Binding of Zn(II) to Tropomyosin Receptor Kinase A in Complex with Its Cognate Nerve Growth Factor: Insights from Molecular Simulation and in Vitro Essays (279 views)
Acs Chem Neurosci (ISSN: 1948-7193electronic, 1948-7193linking), 2018 Jan 12; N/D: N/D-N/D.
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Paper type: Journal Article,
Impact factor: 4.348, 5-year impact factor: 4.51
Url: Not available.
Keywords: Metadynamics Simulation, Metal Complexes, Metal Ions, Neurotrophin, Peptide,
Affiliations:
*** IBB - CNR ***
Dipartimento di Scienze della Salute, Universita di Catanzaro , Viale Europa, 88100 Catanzaro, Italy., IBB-CNR , UOS Catania, via Paolo Gaifami 18, 95126 Catania, Italy., Dipartimento di Scienze Chimiche, Universita degli Studi di Catania , Viale Andrea Doria 6, 95125 Catania, Italy., Institute for Computational Biomedicine (IAS-5/INM-9/INM-9) Forschungszentrum Julich , 52425 Julich, Germany., Department of Physics, RWTH Aachen University , 52056 Aachen, Germany., Department of Pharmacy, University of Pisa , Via Bonanno Pisano 6, 56126 Pisa, Italy.,
References:
Not available.
Acs Chem Neurosci (ISSN: 1948-7193electronic, 1948-7193linking), 2018 Jan 12; N/D: N/D-N/D.
Export to BibTeX Export to EndNote
Paper type: Journal Article,
Impact factor: 4.348, 5-year impact factor: 4.51
Url: Not available.
Keywords: Metadynamics Simulation, Metal Complexes, Metal Ions, Neurotrophin, Peptide,
Affiliations:
*** IBB - CNR ***
Dipartimento di Scienze della Salute, Universita di Catanzaro , Viale Europa, 88100 Catanzaro, Italy., IBB-CNR , UOS Catania, via Paolo Gaifami 18, 95126 Catania, Italy., Dipartimento di Scienze Chimiche, Universita degli Studi di Catania , Viale Andrea Doria 6, 95125 Catania, Italy., Institute for Computational Biomedicine (IAS-5/INM-9/INM-9) Forschungszentrum Julich , 52425 Julich, Germany., Department of Physics, RWTH Aachen University , 52056 Aachen, Germany., Department of Pharmacy, University of Pisa , Via Bonanno Pisano 6, 56126 Pisa, Italy.,
References:
Not available.
Binding of Zn(II) to Tropomyosin Receptor Kinase A in Complex with Its Cognate Nerve Growth Factor: Insights from Molecular Simulation and in Vitro Essays
The binding of the human nerve growth factor (NGF) protein to tropomyosin receptor kinase A (TrkA) is associated with Alzhemeir's development. Owing to the large presence of zinc(II) ions in the synaptic compartments, the zinc ions might be bound to the complex in vivo. Here, we have identified a putative zinc binding site using a combination of computations and experiments. First, we have predicted structural features of the NGF/TrkA complex in an aqueous solution by molecular simulation. Metadynamics free energy calculations suggest that these are very similar to those in the X-ray structure. Here, the "crab" structure of the NGF shape binds tightly to two TrkA "pincers". Transient conformations of the complex include both more extended and more closed conformations. Interestingly, the latter features facial histidines (His60 and His61) among the N-terminal D1-D3 domains, each of which is a potential binding region for biometals. This suggests the presence of a four-His Zn binding site connecting the two chains. To address this issue, we investigated the binding of a D1-D3 domains' peptide mimic by stability constant and nuclear magnetic resonance measurements, complemented by density functional theory-based calculations. Taken together, these establish unambiguously a four-His coordination of the metal ion in the model systems, supporting the presence of our postulated binding site in the NGF/TrkA complex.
The binding of the human nerve growth factor (NGF) protein to tropomyosin receptor kinase A (TrkA) is associated with Alzhemeir's development. Owing to the large presence of zinc(II) ions in the synaptic compartments, the zinc ions might be bound to the complex in vivo. Here, we have identified a putative zinc binding site using a combination of computations and experiments. First, we have predicted structural features of the NGF/TrkA complex in an aqueous solution by molecular simulation. Metadynamics free energy calculations suggest that these are very similar to those in the X-ray structure. Here, the "crab" structure of the NGF shape binds tightly to two TrkA "pincers". Transient conformations of the complex include both more extended and more closed conformations. Interestingly, the latter features facial histidines (His60 and His61) among the N-terminal D1-D3 domains, each of which is a potential binding region for biometals. This suggests the presence of a four-His Zn binding site connecting the two chains. To address this issue, we investigated the binding of a D1-D3 domains' peptide mimic by stability constant and nuclear magnetic resonance measurements, complemented by density functional theory-based calculations. Taken together, these establish unambiguously a four-His coordination of the metal ion in the model systems, supporting the presence of our postulated binding site in the NGF/TrkA complex.
