kappaB (NF-kappaB) transcription factors of a PNA-DNA chimera mimicking NF-kappaB binding sites (404 visite)
Eur J Biochem (ISSN: 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.
Impact Factor: 4.779
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D'Andrea LD, Mazzeo M, Isernia C, Rossi F, Saviano M, Gallo P, Paolillo L, Pedone C
Solution conformational preferences of a peptidic analogue of a natural macrolide (354 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 1997; 42(3): 349-361.
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Saviano M, Rossi F, Pavone V, Di Blasio B, Pedone C
Molecular dynamics simulation in vacuo and in solution of [Aib5, 6-D- Ala8] Cyclolinopeptide A: A conformational and comparative study (418 visite)
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic, 0739-1102linking), 1992 Jun; 9(6): 1045-1060.
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Diaferia C, Sibillano T, Balasco N, Giannini C, Roviello V, Vitagliano L, Morelli G, Accardo A
* Hierarchical Analysis of Self-Assembled PEGylated Hexaphenylalanine Photoluminescent Nanostructures (365 visite)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2016 Nov 7; 22(46): 16586-16597.
Impact Factor: 5.317
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Nastri F, Chino M, Maglio O, Bhagi-damodaran A, Lu Y, Lombardi A
* Design and engineering of artificial oxygen-activating metalloenzymes (205 visite) (PDF 165 visite)
Chem Soc Rev (ISSN: 0306-0012, 1460-4744), 2016 Sep 21; 45(18): 5020-5054.
Impact Factor: 38.618
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Martinez-fernandez L, Pepino AJ, Segarra-marti J, Banyasz A, Garavelli M, Improta R
* Computing the Absorption and Emission Spectra of 5-Methylcytidine in Different Solvents: A Test-Case for Different Solvation Models (189 visite)
J Chem Theory Comput (ISSN: 1549-9618, 1549-9626electronic), 2016 Sep 13; 12(9): 4430-4439.
Impact Factor: 5.245
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Langella E, Calce E, Saviano M, De Luca S
* Structural identification of an HER2 receptor model binding pocket to optimize lead compounds: a combined experimental and computational approach (278 visite)
Mol Biosyst (ISSN: 1742-206x), 2016 Jun 21; 12(7): 2159-2167.
Impact Factor: 2.781
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Banyasz A, Esposito L, Douki T, Perron M, Lepori C, Improta R, Markovitsi D
* Effect of C5-Methylation of Cytosine on the UV-Induced Reactivity of Duplex DNA: Conformational and Electronic Factors (228 visite)
J Phys Chem B (ISSN: 1520-6106, 1520-5207), 2016 May 12; 120(18): 4232-4242.
Impact Factor: 3.177
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Calvanese L, Falcigno L, D'Auria G
* Essential Dynamics Analysis Captures the Concerted Motion of the Integrin-Binding Site in Jerdostatin, an RTS Disintegrin (363 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2015 Mar; 103(3): 158-166.
Impact Factor: 2.248
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Balasco N, Barone D, Vitagliano L
* Structural conversion of the transformer protein RfaH: new insights derived from protein structure prediction and molecular dynamics simulations (363 visite)
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic, 0739-1102linking), 2015 Jan 12; 33(10): 2173-2179.
Impact Factor: 2.3
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Vitiello G, Falanga A, Petruk AA, Merlino A, Fragneto G, Paduano L, Galdiero S, D'Errico G
* Fusion of raft-like lipid bilayers operated by a membranotropic domain of the HSV-type I glycoprotein gH occurs through a cholesterol-dependent mechanism (349 visite)
Soft Matter (ISSN: 1744-683x), 2015; 11(15): 3003-3016.
Impact Factor: 3.798
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Carbonniere P, Pouchan C, Improta R
* Intramolecular vibrational redistribution in the non-radiative excited state decay of uracil in the gas phase: An ab initio molecular dynamics study (310 visite)
Phys Chem Chem Phys (ISSN: 1463-9076, 1463-3907, 1463-9084electronic), 2015; 17(17): 11615-11626.
Impact Factor: 4.449
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Russo L, Palmieri M, Caso JV, Abrosca GD, Diana D, Malgieri G, Baglivo I, Isernia C, Pedone PV, Fattorusso R
* Towards understanding the molecular recognition process in prokaryotic zinc-finger domain (340 visite)
Eur J Med Chem (ISSN: 0223-5234, 1768-3254, 0223-5234linking), 2015; 91: 100-108.
