List of Publications of Paolo Ruggerone (update: September 9th, 2014)
Bacteria and antibiotics: efflux (nr. articles: 8)
1. Vargiu AV, Ruggerone P, Opperman TJ, Nguyen ST, Nikaido H (2014) Inhibition of E.
coli AcrB multidrug efflux pump by MBX2319: molecular mechanism and comparison
with other inhibitors, Antimicrob Agents Chemother, in press.
2. Ruggerone P, Murakami S, Pos KM, Vargiu AV (2013) RND Efflux Pumps: Structural
Information Translated Into Function And Inhibition Mechanisms, Curr Top Med Chem,
13, pp. 3079-100
3. Ruggerone P, Collu F, Vargiu AV, Fischer N, Kandt C (2013) Molecular dynamics
computer simulations of multidrug RND efflux pumps, Comp Struct Biotechnol J 5, pp.
1-11
4. Collu F, Vargiu AV, Dreier J, Cascella M, Ruggerone P (2012) Recognition of
imipenem and meropenem by the RND-transporter MexB studied by computer
simulations, J Am Chem Soc 134, pp. 19146-19158
5. Vargiu AV, Collu F, Schulz R, Pos KM, Zacharias M, Kleinekathöfer U, Ruggerone P
(2011) Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter:
Explanation and Rationale by Molecular Dynamics Simulations, J Am Chem Soc 133,
10704-10707
6. Schulz R, Vargiu AV, Ruggerone P, Kleinekathöfer U (2011) Role of Water during the
Extrusion of Substrates by the Efflux Transporter AcrB, J Phys Chem B 115, 95099509 (Errata)
7. Schulz R, Vargiu AV, Ruggerone P, Kleinekathöfer U (2011) Role of Water during the
Extrusion of Substrates by the Efflux Transporter AcrB, J Phys Chem B 115, 82788287
8. Schulz R, Vargiu AV, Collu F, Kleinekathöfer U, Ruggerone P (2010) Functional
Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations, Plos
Comp Biol 6, art. No. e1000806
Bacteria and antibiotics: influx (nr. articles: 8)
1. Ceccarelli M, Vargiu AV, Ruggerone P (2012) A kinetic Monte Carlo approach to
investigate antibiotic translocation through bacterial porins, J Phys Condens Matter 24,
art. No. 104012
2. Kumar A, Hajjar E, Ruggerone P, Ceccarelli M (2010) Structural and dynamical
properties of the porins OmpF and OmpC: insights from molecular simulations, J Phys
Condens Matter 22, art. No. 454125
3. Hajjar E, Bessonov A, Molitor A, Kumar A, Mahendran KR, Winterhalter M, Pagès JM,
Ruggerone P, Ceccarelli M (2010) Toward screening for antibiotics with enhanced
permeation properties through bacterial porins, Biochemistry 49, pp. 6928-35
4. Kumar A, Hajjar E, Ruggerone P, Ceccarelli M (2010) Molecular simulations reveal the
mechanism and the determinants for ampicillin translocation through OmpF, J Phys
Chem B 114, pp. 9608-16
5. Hajjar E, Kumar A, Ruggerone P, Ceccarelli M (2010) Investigating reaction pathways
in rare events simulations of antibiotics diffusion through protein channels, J Mol Model
16, pp. 1701-8
6. Hajjar E, Mahendran KR, Kumar A, Bessonov A, Petrescu M, Weingart H, Ruggerone
P, Winterhalter M, Ceccarelli M (2010) Bridging timescales and length scales: from
macroscopic flux to the molecular mechanism of antibiotic diffusion through porins,