Binding of Zn(II) to Tropomyosin Receptor Kinase A in Complex with Its Cognate Nerve Growth Factor: Insights from Molecular Simulation and in Vitro Essays
| ▼ Characterization of neurotoxic and neuroprotective factors by using computational methodologies |
| ▼ New peptide–based molecules as NGF mimetics in the therapy of neurological dysfunctions |
Binding of Zn(II) to Tropomyosin Receptor Kinase A in Complex with Its Cognate Nerve Growth Factor: Insights from Molecular Simulation and in Vitro Essays
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Impact Factor: 5.771
View Export to BibTeX Export to EndNote
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Impact Factor: 5.731
View Export to BibTeX Export to EndNote
Bellia F, GrassoG
* The role of copper(II) and zinc(II) in the degradation of human and murine IAPP by insulin-degrading enzyme (760 views)
J Mass Spectrom (ISSN: 1076-5174, 1096-9888), 2014; 49(4): 274-279.
Impact Factor: 2.379
View Export to BibTeX Export to EndNote
Palmieri M, Malgieri G, Russo L, Baglivo I, Esposito S, Netti F, Del Gatto A, De Paola I, Zaccaro L, Pedone PV, Isernia C, Milardi D, Fattorusso R
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Impact Factor: 11.444
View Export to BibTeX Export to EndNote
Di Natale G, Osz K, Kállay C, Pappalardo G, Sanna D, Impellizzeri G, Sóvágó I, Rizzarelli E
* Affinity, speciation, and molecular features of copper(II) complexes with a prion tetraoctarepeat domain in aqueous solution: insights into old and new results (585 views)
Chemistry (ISSN: 1521-3765, 0947-6539, 1521-3765electronic), 2013 Mar 11; 19(11): 3751-3761.
Impact Factor: 5.696
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Grasso G, Spoto G
* Plasmonics for the study of metal ion-protein interactions (652 views)
Anal Bioanal Chem (ISSN: 1618-2642), 2013 Feb; 405(6): 1833-1843.
Impact Factor: 3.578
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Arena G, Attanasio F, Zhang D, Yang Y, Bartsch RA, Sgarlata C
* Selective sensing of Hg2+ by a proton-ionizable calix[4]arene fluoroionophore (455 views)
Anal Bioanal Chem (ISSN: 1618-2642), 2013 Jan; 405(2-3): 1133-1137.
Impact Factor: 3.578
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Bellia F, Pietropaolo A, Grasso G
* Formation of insulin fragments by insulin-degrading enzyme: The role of zinc(II) and cystine bridges (632 views)
J Mass Spectrom (ISSN: 1076-5174, 1096-9888), 2013; 48(2): 135-140.
Impact Factor: 2.709
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Faiella M, Maglio O, Nastri F, Lombardi A, Lista L, Hagen WR, Pavone V
* De Novo Design, Synthesis and Characterisation of MP3, A New Catalytic Four-Helix Bundle Hemeprotein (580 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2012 Dec 7; 18(50): 15960-15971.
Impact Factor: 5.831
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Travaglia A, La Mendola D, Magrì A, Nicoletti VG, Pietropaolo A, Rizzarelli E
* Copper, BDNF and Its N-terminal domain: inorganic features and biological perspectives (676 views)
Chemistry (ISSN: 1521-3765, 0947-6539, 1521-3765electronic), 2012 Dec 3; 18(49): 15618-15631.
Impact Factor: 5.831
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Grasso G, Salomone F, Tundo GR, Pappalardo G, Ciaccio C, Spoto G, Pietropaolo A, Coletta M, Rizzarelli E
* Metal ions affect insulin-degrading enzyme activity (708 views)
J Chem Res (ISSN: 1873-3344, 0162-0134, 0162-0134print), 2012 Dec; 117: 351-358.
Impact Factor: 3.197
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Hua Y, Changenet-Barret P, Improta R, Vaya I, Gustavsson T, Kotlyar AB, Zikich D, Sket P, Plavec J, Markovitsi D
* Cation effect on the electronic excited states of guanine nanostructures studied by time-resolved fluorescence spectroscopy (509 views)
J Phys Chem C (ISSN: 1932-7447), 2012 Jul 12; 116(27): 14682-14689.
Impact Factor: 4.814
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Santoro AM, Lo Giudice MC, D'Urso A, Lauceri R, Purrello R, Milardi D
* Cationic porphyrins are reversible proteasome inhibitors (670 views)
J Am Chem Soc (ISSN: 0002-7863, 0002-2786, 1520-5126), 2012 Jun 27; 134(25): 10451-10457.