Impact Factor: 3.902
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Correale S, de Paola I, Morgillo CM, Federico A, Zaccaro L, Pallante P, Galeone A, Fusco A, Pedone E, Luque FJ, Catalanotti B
* Structural Model of the hUbA1-UbcH10 Quaternary Complex: In Silico and Experimental Analysis of the Protein-Protein Interactions between E1, E2 and Ubiquitin (389 visite)
Plosone (ISSN: 1932-6203, 1932-6203electronic), 2014 Nov 6; 9(11): e112082-e112082.
Impact Factor: 3.234
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Pappalardo M, Shachaf N, Basile L, Milardi D, Zeidan M, Raiyn J, Guccione S, Rayan A
* Sequential Application of Ligand and Structure Based Modeling Approaches to Index Chemicals for Their hH(4)R Antagonism (338 visite)
Plosone (ISSN: 1932-6203, 1932-6203electronic), 2014 Oct 16; 9(10): e109340-e109340.
Impact Factor: 3.234
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Petruk AA, Vergara A, Marasco D, Bikiel D, Doctorovich F, Estrin DA, Merlino A
* Interaction between Proteins and Ir Based CO Releasing Molecules: Mechanism of Adduct Formation and CO Release (365 visite)
Inorg Chem (ISSN: 0020-1669, 1520-510x, 0020-1669linking), 2014 Oct 6; 53(19): 10456-10462.
Impact Factor: 4.762
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Balasco N, Pirone L, Smaldone G, Di Gaetano S, Esposito L, Pedone E, Vitagliano L
* Molecular recognition of Cullin3 by KCTDs: Insights from experimental and computational investigations (327 visite)
Bba-Gen Subjects (ISSN: 0925-4439, 0006-3002, 1570-9639), 2014 Jul; 1844(7): 1289-1298.
Impact Factor: 4.882
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Autiero I, Saviano M, Langella E
* Molecular Dynamics Simulations Of Pna-Pna And Pna-Dna Duplexes By The Use Of New Parameters Implemented In The Gromacs Package: A Conformational And Dynamics Study (403 visite)
Phys Chem Chem Phys (ISSN: 1463-9076, 1463-3907, 1463-9084electronic), 2014; 16(5): 1868-1874.
Impact Factor: 4.493
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Petruk AA, Varriale S, Coscia MR, Mazzarella L, Merlino A, Oreste U
* The Structure Of The Cd3 Zeta Zeta Transmembrane Dimer In Popc And Raft-Like Lipid Bilayer: A Molecular Dynamics Study (385 visite)
Bba-Gen Subjects (ISSN: 0005-2736, 0006-3002e, 0005-2736print), 2013 Nov; 1828(11): 2637-2645.
Impact Factor: 3.498
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Alcides Petruk A, Vergara A, Estrin D, Merlino A
* Molecular basis of the NO trans influence in quaternary T-state human hemoglobin: A computational study (341 visite)
Febs Lett (ISSN: 0014-5793, 0014-5793print, 1873-3468electronic), 2013 Sep 2; 587(15): 2393-2398.
Impact Factor: 3.341
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Vitiello G, Fragneto G, Petruk AA, Falanga A, Galdiero S, D'Ursi A, Merlino A, D'Errico G
* Cholesterol modulates the fusogenic activity of a membranotropic domain of the FIV glycoprotein gp36 (364 visite)
Soft Matter (ISSN: 1744-683x), 2013; 9(28): 6442-6456.
Impact Factor: 4.151
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Autiero I, Langella E, Saviano M
* Insights Into The Mechanism Of Interaction Between Trehalose-Conjugated Beta-Sheet Breaker Peptides And Aβ(1-42) Fibrils By Molecular Dynamics Simulations (477 visite)
Molecular Biosystems (ISSN: 1742-206x, 1742-2206), 2013; 9(11): 2835-2841.
Impact Factor: 3.18
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Caruso P, Causà M, Cimino P, Crescenzi O, D'Amore M, Improta R, Pavone M, Rega N
* Effects of molecular dynamics and solvation on the electronic structure of molecular probes (308 visite)
Theor Chem Acc (ISSN: 1432-881x), 2012 Apr; 131(4): 1211-1212.
