Publications

47. Pietropaolo A, Nakano T. Learning how planarization can affect dichroic patterns in polyfluorenes.
Special issue in honor and memory of Prof. Koji Nakanishi.
Chirality, 2020 32, 661-666.

46. Patrizi B, Cozza C, Pietropaolo A, Foggi P, Siciliani de Cumis M.
Synergistic Approach of Ultrafast Spectroscopy and Molecular Simulations in the Characterization of Intramolecular Charge Transfer in Push-Pull Molecules.

Molecules. 2020, 25, pii: E430.

45. Santoro AM, Lanza V, Bellia F, Sbardella D, Tundo GR, Cannizzo A, Grasso G, Arizzi M, Nicoletti VG, Alcaro S, Costa G, Pietropaolo A, Malgieri G, D’Abrosca G, Fattorusso R, García-Viñuales S, Ahmed IMM, Coletta M, Milardi D. Pyrazolones Activate the Proteasome by Gating Mechanisms and Protect Neuronal Cells from β‐Amyloid Toxicity.
ChemMedChem. 2020, 15, 302-316.

44. Magrì A, Tabbì G, Cucci LM, Satriano C, Pietropaolo A, Malgieri G, Isernia C, La Mendola D.
The curious case of opossum prion: a physicochemical study on copper(ii) binding to the bis-decarepeat fragment from the protein N-terminal domain.

Dalton Trans. 2019 48, 17533-17543.

43. Bonomi et al. PLUMED consortium. Promoting transparency and reproducibility in enhanced molecular simulations. Nature Methods. 2019 16, 670-673.

42. Naletova I, Satriano C, Pietropaolo A, Gianì F, Pandini G, Triaca V, Amadoro G, Latina V, Calissano P, Travaglia A, Nicoletti VG, La Mendola D, Rizzarelli E.
The Copper(II)-Assisted Connection between NGF and BDNF by Means of Nerve Growth Factor-Mimicking Short Peptides.
Cells 2019 8, E301.

41. Bellia F, Lanza V, García-Viñuales S, Ahmed IMN, Pietropaolo A, Iacobucci C, Malgieri G, D’Abrosca G, Fattorusso R, Nicoletti VG, Sbardella D, Tundo GR, Coletta M, Pirone L, Pedone E, Calcagno D, Grasso G, Milardi D.
Ubiquitin binds the amyloid β peptide and interferes with its clearance pathways.

Chem. Sci. 2019,10:2732-

40. Cozza C, Bonomi M, Pietropaolo A.
A Versatile Computational Strategy To Characterize the Free-Energy Landscape of Excited States in Oligofluorenes.

J. Chem Theory Comput. 2018,14:5441–5445.

39. Pietropaolo A, Cozza C, Zhang Z, Nakano T.  
Temperature-dependent UV absorption of biphenyl based on intra-molecular rotation investigated within a combined experimental and TD-DFT approach.

Liq. Cryst.  2018, 45, 2048-2053.

38. Pietropaolo A, Magrì A, Greco V, Losasso V, La Mendola D, Sciuto S, Carloni P, Rizzarelli E.
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.

ACS Chem Neurosci. 2018,16:1095-1103.

37. Magrì A, Pietropaolo A, Tabbì G, La Mendola D, Rizzarelli E.
From Peptide Fragments to Whole Protein: Copper(II) Load and Coordination Features of IAPP.

Chem. Eur. J.2017,23:17898-17902.

36. Pietropaolo A, Tang S, Raymo FM.
Free-energy predictions and absorption spectra calculations for supramolecular nanocarriers and their photoactive cargo.

Nanoscale, 2017,9:4989-4994.

35. Oliveri V, Pietropaolo A, Sgarlata C, Vecchio G.
Zinc Complexes of Cyclodextrin-bearing 8-Hydroxyquinoline Ligands: a Comparative Study.
Chem Asian J. 2017, 12:110-115.

34. Pandini G, Satriano C, Pietropaolo A, Gianì F, Travaglia A, La Mendola D, Nicoletti VG, Rizzarelli E.
The Inorganic Side of NGF: Copper(II) and Zinc(II) Affect the NGF Mimicking Signaling of the N-Terminus Peptides Encompassing the Recognition Domain of TrkA Receptor.

Front Neurosci. 2016, 10:569.

33. Naletova I, Nicoletti VG, Milardi D, Pietropaolo A, Grasso G.
Copper, differently from zinc, affects the conformation, oligomerization state and activity of bradykinin.
Metallomics, 2016, 8:750-61.

32. Oliveri V, Bellia F, Grasso GI, Pietropaolo A, Vecchio G.
Trehalose-8-hydroxyquinoline conjugates as antioxidant modulators of Aß aggregation.
RSC Advances 2016,6: 47229-47236.