Impact Factor: 10.677
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Travaglia A, Pietropaolo A, La Mendola D, Nicoletti VG, Rizzarelli E
* The inorganic perspectives of neurotrophins and Alzheimer's disease (869 views)
J Chem Res (ISSN: 1873-3344, 0162-0134, 0162-0134print), 2012 Jun; 111: 130-137.
Impact Factor: 3.197
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Arena G, Fattorusso R, Grasso G, Grasso GI, Isernia C, Malgieri G, Milardi D, Rizzarelli E
* Zinc(II) complexes of ubiquitin: speciation, affinity and binding features (836 views)
Chemistry (ISSN: 1521-3765, 0947-6539, 1521-3765electronic), 2011 Oct 4; 17(41): 11596-11603.
Impact Factor: 5.925
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Grasso GI, Arena G, Bellia F, Maccarrone G, Parrinello M, Pietropaolo A, Vecchio G, Rizzarelli E
* Intramolecular weak interactions in the thermodynamic stereoselectivity of copper(II) complexes with carnosine-trehalose conjugates (654 views)
Chemistry (ISSN: 1521-3765, 0947-6539, 1521-3765electronic), 2011 Sep 16; 17(34): 9448-9455.
Impact Factor: 5.925
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Kállay C, Turi I, Timári S, Nagy Z, Sanna D, Pappalardo G, De Bona P, Rizzarelli E, Sóvágó I
* The effect of point mutations on copper(II) complexes with peptide fragments encompassing the 106-114 region of human prion protein (835 views)
Monatshefte Fur Chemie (ISSN: 0026-9247), 2011 Apr; 142(4): 411-419.
Impact Factor: 1.532
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Grasso G, Pietropaolo A, Spoto G, Pappalardo G, Tundo GR, Ciaccio C, Coletta M, Rizzarelli E
* Copper(I) and Copper(II) Inhibit A beta Peptides Proteolysis by Insulin-Degrading Enzyme Differently: Implications for Metallostasis Alteration in Alzheimer's Disease (696 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2011 Feb 25; 17(9): 2752-2762.
Impact Factor: 5.925
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Grasso G, La Mendola D, Milardi D
Metal Ions and the Clearance of Misfolded Proteins (292 views)
Neurodegeneration (ISSN: 2041-3203), 2011; (7): N/D-N/D.
Impact Factor: 2.082
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La Mendola D, Magrì A, Vagliasindi LI, Hansson Ö, Bonomo RP, Rizzarelli E
* Copper(II) complex formation with a linear peptide encompassing the putative cell binding site of angiogenin (567 views)
Dalton T (ISSN: 1477-9234, 1477-9226, 1477-9234electronic), 2010 Nov 28; 39(44): 10678-10684.
Impact Factor: 3.647
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Stanzione F, Esposito L, Paladino A, Pedone C, Morelli G, Vitagliano L
* Role of the conformational versatility of the neurotrophin N-terminal regions in their recognition by Trk receptors (665 views)
Biophys J (ISSN: 1542-0086, 0006-3495, 0006-3495linking), 2010 Oct 6; 99(7): 2273-2278.
Impact Factor: 4.218
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Józsa E, Osz K, Kállay C, de Bona P, Damante CA, Pappalardo G, Rizzarelli E, Sóvágó I
* Nickel(ii) and mixed metal complexes of amyloid-β N-terminus (577 views)
Dalton T (ISSN: 1477-9226, 1477-9234, 1477-9234electronic), 2010 Sep 14; 39(30): 7046-7053.
Impact Factor: 3.647
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La Mendola D, Magrì A, Campagna T, Campitiello MA, Raiola L, Isernia C, Hansson O, Bonomo RP, Rizzarelli E
* A doppel alpha-helix peptide fragment mimics the copper(II) interactions with the whole protein (1373 views)
Chemistry (ISSN: 0947-6539, 1521-3765, 1521-3765electronic), 2010 Jun 1; 16(21): 6212-6223.
Impact Factor: 5.476
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Torres Martin De Rosales R, Faiella M, Farquhar E, Que L, J , Andreozzi C, Pavone V, Maglio O, Nastri F, Lombardi A
* Spectroscopic and metal-binding properties of DF3: an artificial protein able to accommodate different metal ions (428 views)
J Biol Inorg Chem (ISSN: 1432-1327electronic, 0949-8257linking, 0949-8257print), 2010 Jun; 15(5): 717-728.