Biophys J 98, pp. 569-75
7. Mach T, Neves P, Spiga E, Weingart H, Winterhalter M, Ruggerone P, Ceccarelli M,
Gameiro P (2008) Facilitated permeation of antibiotics across membrane channels--
interaction of the quinolone moxifloxacin with the OmpF channel, J Am Chem Soc 130,
pp. 13301-9
8. Ceccarelli M, Ruggerone P (2008) Physical insights into permeation of and resistance
to antibiotics in bacteria, Curr Drug Targets 9, pp. 779-88
TatA system (nr. articles: 1)
1. Walther TH, Gottselig C, Grage SL, Wolf M, Vargiu AV, Klein MJ, Vollmer S, Prock S,
Hartmann M, Afonin S, Stockwald E, Heinzmann H, Nolandt OV, Wenzel W,
Ruggerone P, Ulrich AS (2013) Folding and self-assembly of the TatA translocation
pore based on a charge zipper mechanism, Cell 152, pp 316-26
Delta-opioid receptors (nr. articles: 1)
1. Collu F, Ceccarelli M, Ruggerone P (2012) Exploring binding properties of agonists
interacting with a δ-opioid receptor, Plos One 7, art. no. e52633
Antimicrobial peptides (nr. articles: 1)
1. Scorciapino MA, Pirri G, Vargiu AV, Ruggerone P, Giuliani A, Casu M, Buerck J,
Wadhwani P, Ulrich AS, Rinaldi AC (2012) A novel dendrimeric peptide with
antimicrobial properties: structure-function analysis of SB056, Biophys J 102, pp. 103948
Hemoglobins (nr. articles: 2)
1. Fais A, Casu M, Ruggerone P, Ceccarelli M, Porcu S, Era B, Anedda R, Sollaino MC,
Galanello R, Corda M (2011) Structural and Functional Characterization of a New
Double Variant Haemoglobin (HbG-Philadelphia/Duarte α(2)β(2)), ISRN Hematol 2011,
art. No. 735314
2. Ceccarelli M, Ruggerone P, Anedda R, Fais A, Era B, Sollaino MC, Corda M, Casu M
(2006) Structure-function relationship in a variant hemoglobin: a combined
computational-experimental approach, Biophys J 91, pp. 3529-41
Myoglobins (nr. articles: 4)
1. Scorciapino MA, Robertazzi A, Casu M, Ruggerone P, Ceccarelli M (2010) Heme
proteins: the role of solvent in the dynamics of gates and portals, J Am Chem Soc 132,
pp. 5156-63
2. Scorciapino MA, Robertazzi A, Casu M, Ruggerone P, Ceccarelli M (2009) Breathing
motions of a respiratory protein revealed by molecular dynamics simulations, J Am
Chem Soc 131, pp. 11825-32
3. Anedda R, Era B, Casu M, Fais A, Ceccarelli M, Corda M, Ruggerone P (2008)
Evidences of xenon-induced structural changes in the active site of cyanometmyoglobins: a 1H NMR study, J Phys Chem B 112, 15856-66
4. Ceccarelli M, Anedda R, Casu M, Ruggerone P (2008) CO escape from myoglobin
with metadynamics simulations, Proteins 71, pp. 1231-6
Compound-DNA interactions (nr. articles: 5)
1. Robertazzi A, Vargiu AV, Magistrato A, Ruggerone P, Carloni P, de Hoog P, Reedijk J
(2009) Copper-1,10-phenanthroline complexes binding to DNA: structural predictions
from molecular simulations, J Phys Chem B 113, pp. 10881-90
2. Vargiu AV, Ruggerone P, Magistrato A, Carloni P (2008) Dissociation of minor groove
binders from DNA: insights from metadynamics simulations, Nucleic Acids Res 36, pp.