31. Pietropaolo A, Pierri CL, Palmieri F, Klingenberg M.
Dataset of the AAC2 conformations in the c-, intermediate- and m-states obtained from free-energy simulations
Data in Brief, 2016 7: 1355–1357. (* The coordinates in pdb format of the work of Ref. 30)

30. Pietropaolo A, Pierri CL, Palmieri F, Klingenberg M.
The switching mechanism of the mitochondrial ADP/ATP carrier explored by free-energy landscapes.

BBA-Bioenergetics 2016 1857:772-781.[pdf]

29. Heng W, Pietropaolo A, Wenbin W, Chen-Yi C, Hisaki I, Toonai N, Miata M, Nakano T.
Right-handed 2/1 helical arrangement of benzene molecules in cholic acid crystal established by experimental and theoretical circular dichroism.

RSC Advances 2015 5:101110-101114.[pdf]

28. Grasso G, Lanza V, Malgieri G, Fattorusso R, Pietropaolo A, Rizzarelli E, Milardi D.
The insulin degrading enzyme activates ubiquitin and promotes the formation of K48 and K63 diubiquitin.

Chem Commun. 2015 DOI: 10.1039/C5CC06786C. [pdf]

27. Pietropaolo A, D’urso A, Purrello R, Berova N.
Effect of Different Z-Inducers on the Stabilization of Z Portion in BZ-DNA Sequence: Correlation Between Experimental and Simulation Data.
Chirality. 2015 DOI: 10.1002/chir.22502.[pdf]

26. Pietropaolo A, Satriano C, Strano G, La Mendola D, Rizzarelli E.
Different zinc(II) complex species and binding modes at Aβ N-terminus drive distinct long range cross-talks in the Aβ monomers.
J Inorg Biochem. 2015, 153:367-376.[pdf]

25. Oliveri V, Bellia F, Pietropaolo A, Vecchio G.
Unusual Cyclodextrin Derivatives as a New Avenue to Modulate Self- and Metal-Induced Aβ Aggregation.
Chem. Eur. 2015 21:14047-14059.[pdf]

24. Travaglia A, Pietropaolo A, Di Martino R, Nicoletti VG, La Mendola D, Calissano P, Rizzarelli E.
A small linear peptide encompassing the NGF N-terminus partly mimics the biological activities of the entire neurotrophin in PC12 cells.
ACS Chem Neurosci 2015 6:1379-1392. [pdf]

23. A. Pietropaolo, Y. Wang, T. Nakano.
Predicting the switchable screw-sense in fluorene based polymers.
Angew. Chem. Int. Ed. 2015, 54:2688-2692.[pdf]

22. G. Grasso, A. Magrì, F. Bellia, A. Pietropaolo, D. La Mendola, E. Rizzarelli.
The copper(II) and zinc(II) coordination mode of HExxH and HxxEH motif in small peptides: The role of carboxylate location and hydrogen bonding network.
J Inorg Biochem. 2014, 130C:92-102.[pdf]

21. A. Travaglia, D. La Mendola, A. Magrì, A. Pietropaolo, V.G. Nicoletti, G. Grasso, G. Malgieri, R. Fattorusso, C. Isernia, E. Rizzarelli.
Zinc(II) Interactions with Brain-Derived Neurotrophic Factor N-Terminal Peptide Fragments: Inorganic Features and Biological Perspectives.
Inorg Chem.  2013, 52:11075-11083.[pdf]

20. A. Pietropaolo and T. Nakano.
Molecular mechanism of polyacrylate helix sense switching across its free-energy landscape
J. Am. Chem. Soc. 2013 135:5509–5512. (* pdf file available upon request)

19. F. Bellia, A. Pietropaolo and G. Grasso.
Formation of insulin fragments by insulin-degrading enzyme: the role of zinc(II) and cystine bridges
J Mass Spectrom 2013 148:135-140.[pdf]

18. A.Pietropaolo and P. Carloni.
Molecular Simulations of the NGF Protein in Encyclopedia of Biophysics Springer-Verlag Berlin Heidelberg pp 1590-1593 2013.[pdf]

17. A. Travaglia, D. La Mendola, A. Magrì, V. Nicoletti, A. Pietropaolo and E. Rizzarelli.

Copper, BDNF and its N-terminal domain: inorganic features and biological perspectives. Chem Eur J 2012 18:15618-15631.[pdf]

16. G. Grasso, F. Salomone, G. R. Tundo, G. Pappalardo, C. Ciaccio, G. Spoto, A. Pietropaolo, M. Coletta and E. Rizzarelli.
Metal ions affect insulin-degrading enzyme activity J Inorg Biochem 2012 117:351-358.[pdf]