Impact Factor: 3.287
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Jozsa E, Hosz K, Kallay C, De Bona P, Damante CA, Pappalardo G, Rizzarelli E, Sovago I
* Nickel (ii) And Mixed Metal Complexes Of Amyloid-B N-Terminus. Results Of Potentiometric And Spectroscopic Studies On The Binary Nickel (ii) And Mixed Metal Nickel (ii)-Copper (ii) And Nickel (ii)-Copper (ii)-Zinc (ii) Complexes Of Peptide Fragments (685 views)
Dalton T (ISSN: 1477-9226, 1477-9234, 1477-9234electronic), 2010; 39(30): 7046-7053.
Impact Factor: 3.647
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Bellia F, La Mendola D, Pedone C, Rizzarelli E, Saviano M, Vecchio G
* Selectively functionalized cyclodextrins and their metal complexes (758 views)
Chem Soc Rev (ISSN: 1460-4744, 0306-0012, 1460-4744electronic), 2009 Sep; 38(9): 2756-2781.
Impact Factor: 20.086
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Grasso G, Rizzarelli E, Spoto G
* The proteolytic activity of insulin-degrading enzyme: a mass spectrometry study (717 views)
J Mass Spectrom (ISSN: 1096-9888, 1076-5174), 2009 May; 44(5): 735-741.
Impact Factor: 3.411
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Di Natale G, Damante CA, Nagy Z, Osz K, Pappalardo G, Rizzarelli E, Sóvágó I
* Copper(II) binding to two novel histidine-containing model hexapeptides: evidence for a metal ion driven turn conformation (545 views)
J Chem Res (ISSN: 1873-3344, 0162-0134, 0162-0134print), 2008 Nov; 102(11): 2012-2019.
Impact Factor: 3.133
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Hilvo M, Baranauskiene L, Salzano AM, Scaloni A, Matulis D, Innocenti A, Scozzafava A, Monti SM, Di Fiore A, De Simone G, Lindfors M, Janis J, Valjakka J, Pastorekova S, Pastorek J, Kulomaa MS, Nordlund HR, Supuran CT, Parkkila S
* Biochemical characterization of CA IX, one of the most active carbonic anhydrase isozymes (896 views)
Jbc Papers (ISSN: 0021-9258, 1083-351x, 0021-9258linking), 2008 Oct 10; 283(41): 27799-27809.
Impact Factor: 5.52
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Sciacca MFM, Pappalardo M, Milardi D, Grasso DM, La Rosa C
* Calcium-Activated Membrane Interaction Of The Islet Amyloid Polypeptide: Implications In The Pathogenesis Of Type Ii Diabetes Mellitus (1280 views)
Arch Biochem Biophys, 2008 Sep 15; 65(1-2): 291-298.
Impact Factor: 3.043
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Pappalardo M, Sciacca MFM, Milardi D, Grasso DM, La Rosa C
* Thermodynamics Of Azurin Folding: The Role Of The Copper Ion (424 views)
Journal Of Thermal Analysis And Calorimetry (ISSN: 1388-6150), 2008 Sep; 93(2): 575-581.
Impact Factor: 1.63
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Milardi D, Arnesano F, Grasso G, Magrì A, Tabbì G, Scintilla S, Natile G, Rizzarelli E
* Ubiquitin stability and the Lys63-linked polyubiquitination site are compromised on copper binding (505 views)
Angew Chem Int Ed (ISSN: 1433-7851, 1521-3773electronic, 1433-7851linking), 2007; 46(42): 7993-7995.
Impact Factor: 10.031
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Joszal V, Nagy Z, Osz K, Sanna D, Di Natale G, La Mendola D, Pappalardo G, Rizzarelli E, Sovago I
* Transition metal complexes of terminally protected peptides containing histidyl residues (678 views)
J Chem Res (ISSN: 0162-0134, 1873-3344, 0162-0134print), 2006 Sep; 100(8): 1399-1409.
Impact Factor: 2.654
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Pappalardo G, Impellizzeri G, Campagna T
* Copper(II) binding of prion protein's octarepeat model peptides (668 views)
Inorg Chim Acta (ISSN: 0020-1693), 2004; 357(1): 185-194.
Impact Factor: 1.554
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D'Auria G, Flores G, Falcigno L, Oliva R, Vacatello M, Corsaro MM, Parrilli M, Paolillo L
* Hyaluronate tetrasaccharide-Cu(II) interaction: A NMR study (437 views)
Biopolymers (ISSN: 0006-3525, 0006-6352, 0006-3525print), 2003 Oct; 70(2): 260-269.
Impact Factor: 2.733
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43 Records (42 excluding Abstracts).
Total impact factor: 212.741 (210.659 excluding Abstracts).
Total 5 year impact factor: 212.042 (209.796 excluding Abstracts).
Total impact factor: 212.741 (210.659 excluding Abstracts).
Total 5 year impact factor: 212.042 (209.796 excluding Abstracts).
279 views. Last view on Sunday 01 December 2024, 7:17:02
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