5910-21
3. Vargiu AV, Ruggerone P, Magistrato A, Carloni P (2008) Sliding of alkylating
anticancer drugs along the minor groove of DNA: new insights on sequence selectivity,
Biophys J 94, pp. 550-61
4. Vargiu AV, Ruggerone P, Magistrato A, Carloni P (2006) Anthramycin-DNA binding
explored by molecular simulations, J Phys Chem B 110, pp. 24687-95
5. Magistrato A, Ruggerone P, Spiegel K, Carloni P, Reedijk J (2006) Binding of novel
azole-bridged dinuclear platinum(II) anticancer drugs to DNA: insights from hybrid
QM/MM molecular dynamics simulations, J Phys Chem B 110, pp. 3604-13
Methods (nr. articles: 3)
1. Biarnés X, Bongarzone S, Vargiu AV, Carloni P, Ruggerone P (2011) Molecular
motions in drug design: the coming age of the metadynamics method, J Comput Aided
Mol Des 25, pp. 395-402
2. Spiegel K, Magistrato A, Maurer P, Ruggerone P, Rothlisberger U, Carloni P, Reedijk
J, Klein ML (2008) Parameterization of azole-bridged dinuclear platinum anticancer
drugs via a QM/MM force matching procedure, J Comput Chem 29, pp. 38-49
3. Dal Peraro M, Ruggerone P, Raugei S, Gervasio FL, Carloni P (2007) Investigating
biological systems using first principles Car-Parrinello molecular dynamics simulations,
Curr Opin Struct Biol 17, pp. 149-56
Viral enzyme inhibitors (nr. articles: 1)
1. Asthana S, Shukla S, Vargiu AV, Ceccarelli M, Ruggerone P, Paglietti G, Marongiu
ME, Blois S, Giliberti G, La Colla P (2013) Different Molecular Mechanisms of Inhibition
of Bovine Viral Diarrhea Virus and Hepatitis C Virus RNA-Dependent RNA
Polymerases by a Novel Benzimidazole, Biochemistry 52, pp 3752–3764
Metal compounds (nr. articles: 1)
1. Vargiu AV, Robertazzi A, Magistrato A, Ruggerone P, Carloni P (2008) The hydrolysis
mechanism of the anticancer ruthenium drugs NAMI-A and ICR investigated by DFTPCM calculations, J Phys Chem B 112, pp. 4401-9
Miscellaneous (nr. articles: 2)
1. Giorgetti A, Ruggerone P, Pantano S, Carloni P (2012) Advanced computational
methods in molecular medicine, J Biomed Biotechnol 2012, art. No. 709085
2. Collu F, Spiga E, Kumar A, Hajjar E, Vargiu AV, Ceccarelli M, Ruggerone P (2009)
Drug design: Insights from atomistic simulations, Nuovo Cimento C 32, pp. 67-71
Surface physics (nr. articles: 58)
1. Braun J, Ruggerone P, Zhang G, Toennies JP, Benedek G (2009) Surface phonon
dispersion curves of thin Pb films on Cu(111), Phys Rev B 79, art. no. 205423
2. Mura M, Ruggerone P, Fiorentini V (2003) Ordered versus disordered growth of
copper quantum wires on Mo and W vicinal surfaces, Phys Rev B 67, pp. 15340611534064
3. Trudu F, Fiorentini V, Ruggerone P, Hansen U (2001) Roughening of close-packed
singular surfaces, Phys Rev B 63, pp. 1534021-1534024
4. Jacobi K, Platen J, Setzer C, Marquez J, Geelhaar L, Meyne C, Richter W, Kley A,
Ruggerone P, Scheffler M (1999) Morphology, surface core-level shifts, and surface
energy of the faceted GaAs(112)A and (-1-1-2) surfaces, Surf Sci 439, pp. 59-72
5. Platen J, Kley A, Setzer C, Jacobi K, Ruggerone P, Scheffler M (1999) The
importance of high-index surfaces for the morphology of GaAs quantum dots, J Appl
Phys 85, 3597-3601
6. Geelhaar L, Marquez J, Jacobi K, Kley A, Ruggerone P, Scheffler M (1999) A
scanning tunneling microscopy study of the GaAs(112) surface, Microelectronics
Journal 30, 393-396
7. Ruggerone P, Kley A, Scheffler M (1998) Bridging the length and time scales: from ab
initio electronic structure calculations to macroscopic proportions, Comm. Condensed
Matter Physics 18, 261
8. Lange G, Toennies JP, Ruggerone P, Benedek G (1998) First Study of the Dynamics
of the (7x7) Reconstructed Si(111) Surface using High-Resolution Helium Atom
Scattering, Europhys Lett 41, 647
9. Ratsch C, Ruggerone P, Scheffler M: Strain - and Temperature Dependence of Metal
Epitaxy studied by Density Functional Theory, in Morphological Organizations
During Epitaxial Growth and Removal, eds. Z. Zhang, M. Lagally (World Scientific,
Singapore 1998), p. 3
10. Ruggerone P, Ratsch C, Scheffler M: Density-Functional Theory of Epitaxial Growth of
Metals, in The Chemical Physics of Solid Surfaces vol. 8, eds. D.A. King, D.P.
