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1

Folding and Self-Assembly of the TatA Translocation Pore Based on a Charge Zipper Mechanism

Walther, Torsten H., Gottselig, Christina, Grage, Stephan L., Wolf, Moritz, Vargiu, Attilio V., Klein, Marco J., Vollmer, Stefanie, Prock, Sebastian, Hartmann, Mareike, Afonin, Sergiy, Stockwald, Eva,

Journal:

Year:

2013

Language:

english

File:

PDF, 1.82 MB

english, 2013

2

Molecular Recognition Routes Of DNA By Anticancer Ligands: Mechanisms and Free Energies Explored Via Molecular Dynamics Simulations

Vargiu, Attilio Vittorio, Magistrato, Alessandra, Carloni, Paolo, Ruggerone, Paolo

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 114 KB

english, 2009

3

Relevance of Ebola virus VP35 homo-dimerization on the type I interferon cascade inhibition

Di Palma, Francesco, Daino, Gian Luca, Ramaswamy, Venkata Krishnan, Corona, Angela, Frau, Aldo, Fanunza, Elisa, Vargiu, Attilio V, Tramontano, Enzo, Ruggerone, Paolo

Journal:

Antiviral Chemistry & Chemotherapy

Year:

2019

Language:

english

File:

PDF, 1.15 MB

english, 2019

4

Molecular motions in drug design: the coming age of the metadynamics method

Xevi Biarnés, Salvatore Bongarzone, Attilio Vittorio Vargiu, Paolo Carloni, Paolo Ruggerone

Journal:

Journal of Computer-Aided Molecular Design

Year:

2011

Language:

english

File:

PDF, 434 KB

english, 2011

5

Role of Water during the Extrusion of Substrates by the Efflux Transporter AcrB

Schulz, Robert, Vargiu, Attilio V., Ruggerone, Paolo, Kleinekathöfer, Ulrich

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 4.79 MB

english, 2011

6

A Novel Dendrimeric Peptide with Antimicrobial Properties: Structure-Function Analysis of SB056

Scorciapino, Mariano A., Pirri, Giovanna, Vargiu, Attilio V., Ruggerone, Paolo, Giuliani, Andrea, Casu, Mariano, Buerck, Jochen, Wadhwani, Parvesh, Ulrich, Anne S., Rinaldi, Andrea C.

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 597 KB

english, 2012

7

Sliding of Alkylating Anticancer Drugs along the Minor Groove of DNA: New Insights on Sequence Selectivity

Vargiu, Attilio V., Ruggerone, Paolo, Magistrato, Alessandra, Carloni, Paolo

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 1.47 MB

english, 2008

8

The Hydrolysis Mechanism of the Anticancer Ruthenium Drugs NAMI-A and ICR Investigated by DFT−PCM Calculations

Vargiu, Attilio V., Robertazzi, Arturo, Magistrato, Alessandra, Ruggerone, Paolo, Carloni, Paolo

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 195 KB

english, 2008

9

Different Molecular Mechanisms of Inhibition of Bovine Viral Diarrhea Virus and Hepatitis C Virus RNA-Dependent RNA Polymerases by a Novel Benzimidazole

Asthana, Shailendra, Shukla, Saumya, Vargiu, Attilio V., Ceccarelli, Matteo, Ruggerone, Paolo, Paglietti, Giuseppe, Marongiu, Maria E., Blois, Sylvain, Giliberti, Gabriele, La Colla, Paolo

Journal:

Year:

2013

Language:

english

File:

PDF, 4.60 MB

english, 2013

10

A kinetic Monte Carlo approach to investigate antibiotic translocation through bacterial porins

Ceccarelli, Matteo, Vargiu, Attilio V, Ruggerone, Paolo

Journal:

Journal of Physics Condensed Matter

Year:

2012

Language:

english

File:

PDF, 563 KB

english, 2012

11

Anthramycin−DNA Binding Explored by Molecular Simulations

Vargiu, Attilio V., Ruggerone, Paolo, Magistrato, Alessandra, Carloni, Paolo

Journal:

Journal of Physical Chemistry B

Year:

2006

Language:

english

File:

PDF, 560 KB

english, 2006

12

Copper−1,10-Phenanthroline Complexes Binding to DNA: Structural Predictions from Molecular Simulations

Robertazzi, Arturo, Vargiu, Attilio Vittorio, Magistrato, Alessandra, Ruggerone, Paolo, Carloni, Paolo, de Hoog, Paul, Reedijk, Jan