Impact Factor: 2.233
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Merlino A, Vitiello G, Grimaldi M, Sica F, Busi E, Basosi R, D’Ursi A, Fragneto G, Paduano L, D’Errico G
* Destabilization of Lipid Membranes by a Peptide Derived from Glycoprotein gp36 of Feline Immunodeficiency Virus: A Combined Molecular Dynamics/Experimental Study (409 visite)
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2012 Jan 12; 116(1): 401-412.
Impact Factor: 3.607
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Boechi L, Marti MA, Vergara A, Sica F, Mazzarella L, Estrin DA, Merlino A
* Protonation of Histidine 55 Affects the Oxygen Access to Heme in the Alpha Chain of the Hemoglobin from the Antarctic Fish Trematomus bernacchii (351 visite)
Iubmb Life (ISSN: 1521-6543, 1521-6551), 2011 Mar; 63(3): 175-182.
Impact Factor: 3.514
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Milardi D, Sciacca MFM, Pappalardo M, Grasso DM, La Rosa C
* The Role Of Aromatic Side-Chains In Amyloid Growth And Membrane Interaction Of The Islet Amyloid Polypeptide Fragment Lanflvh (403 visite)
Eur Biophys J, 2011 Jan; 40(1): 1-12.
Impact Factor: 3.832
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Varriale S, Merlino A, Coscia MR, Mazzarella L, Oreste U
* An evolutionary conserved motif is responsible for Immunoglobulin heavy chain packing in the B cell membrane (312 visite)
Molecular Phylogenetics And Evolution (ISSN: 1055-7903), 2010 Dec; 57(3): 1238-1244.
Impact Factor: 3.889
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D'Auria G, Esposito C, Falcigno L, Calvanese L, Iaccarino E, Ruggiero A, Pedone C, Pedone E, Berisio R
* Dynamical properties of cold shock protein A from Mycobacterium tuberculosis (285 visite)
Biochem Biophys Res Commun (ISSN: 0006-291x, 1090-2104, 1090-2104electronic), 2010 Nov 26; 402(4): 693-698.
Impact Factor: 2.595
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Merlino A, Vergara A, Sica F, Aschi M, Amadei A, Di Nola A, Mazzarella L
* Free-Energy Profile for CO Binding to Separated Chains of Human and Trematomus newnesi Hemoglobin: Insights from Molecular Dynamics Simulations and Perturbed Matrix Method (278 visite)
J Phys Chem B (ISSN: 1520-6106, 1520-5207, 1520-5207electronic), 2010 May 27; 114(20): 7002-7008.
Impact Factor: 3.603
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Diana D, Ziaco B, Scarabelli G, Pedone C, Colombo G, D'Andrea LD, Fattorusso R
* Structural analysis of a helical peptide unfolding pathway (404 visite)
Chemistry (ISSN: 1521-3765, 0947-6539, 1521-3765electronic), 2010 May 10; 16(18): 5400-5407.
Impact Factor: 5.476
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Vitagliano L, Stanzione F, De Simone A, Esposito L
* Dynamics and Stability of Amyloid-Like Steric Zipper Assemblies with Hydrophobic Dry Interfaces (379 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2009 Dec; 91(12): 1161-1171.
Impact Factor: 2.605
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Pietropaolo A, Muccioli L, Zannoni C, Rizzarelli E
* Conformational preferences of the full chicken prion protein in solution and its differences with respect to mammals (319 visite)
Chemphyschem (ISSN: 1439-7641, 1439-4235, 1439-7641electronic), 2009 Jul 13; 10(9-10): 1500-1510.
Impact Factor: 3.453
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Vitagliano L, Esposito L, Pedone C, De Simone A
* Stability of single sheet GNNQQNY aggregates analyzed by replica exchange molecular dynamics: antiparallel versus parallel association (539 visite)
Biochem Biophys Res Commun (ISSN: 1090-2104, 0006-291x, 1090-2104electronic), 2008 Dec 26; 377(4): 1036-1041.
Impact Factor: 2.648
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De Simone A, Vitagliano L, Berisio R
* Role of hydration in collagen triple helix stabilization (348 visite)
Biochem Biophys Res Commun (ISSN: 0006-291x), 2008 Jul 18; 372(1): 121-125.
Impact Factor: 2.648
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Esposito L, Paladino A, Pedone C, Vitagliano L
* Insights into structure, stability, and toxicity of monomeric and aggregated polyglutamine models from molecular dynamics simulations (372 visite)
Biophysical Journal (ISSN: 1542-0086, 0006-3495), 2008 May 15; 94(10): 4031-4040.