Woodruff (Elsevier Science, Amsterdam, 1997), p. 490
11. Ratsch C, Ruggerone P, Scheffler M: The Microscopic Processes governing Epitaxial
Growth, in Surface Diffusion: Atomistic and Collective Processes, ed. M. Tringides
(Plenum Press, New York, 1997), p. 83
12. Ruggerone P, Kley A, Scheffler M: Microscopic processes behind metal homoepitaxy,
in Advances in Computational Materials Science, eds. V. Fiorentini e F. Meloni
(SIF, Bologna, 1997), p. 33
13. Petersen M, Ruggerone P, Scheffler M: He scattering from metal surfaces, in
Advances in Computational Materials Science, eds. V. Fiorentini e F. Meloni (SIF,
Bologna, 1997), p. 43
14. Kley A, Ruggerone P, Scheffler M (1997) Novel diffusion mechanism on the
GaAs(001) surface: the role of adatom-dimer interaction, Phys Rev Lett 79, 5278
15. Kohler B, Ruggerone P, Scheffler M (1997) Ab initio study of the anomalies in the He
atom scattering spectra of H/Mo(110) and H/W(110), Phys Rev B 56, 13503
16. Ruggerone P, Kley A, Scheffler M (1997) Microscopic aspects of homoepitaxial
growth, Progr Surf Sci 54, 331
17. Kohler B, Ruggerone P, Scheffler M (1996) Anomalies in He atom scattering spectra
of the H-covered Mo(110) and W(110) surfaces, Surf Sci 368, 213
18. Kohler B, Ruggerone P, Scheffler M, Tosatti E (1996) H-induced Phonon Anomaly of
Mo(110) and W(110) surfaces, Z Phys Chem 197, 193
19. Ruggerone P (1996) Role of the Electronic Degrees of Freedom in Surface Lattice
Dynamics: a Phenomenological Model Study, La Rivista del Nuovo Cimento 18, 1
20. Petersen M, Wilke S, Ruggerone P, Kohler B, Scheffler M (1996) Theoretical Study of
the Anticorrugating Effect of the He Interaction potential with Metal Surfaces, Phys Rev
Lett 76, 995
21. Luo NS, Ruggerone P, Toennies JP (1996) Theory of Surface Vibrations in Epitaxial
Thin Films, Phys Rev B 54, 5051
22. Ruggerone P, Kohler B, Wilke S, Scheffler M: Frustrated H - induced instability of
Mo(110), in Electronic Surface and Interface States on Metallic Systems, eds. E.
Bertel, M. Doniath (World Scientific, Singapore, 1995), p. 113
23. Kohler B, Ruggerone P, Wilke S, Scheffler M (1995) Frustrated H-induced instability of
Mo(110), Phys Rev Lett 74, 1387
24. Benedek G, Luo NS, Reichmuth A, Ruggerone P, Toennies JP (1994) Diagnostics of
the epitaxial growth of ultrathin metal films by helium atom scattering, Il Vuoto 23, 12
25. Benedek G, Ellis J, Ruggerone P, Toennies JP (1994) Confined resonances in sodium
ultrathin films on Cu(001) observed by inelastic helium atom scattering, Il Vuoto 23, 30
26. Luo NS, Ruggerone P, Toennies JP, Benedek G: Analysis of inelastic He atom
scattering spectra on Cu(001): evidence for contribution of surface electronic
oscillations, in Energy Transfer in Interactions with Surfaces and Adsorbates,
eds. V. Bortolani, K. Gummhalter, A.C. Levi (World Scientific, Singapore, 1994), p. 67
27. Bunjes N, Luo NS, Ruggerone P, Toennies JP, Witte G (1994) Helium Atom
Scattering Study and Theoretical Analysis of the Electron-Phonon Resonance in
Ag(001), Phys Rev B 50, 8897
28. Miglio L, Onida G, Benedek G, Hofmann F, Ruggerone P (1994) Surface phonons in
layered crystals: theoretical issues, Surf Sci Reports 20, 1