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 4.26 MB

english, 2009

13

Modeling Assembly of the Tata Pore Forming Complex using an Implicit Membrane Model

Wolf, Moritz, Walther, Torsten H., Gottselig, Christina, Grage, Stephan L., Vargiu, Attilio, Klein, Marco J., Vollmer, Stefanie, Prock, Sebastian, Hartmann, Mareike, Afonin, Sergiy, Stockwald, Eva, He

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 42 KB

english, 2013

14

Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations

Vargiu, Attilio Vittorio, Schulz, Robert, Collu, Francesca, Kleinekathoefer, Ulrich, Ruggerone, Paolo

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 35 KB

english, 2010

15

Contents

Ruggerone, Paolo, Vargiu, Attilio V., Collu, Francesca

Journal:

Clinics in Geriatric Medicine

Year:

2009

Language:

english

File:

PDF, 30 KB

english, 2009

16

Effects of Point Mutations on the Activity of AcrB

Ruggerone, Paolo, Vargiu, Attilio V., Collu, Francesca

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 39 KB

english, 2012

17

Simulating Efflux Pumps: The Extrusion Mechanism of Substrates

Schulz, Robert, Vargiu, Attilio V., Collu, Francesca, Ceccarelli, Matteo, Kleinekathöfer, Ulrich, Ruggerone, Paolo

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 111 KB

english, 2009

18

Functional Rotation of the Transporter AcrB: The Essentials of Peristaltic Motion and Subsequent Substrate Extrusion

Schulz, Robert, Vargiu, Attilio Vittorio, Collu, Francesca, Kleinekathöfer, Ulrich, Ruggerone, Paolo

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 39 KB

english, 2010

19

Simulations of Copper-1,10-Phenanthroline Complexes Binding the DNA

Robertazzi, Arturo, Vargiu, Attilio Vittorio, Ruggerone, Paolo, Magistrato, Alessandra, de Hoog, Paul, Carloni, Paolo, Reedijk, Jan

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 39 KB

english, 2009

20

Multidrug Binding Properties of the AcrB Efflux Pump Characterized by Molecular Dynamics Simulations

Vittorio Vargiu, Attilio, Nikaido, Hiroshi

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 54 KB

english, 2013

21

Point Mutation I261M Affects the Dynamics of BVDV and its Interaction with Benzimidazole Antiviral 227G

Asthana, Shailendra, Shukla, Saumya, Ruggerone, Paolo, Ceccarelli, Matteo, Giliberti, Gabriele, La Colla, Paolo, Vargiu, Attilio Vittorio

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 51 KB

english, 2011

22

Folding and Self-Assembly of the Pore-Forming Unit Tat-A of the Bacterial Twin-Arginine Translocase

Grage, Stephan L., Walther, Torsten H., Wolf, Moritz, Vargiu, Attilio, Klein, Marco J., Ruggerone, Paolo, Wenzel, Wolfgang, Ulrich, Anne S.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 36 KB

english, 2011

23

MOLECULAR DYNAMICS COMPUTER SIMULATIONS OF MULTIDRUG RND EFFLUX PUMPS

Ruggerone, Paolo, Vargiu, Attilio V., Collu, Francesca, Fischer, Nadine, Kandt, Christian

Journal:

Computational and Structural Biotechnology Journal

Year:

2013

Language:

english

File:

PDF, 5.20 MB

english, 2013

24

Some Ligands Enhance the Efflux of Other Ligands by the Escherichia coli Multidrug Pump AcrB

Kinana, Alfred D., Vargiu, Attilio V., Nikaido, Hiroshi

Journal:

Year:

2013

Language:

english

File:

PDF, 4.32 MB

english, 2013

25

Ru[(bpy) 2 (dppz)] 2+ and Rh[(bpy) 2 (chrysi)] 3+ Targeting Double Strand DNA: The Shape of the Intercalating Ligand Tunes the Free Energy Landscape of Deintercalation

Franco, Duvan, Vargiu, Attilio V., Magistrato, Alessandra

Journal:

Inorganic Chemistry

Year:

2014

Language:

english

File:

PDF, 5.76 MB

english, 2014

26

Detecting DNA Mismatches with Metallo-Insertors: A Molecular Simulation Study

Vargiu, Attilio V., Magistrato, Alessandra

Journal:

Inorganic Chemistry

Year:

2012

Language:

english

File:

PDF, 3.81 MB

english, 2012

27

Recognition of Imipenem and Meropenem by the RND-Transporter MexB Studied by Computer Simulations

Collu, Francesca, Vargiu, Attilio V., Dreier, Jürg, Cascella, Michele, Ruggerone, Paolo

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 1.75 MB

english, 2012

28

Role of Water during the Extrusion of Substrates by the Efflux Transporter AcrB

Schulz, Robert, Vargiu, Attilio V., Ruggerone, Paolo, Kleinekathöfer, Ulrich

Journal:

Journal of Physical Chemistry B

Year:

2011

File:

PDF, 592 KB

2011

29

Magnetic Coupling between Copper(II) Ions Mediated by Hydrogen-Bonded (Neutral) Water Molecules

Tang, Jinkui, Sánchez Costa, José, Golobič, Amalija, Kozlevčar, Bojan, Robertazzi, Arturo, Vargiu, Attilio V., Gamez, Patrick, Reedijk, Jan

Journal:

Inorganic Chemistry

Year:

2009

Language:

english

File:

PDF, 2.35 MB

english, 2009

30

Effect of the F610A Mutation on Substrate Extrusion in the AcrB Transporter: Explanation and Rationale by Molecular Dynamics Simulations

Vargiu, Attilio V., Collu, Francesca, Schulz, Robert, Pos, Klaas M., Zacharias, Martin, Kleinekathöfer, Ulrich, Ruggerone, Paolo

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 2.66 MB

english, 2011

31

Molecular Mechanism of Viral Resistance to a Potent Non-nucleoside Inhibitor Unveiled by Molecular Simulations

Asthana, Shailendra, Shukla, Saumya, Ruggerone, Paolo, Vargiu, Attilio V.

Journal:

Year:

2014

Language:

english

File:

PDF, 5.48 MB

english, 2014

32

Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations

Vargiu, Attilio V., Magistrato, Alessandra

Journal:

Year:

2014

Language:

english

File:

PDF, 3.90 MB

english, 2014

33

Publisher's Note: “Molecular recognition of DNA by ligands: Roughness and complexity of the free energy profile” [J. Chem. Phys. 139, 145102 (2013)]

Zheng, Wenwei, Vargiu, Attilio Vittorio, Rohrdanz, Mary A., Carloni, Paolo, Clementi, Cecilia

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 265 KB

english, 2013

34

AcrB drug-binding pocket substitution confers clinically relevant resistance and altered substrate specificity

Blair, Jessica M. A., Bavro, Vassiliy N., Ricci, Vito, Modi, Niraj, Cacciotto, Pierpaolo, Kleinekathӧfer, Ulrich, Ruggerone, Paolo, Vargiu, Attilio V., Baylay, Alison J., Smith, Helen E., Brandon, Yvo

Journal:

Proceedings of the National Academy of Sciences

Year:

2015

Language:

english

File:

PDF, 882 KB

english, 2015

35

Functional Rotation of the Transporter AcrB: Insights into Drug Extrusion from Simulations

Schulz, Robert, Vargiu, Attilio V., Collu, Francesca, Kleinekathöfer, Ulrich, Ruggerone, Paolo, Tajkhorshid, Emad

Journal:

PLoS Computational Biology

Year:

2010

Language:

english

File:

PDF, 505 KB

english, 2010

36

Structure–Activity Relationship Study of Hydroxycoumarins and Mushroom Tyrosinase

Asthana, Shailendra, Zucca, Paolo, Vargiu, Attilio V., Sanjust, Enrico, Ruggerone, Paolo, Rescigno, Antonio

Journal:

Journal of Agricultural and Food Chemistry

Year:

2015

Language:

english

File:

PDF, 4.20 MB

english, 2015

37

Molecular basis for inhibition of AcrB multidrug efflux pump by novel and powerful pyranopyridine derivatives

Sjuts, Hanno, Vargiu, Attilio V., Kwasny, Steven M., Nguyen, Son T., Kim, Hong-Suk, Ding, Xiaoyuan, Ornik, Alina R., Ruggerone, Paolo, Bowlin, Terry L., Nikaido, Hiroshi, Pos, Klaas M., Opperman, Timo

Journal:

Proceedings of the National Academy of Sciences

Year:

2016

Language:

english

File:

PDF, 1.73 MB

english, 2016

38

Design of a hydrophobic tripeptide that self-assembles into amphiphilic superstructures forming a hydrogel biomaterial