Impact Factor: 4.683
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Improta R, Berisio R, Vitagliano L
* Contribution of dipole-dipole interactions to the stability of the collagen triple helix (370 visite)
Protein Sci (ISSN: 0961-8368, 1469-896xelectronic), 2008 May; 17(5): 955-961.
Impact Factor: 3.115
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Vergara A, Merlino A, Pizzo E, D'Alessio G, Mazzarella L
* A novel method for detection of selenomethionine incorporation in protein crystals via Raman microscopy (286 visite)
Acta Crystallogr D Biol Crystallogr (ISSN: 0907-4449, 0907-4449linking), 2008 Feb; 64: 167-171.
Impact Factor: 2.943
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Staiano M, Saviano M, Herman P, Grycznyski Z, Fini C, Varriale A, Parracino A, Kold AB, Rossi M, D'Auria S
* Time-resolved fluorescence spectroscopy and molecular dynamics simulations point out the effects of pressure on the stability and dynamics of the porcine odorant-binding protein (480 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2008; 89(4): 284-291.
Impact Factor: 2.823
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Vitale RM, Pedone C, Amodeo P, Antel J, Wurl M, Scozzafava A, Supuran CT, De Simone G
* Molecular modeling study for the binding of zonisamide and topiramate to the human mitochondrial carbonic anhydrase isoform VA (314 visite)
Bioorg Med Chem (ISSN: 0968-0896, 1464-3391, 1464-3391electronic), 2007 Jun 15; 15(12): 4152-4158.
Impact Factor: 2.662
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Ronga L, Langella E, Palladino P, Marasco D, Tizzano B, Saviano M, Pedone C, Improta R, Ruvo M
* Does Tetracycline Bind Helix 2 Of Prion? An Integrated Spectroscopical And Computational Study Of The Interaction Between The Antibiotic And Alpha Helix 2 Human Prion Protein Fragments (435 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2007 Feb 15; 66(3): 707-715.
Impact Factor: 3.354
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Pappalardo M, Milardi D, Grasso D, La Rosa C
* Steered molecular dynamics studies reveal different unfolding pathways of prions from mammalian and non-mammalian species (279 visite)
New J Chem (ISSN: 1144-0546), 2007; 31(6): 901-905.
Impact Factor: 2.651
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Esposito L, Pedone C, Vitagliano L
* Molecular dynamics analyses of cross-beta-spine steric zipper models: beta-sheet twisting and aggregation (568 visite)
P Natl Acad Sci Usa (ISSN: 0027-8424, 1091-6490, 0027-8424print), 2006 Sep 1; 103(31): 11533-11538.
Impact Factor: 9.643
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Langella E, Improta R, Crescenzi O, Barone V
* Assessing the acid-base and conformational properties of histidine residues in human prion protein (125-228) by means of pKα calculations and molecular dynamics simulations (457 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jul 1; 64(1): 167-177.
Impact Factor: 3.73
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Merlino A, Esposito L, Vitagliano L
* Polyglutamine Repeats And Beta-Helix Structure: Molecular Dynamics Study (470 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2006 Jun 1; 63(4): 918-927.
Impact Factor: 3.73
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De Simone A, Dodson GG, Fraternali F, Zagari A
* Water molecules as structural determinants among prions of low sequence identity (308 visite)
Febs Lett (ISSN: 0014-5793print, 0014-5793linking, 1873-3468electronic), 2006 May 1; 580(10): 2488-2494.
Impact Factor: 3.372
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De Capua A, Goodman M, Amino Y, Saviano M, Benedetti E
* Conformation analysis of aspartame-based sweeteners by NMR spectroscopy, molecular dynamics simulations, and X-ray diffraction studies (595 visite)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2006 Feb; 7(2): 377-387.
Impact Factor: 4.1
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Esposito L, Daggett V
* Insight into ribonuclease A domain swapping by molecular dynamics unfolding simulations (398 visite)
Biochemistry (ISSN: 0006-2960, 1520-4995, 1520-4995electronic), 2005 Mar 8; 44(9): 3358-3368.
Impact Factor: 3.848
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Merlino A, Ceruso MA, Vitagliano L, Mazzarella L
* Open interface and large quaternary structure movements in 3D domain swapped proteins: Insights from molecular dynamics simulations of the C-terminal swapped dimer of ribonuclease (525 visite)
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2005 Mar; 88(3): 2003-2012.