29. Gester M, Kleinhesselink D, Ruggerone P, Toennies JP (1994) Combined heliumatom scattering and molecular dynamics study of aluminium surface-phonon
anharmonicities and linewidths, Phys Rev B 49, 5777
30. Benedek G, Brusdeylins G, Hofmann F, Ruggerone P, Toennies JP, Vollmer R,
Skofronick JG (1994) Strong coupling of Rayleigh phonons to charge density wave in
1T-TaS2, Surf Sci 304, 185
31. Benedek G, Luo NS, Ruggerone P, Reichmuth A, Toennies JP (1994) Vibrational
Diagnostics of the Epitaxial Growth of Ultrathin Films of Sodium on Cu(001), Materials
Science and Engineering B 23, 123
32. Luo NS, Ruggerone P, Toennies JP, Benedek G, Celli V (1993) Theoretical analysis of
confined vibrations in epitaxial films, J Electron Spectrosc Relat Phenom 64/65, 755
33. Luo NS, Ruggerone P, Toennies JP, Benedek G (1993) Electron-phonon coupling at
metal surfaces probed by helium atom scattering, Physica Scripta T 49, 584
34. Benedek G, Ellis J, Luo NS, Reichmuth A, Ruggerone P, Toennies JP (1993)
Enhanced helium atom scattering from longitudinal surface phonons in Cu(001), Phys
Rev B 48, 4917
35. Safron SA, Bishop GG, Duan J, Gillman ES, Skofronick JG, Luo NS, Ruggerone P
(1993) Surface dynamics of epitaxially grown KBr overlayers on a NaCl substrate, J
Phys Chem 97, 2270
36. Benedek G, Ellis J, Reichmuth A, Ruggerone P, Schief H, Toennies JP (1992) Organ
Pipe Modes of Sodium Epitaxial Multilayers on Cu(001) Observed by Inelastic Helium
Atom Scattering, Phys Rev Lett 69, 2951
37. Kaden C, Ruggerone P, Toennies JP, Benedek G (1992) Surface Lattice Dynamics
and Inelastic He Scattering in Cu(111), Nuovo Cimento D14, 627
38. Santini P, Ruggerone P, Miglio L, Doak B (1992) Intrinsic and Extrinsic Effects in
Surfaces: Acoustic Phonon Softening of Capped Si(111) Surfaces, Phys Rev B 46,
9865
39. Kaden C, Ruggerone P, Toennies JP, Zhang G, Benedek G (1992) An Electronic
Pseudocharge Model for the Cu(111) Longitudinal Surface Phonon Anomaly Observed
by Helium Atom Scattering, Phys Rev B 46, 13509
40. Brusdeylins G, Luo NS, Ruggerone P, Schmicker D, Toennies JP, Vollmer R, Wach
Th (1992) Interface Mode for NaCl overlayers on the Ge(001) surface, Surf Sci 272,
358
41. Santini P, Ruggerone P, Miglio L, Benedek G (1991) Lattice dynamics of GaAs(110)
and Ge(111) 2x1: A critical comparison, Surf Sci 241, 346
42. Santini P, Ruggerone P, Miglio L, Doak B (1991) Isotropic and Bond-breaking in
Capped Silicon Surfaces: Si(111):As 1x1, Vuoto 21, 198
43. Ruggerone P, Santini P, L. Miglio, G. Benedek (1990) Lattice dynamics of GaAs(110)
and Ge(111) 2x1, Vacuum 41, 605
44. Santini P, Miglio L, Benedek G, Harten U, Ruggerone P, Toennies JP (1990)
Dynamics and structural assessment of open semiconductor surfaces: GaAs(110),
Phys Rev B 42, 11942
45. Kaden C, Ruggerone P, Toennies JP, Benedek G (1990) Lattice dynamics of Cu(111),
Il Vuoto 20, 38
46. Brusdeylins G, Hofmann F, Ruggerone P, Toennies JP, Vollmer R, Benedek G,
Skofronick JG (1990) Charge density wave coupled phonons on a 1T-TaS2(001) single
crystal surface, Il Vuoto 20, 72
47. Brusdeylins G, Hofmann F, Ruggerone P, Toennies JP, Vollmer R, Benedek G,
Skofronick JG: Charge density wave coupled phonons on a 1T-TaS2(001) single crystal
surface measured by helium atom scattering, in Phonons 89, eds. S. Hunklinger, W.