15. A. Pietropaolo.

Exploring metal-driven stereoselectivity of glycopeptides by free energy calculations. Pure and Applied Chemistry 2012, 84: 1919-1930.[pdf]

14. A. Travaglia, A. Pietropaolo, D La Mendola, VG Nicoletti, E Rizzarelli.
The inorganic perspectives of neurotrophins and Alzheimer’s disease J Inorg Biochem 2012, 111:130-137.[pdf]

13. V. Losasso, A. Pietropaolo, C. Zannoni, S. Gustincich and P. Carloni.
Structural Role of Compensatory Aminoacid Replacements in the Alpha-Synuclein Protein Biochemistry  2011,50:6994-7001.[pdf]

12. A. Pietropaolo, D. Branduardi, M. Bonomi and M. Parrinello.
A chirality-based metrics for free-energy calculations in biomolecular systems J Comput Chem, 2011 32:2627-2637.[pdf]

11. G.I. Grasso, G. Arena, F. Bellia, G. Maccarrone, M. Parrinello, A.Pietropaolo, G. Vecchio and E. Rizzarelli.
Intramolecular Weak Interactions in the Thermodynamic Stereoselectivity of Copper(II) Complexes with Carnosine-trehalose Conjugates Chem Eur J 2011, 17:9448-9455.[pdf]

10. A. Pietropaolo and M. Parrinello  A quantitative measure of chirality inside nucleic acid databank Chirality 2011, 23:534-542.[pdf]

9. G. Grasso, A. Pietropaolo, G. Spoto,G. Pappalardo, G. R. Tundo, C. Ciaccio, M. Coletta and E. Rizzarelli Copper(I) and copper(II) inhibit Aβ peptides proteolysis by insulin-degrading enzyme differently: implications for metallostasis alteration in Alzheimer’s disease. Chem Eur J 2011, 17:2752-2762.[pdf]

8. A. Pietropaolo Chirality in Biochemistry: A Computational Approach for Investigating Biomolecule Conformations in Where Chemistry Meets Life Wiley-VCH 2010, ISBN: 978-3-527-32541-2.[pdf]

7. A. Pietropaolo, L. Muccioli, E. Rizzarelli, C. Zannoni. Conformational preferences of the full chicken prion protein in solution and its differences with respect to mammals
ChemPhysChem, Special Issue : Biophysics, 2009, 10, 1500-1510.[pdf]

6. D. La Mendola, R. P. Bonomo, S. Caminati, G. Di Natale, S. Emmi, Ö.Hansson, G. Maccarrone, G.Pappalardo, A. Pietropaolo, E. Rizzarelli. Copper(II) complexes with an avian prion N-terminal region and their potential SOD-like activity, J Inorg. Biochem. 2009, 103, 195-204.[pdf]

5. D. La Mendola, A. Pietropaolo, G. Pappalardo, C. Zannoni and E. Rizzarelli. Prion proteins leading to neurodegeneration. Curr. Alzheimer Res., 2008, 5, 579-590. [pdf]

4. A. Pietropaolo, L. Muccioli, C. Zannoni, D. La Mendola, G. Maccarone, G. Pappalardo, E. Rizzarelli. Unveiling the role of histidine and tyrosine residues on the conformation of the avian prion hexarepeat domain J. Phys. Chem. B, 2008, 112, 5182 -5188.[pdf]

3. A. Pietropaolo, L. Muccioli, R. Berardi and C. Zannoni. A chirality index for investigating protein secondary structures and their time evolution PROTEINS: Structure, Function, and Bioinformatics,2008, 70, 667-677.[pdf]

2. A. Pietropaolo, L. Raiola, L. Muccioli, G. Tiberio, C. Zannoni, R. Fattorusso, C. Isernia, D. La Mendola, G. Pappalardo, E. Rizzarelli. An NMR and Molecular Dynamics investigation of the avian prion hexarepeat
conformational features in solution. Chem. Phys. Lett., 2007, 442, 110-118. [pdf]

1. D. La Mendola, R. P. Bonomo, G. Impellizzeri, G. Maccarrone, G. Pappalardo,
A. Pietropaolo, E. Rizzarelli, V. Zito. Copper (II) complexes with chicken prion repeats. Influence of proline and tyrosine residues on the coordination feautures. J. Biol. Inorg. Chem, 2005, 10, 463-475.[pdf]

Conference Proceedings

A. Pietropaolo and T. Nakano. Helical Polymer Switching Using Molecular Simulations.  JPS Conf. Proc. 2014