Impact Factor: 4.507
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Vergara A, Lorber B, Sauter C, Giege R, Zagari A
* Lessons from crystals grown in the Advanced Protein Crystallisation Facility for conventional crystallisation applied to structural biology (299 visite)
Biophys Chem (ISSN: 0301-4622, 0301-4622linking), 2005; 118(2-3): 102-112.
Impact Factor: 1.925
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Langella E, Improta R, Barone V
* Checking the pH-induced conformational transition of prion protein by molecular dynamics simulations: Effect of protonation of histidine residues (334 visite)
Biophysical Journal (ISSN: 0006-3495, 1542-0086), 2004 Dec; 87(6): 3623-3632.
Impact Factor: 4.585
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Vitale RM, Pedone C, De Benedetti PG, Fanelli F
* Structural features of the inactive and active states of the melanin-concentrating hormone receptors: Insights from molecular simulations (432 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2004 Sep 15; 56(3): 430-448.
Impact Factor: 4.429
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Merlino A, Vitagliano L, Ceruso MA, Mazzarella L
* Subtle functional collective motions in pancreatic-like ribonucleases: From ribonuclease A to angiogenin (349 visite)
Proteins (ISSN: 0887-3585, 1097-0134, 1097-0134electronic), 2003 Oct 1; 53(1): 101-110.
Impact Factor: 4.313
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Oliva R, Falcigno L, D'Auria G, Dettin M, Scarinci C, Pasquato A, Di Bello C, Paolillo L
* Structural investigation of the HIV-1 envelope glycoprotein gp160 cleavage site (347 visite)
Chembiochem (ISSN: 1439-4227, 1439-7633, 1439-7633electronic), 2003 Sep 4; 4(8): 727-733.
Impact Factor: 3.992
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Pappalardo M, Milardi D, Grasso DM, La Rosa C
* Free energy perturbation and molecular dynamics calculations of copper binding to azurin (361 visite)
J Comput Chem (ISSN: 0192-8651, 1096-987xelectronic), 2003 Apr 30; 24(6): 779-785.
Impact Factor: 3.186
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Merlino A, Vitagliano L, Ceruso M, Di Nola A, Mazzarella L
* Global and local motions in ribonuclease A: A molecular dynamics study (390 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2002 Nov 15; 65(4): 274-283.
Impact Factor: 2.372
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Oliva R, Leone M, Falcigno L, D'Auria G, Dettin M, Scarinci C, Di Bello C, Paolillo L
* Structural investigation of the HIV-1 envelope glycoprotein gp160 cleavage site (363 visite)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2002 Mar 15; 8(6): 1467-1473.
Impact Factor: 4.238
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Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
* Molecular interactions between nuclear factor κB (NF-κB) transcription factors and a PNA-DNA chimera mimicking NF-κB binding sites (393 visite)
Eur J Biochem (ISSN: 0014-2956, 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.
Impact Factor: 2.849
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Romanelli A, Pedone C, Saviano M, Bianchi N, Borgatti M, Mischiati C, Gambari R
* Molecular interactions with nuclear factor kappaB (NF-kappaB) transcription factors of a PNA-DNA chimera mimicking NF-kappaB binding sites (404 visite)
Eur J Biochem (ISSN: 0014-2956print, 0014-2956linking), 2001 Dec; 268(23): 6066-6075.
Impact Factor: 4.779
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D'Andrea LD, Mazzeo M, Isernia C, Rossi F, Saviano M, Gallo P, Paolillo L, Pedone C
Solution conformational preferences of a peptidic analogue of a natural macrolide (354 visite)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 1997; 42(3): 349-361.
Impact Factor: 2.425
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Saviano M, Rossi F, Pavone V, Di Blasio B, Pedone C
Molecular dynamics simulation in vacuo and in solution of [Aib5, 6-D- Ala8] Cyclolinopeptide A: A conformational and comparative study (418 visite)
J Biomol Struct Dyn (ISSN: 0739-1102, 1538-0254electronic, 0739-1102linking), 1992 Jun; 9(6): 1045-1060.
Impact Factor: 1.283
Dettagli Esporta in BibTeX Esporta in EndNote
87 Records (85 escludendo Abstract e Conferenze).
Impact factor totale: 361.639 (355.171 escludendo Abstract e Conferenze).
Impact factor a 5 anni totale: 336.114 (328.71 escludendo Abstract e Conferenze).
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