Ludwig, G. Weiss (World Scientific, Singapore, London, 1990), p. 892
48. Santini P, Miglio L, Benedek G, Ruggerone P: Surface phonons in GaAs(110) and
Ge(111) 2x1: a bond charge model calculation, in Phonons 89, eds. S.Hunklinnger,
W.Ludwig, G.Weiss (World Scientific, Singapore, London, 1990), 937
49. Miglio L, Santini P, Ruggerone P, Benedek G (1989) Dynamics of extensively
reconstructed surfaces: Si(111) 2x1, Phys Rev Lett 62, 3070
50. Miglio L, Santini P, Ruggerone P, Benedek G (1989) Surface lattice dynamics of the
Pandey-reconstructed Si(111) 2x1: No pathologies in the experimental findings, Surf.
Sci. 211-212, 335
51. Miglio L, Santini P, Ruggerone P, Benedek G (1989) Surface phonons in Si(111) 2x1:
Folding and chain effects of the reconstruction, Physica Scripta T25, 305
52. Santini P, Ruggerone P, Miglio L, Benedek G (1989) Surface crystallography and
lattice dynamics: GaAs(110) vs. Si(111) 2x1, Helvetica Physica Acta 62, 834
53. Santini P, Ruggerone P, Miglio L, Colombo L, Benedek G (1989) Surface dynamics of
GaAs(110), Il Vuoto 19, 223
54. Harten U, Toennies JP, Wöll C, Miglio L, Ruggerone P, Colombo L, Benedek G (1988)
Surface phonons in Si(111)+H(1x1), Phys Rev B 38, 3305
55. Miglio L, Ruggerone P, Benedek G, Colombo L (1988) Surface phonon calculation for
Si(111):H(1x1), Physica Scripta 37, 768
56. Santini P, Ruggerone P, Miglio L, Benedek G (1988) Lattice dynamics of the Si(111)
2x1 reconstructed surface, Il Vuoto 18, 36
57. Miglio L, Ruggerone P, Benedek G (1987) Lattice dynamics of the Si(111) surface:
folding effects in the 2x1 structure, J Electron Spectrosc Relat Phenom 44, 281
58. Miglio L, Ruggerone P, Colombo L, Benedek G (1986) Surface phonons in
Si(111):H(1x1), Il Vuoto 16, 198
Solid state (nr. articles: 6)
1. Alippi P, Ruggerone P, Colombo L (2004) Neutral boron-interstitial clusters in
crystalline silicon, Phys Rev B 69, pp. 1252051-1252057
2. Alippi P, Ruggerone P, Colombo L (2002) Atomistic study of boron clustering in silicon,
Solid State Phenomena 82-84, pp. 163-170
3. Alippi P, Colombo L, Ruggerone P (2001) Energetics and diffusivity of atomic boron in
silicon by density-functional-based tight-binding simulations, Computational Materials
Science 22, pp. 44-48
4. Alippi P, Colombo L, Ruggerone P, Sieck A, Seifert G, Frauenheim Th (2001) Atomicscale characterization of boron diffusion in silicon, Phys Rev B 64, pp. 752071-752074
5. Zoroddu A, Bernardini F, Ruggerone P, Fiorentini V (2001) First-principles prediction
of structure, energetics, formation enthalpy, elastic constants, polarization, and
piezoelectric constants of AlN, GaN, and InN: Comparison of local and gradientcorrected density-functional theory, Phys Rev B 64, pp. 452081-452086
6. Benedek G, Ruggerone P: Polarization phenomena in lattice dynamics, in Highlights
on spectroscopies of semiconductors and insulators, eds. A. Balzarotti, G.
Guizzetti, A. Stella (World Publ.Co., Singapore, 1989), pp. 79