Vargiu, Attilio V, Iglesias, Daniel, Styan, Katie, Waddington, Lynne -, Easton, Christopher D., Marchesan, Silvia

Journal:

Chemical Communications

Year:

2016

Language:

english

File:

PDF, 1.14 MB

english, 2016

39

Water−Chloride and Water−Bromide Hydrogen-Bonded Networks: Influence of the Nature of the Halide Ions on the Stability of the Supramolecular Assemblies

Dey, Biswajit, Choudhury, Somnath Ray, Gamez, Patrick, Vargiu, Attilio Vittorio, Robertazzi, Arturo, Chen, Chih-Yuan, Lee, Hon Man, Jana, Atish Dipankar, Mukhopadhyay, Subrata

Journal:

Journal of Physical Chemistry A

Year:

2009

Language:

english

File:

PDF, 3.12 MB

english, 2009

40

Effect of site-directed mutations in multidrug efflux pump AcrB examined by quantitative efflux assays

Kinana, Alfred D., Vargiu, Attilio V., Nikaido, Hiroshi

Journal:

Biochemical and Biophysical Research Communications

Year:

2016

Language:

english

File:

PDF, 914 KB

english, 2016

41

HIV-1 Protease Dimerization Dynamics Reveals a Transient Druggable Binding Pocket at the Interface

Pietrucci, Fabio, Vargiu, Attilio Vittorio, Kranjc, Agata

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 2.03 MB

english, 2015

42

Molecular Rationale Behind the Differential Substrate Specificity of RND Transporters AcrB and AcrD

Krishnan Ramaswamy, Venkata, Malloci, Giuliano, Vittorio Vargiu, Attilio, Ruggerone, Paolo

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 44 KB

english, 2017

43

Molecular Insights into Compound-Transporter Interactions: The Case of Inhibitors of Gram-Negative Bacteria Efflux Pumps

Sjuts, Hanno, Vargiu, Attilio V., Kwasny, Steven M., Nguyen, Son T., Kim, Hong-Suk, Ding, Xiaoyuan, Ornik, Alina R., Ruggerone, Paolo, Bowlin, Terry L., Nikaido, Hiroshi, Pos, Klaas M., Opperman, Timo

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 44 KB

english, 2017

44

Computational Study of the Interaction between Antimicrobial Compounds and Efflux Systems of Gram-Negative Bacteria

Atzori, Alessio, Vittorio Vargiu, Attilio, Malloci, Giuliano, Ruggerone, Paolo

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 44 KB

english, 2017

45

Transport Mechanism in the RND Transporter AcrD of E. coli

Vargiu, Attilio V., Krishnan, Venkata R., Malloci, Giuliano, Ruggerone, Paolo

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 43 KB

english, 2017

46

Molecular Insights on the Recognition of Substrates by the Promiscuous Efflux Pump AcrB

Malvacio, Ivana, Ombrato, Rosella, Ruggerone, Paolo, Vargiu, Attilio V.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 69 KB

english, 2017

47

Binding of Antibiotics to the Multidrug Efflux Pump AcrB of E. coli Investigated by Molecular Docking

Malloci, Giuliano, Serra, Giovanni, Bosin, Andrea, Vittorio Vargiu, Attilio, Ruggerone, Paolo

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 61 KB

english, 2017

48

Molecular Rationale behind the Differential Substrate Specificity of Bacterial RND Multi-Drug Transporters

Ramaswamy, Venkata Krishnan, Vargiu, Attilio V., Malloci, Giuliano, Dreier, Jürg, Ruggerone, Paolo

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 5.11 MB

english, 2017

49

Water-mediated interactions enable smooth substrate transport in a bacterial efflux pump

Vargiu, Attilio Vittorio, Ramaswamy, Venkata Krishnan, Malvacio, Ivana, Malloci, Giuliano, Kleinekathöfer, Ulrich, Ruggerone, Paolo

Journal:

Biochimica et Biophysica Acta (BBA) - General Subjects

Year:

2018

Language:

english

File:

PDF, 1.68 MB

english, 2018

50

Computer simulations of the activity of RND efflux pumps

Vargiu, Attilio Vittorio, Ramaswamy, Venkata Krishnan, Malloci, Giuliano, Malvacio, Ivana, Atzori, Alessio, Ruggerone, Paolo

Journal:

Research in Microbiology

Year:

2018

Language:

english

File:

PDF, 2.67 MB

english, 2018

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