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Journal, Book
DOI

Title

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Year

138

Mariano A. Scorciapino, Giuliano Malloci, Ilaria Serra, Stefan Milenkovic, Lucile Moynie, James H. Naismith, Eric Desarbre, Malcolm G. P. Page, Matteo Ceccarelli
J. Am. Chem Soc.

Complexes formed by the siderophore-monosulfactam conjugate BAL30072 and their interaction with the outer membrane receptor PiuA of P. aeruginosa

UNICA, USTAN, BASILEA

2018 submitted

137

Vinaya Kumar Golla, Eulália Sans-Serramitjana, Karunakar Reddy Pothula, Lorraine Benier, Jayesh Arun Bafna, Mathias Winterhalter, Ulrich Kleinekathöfer
Biophys. J.

Fosfomycin permeation through the outer membrane porin OmpF

JUB

2018 in press

136

Watcharin Chumjan; Mathias Winterhalter; Wipa Siginta
BBA - Biomembranes

Effects of H-Bonds on Sugar Binding to Chitoporin from Vibrio harveyi

JUB

2018 in press

135

Estelle Dumont, Julia Vergalli, Jelena Pajovic, Satya P. Bhamidimarri, Koldo Morante, Jiajun Wang, Dmitrijs Lubriks, Edgars Suna, Robert A. Stavenger, Mathias Winterhalter, Matthieu Réfrégiers, Jean-Marie Pagès
In Life Science Alliance

Mechanistic aspects of maltotriose-conjugate translocation to the Gram-negative bacteria cytoplasm

AMU, SYN JUB, GSK, NEW

2018 in press

134

Jiajun Wang, Lorraine Benier, Mathias Winterhalter
ACS Omega, 2018, 3 (12), pp 17481–17486
DOI:10.1021/acsomega.8b01611

Quantifying permeation of small charged molecules across channels: electrophysiology in small volumes

JUB

2018

133

Dumont E, Vergalli J, Conraux L, Tailler C, Pajovic J, Vassort A, Réfrégiers M, Mourez M, Pagès JM
J Antimicrob Chemother
DOI:10.1093/jac/dky396

Antibiotic and efflux: Combined spectrofluorimetry and mass spectrometry to evaluate the involvement of concentration and efflux activity in antibiotic intracellular accumulation

AMU, SANOFI, SYN

2018

132

Atzori A, Malviya V, Malloci G, Dreier J, Pos KM, Vargiu AV, Ruggerone P
Biochim Biophys Acta - Biomembranes
DOI:10.1016/j.bbamem.2018.10.012

Identification and characterization of carbapenem binding sites within the RND-transporter AcrB

UNICA, BASILEA, GUF

2018

131

Matthew P. McCusker, Daniela Alves Ferreira, Donal Cooney, Bruno Martins Alves, Seámus Fanning, Jean-Marie Pagès, Marta Martins, Anne Davin-Regli.
Global Antimicrobial Resistance
DOI:10.1016/j.jgar.2018.10.009

Modulation of antibiotic resistance in clinical isolates of Enterobacter aerogenes - a strategy combining antibiotics and chemosensitiser

AMU, UCD

2018

130

Terrasse R, Winterhalter M.
M. Eur. Phys. J. E, 41: 111.
DOI:10.1140/epje/i2018-11721-9

Translocation of small molecules through engineered outer-membrane channels from Gram-negative bacteria

JUB

2018

129

Bodrenko I, Salis S, Acosta-Gutierrez S, Ceccarelli M
Physical Review Letter
arXiv preprint arXiv:1805.12541

Diffusion of large particles through small pores: from entropic to enthalpic transport

UNICA

2018

128

Heng-Keat Tam, Viveka Nand Malviya and Klaas M. Pos
In: Yamaguchi A., Nishino K. (eds) Bacterial Multidrug Exporters. Methods in Molecular Biology, vol 1700. Humana Press, New York, NY
DOI:10.1007/978-1-4939-7454-2_1

High resolution crystallographic analysis of AcrB using Designed Ankyrin Repeat Proteins (DARPins)

GUF

2018

127

Cacciotto P, Ramaswamy VK, Malloci G, Ruggerone P, Vargiu AV
In: Yamaguchi A., Nishino K. (eds) Bacterial Multidrug Exporters. Methods in Molecular Biology, vol 1700. Humana Press, New York, NY
DOI:10.1007/978-1-4939-7454-2_11

Molecular modeling of multi-drug properties of Resistance Nodulation Division (RND) transporters

UNICA

2018

126

Vargiu AVV, Ramaswamy VK, Malvacio I, Malloci G, Kleinekathöfer U, Ruggerone P
Biochimica et Biophysica Acta (BBA) - General Subjects, Volume 1862, Issue 4, Pages 836-845, ISSN 0304-4165
DOI:10.1016/j.bbagen.2018.01.010

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

UNICA, JUB

2018

125

Citak F, Ghai I, Rosenkötter F, Benier L, Winterhalter M, Wagner R
Biochem Biophys Res Commun 495(1): 1454-1460
DOI:10.1016/j.bbrc.2017.11.188

Probing transport of fosfomycin through substrate specific OprO and OprP from Pseudomonas aeruginosa

JUB, ION

2018

124

Ganguly S, Kesireddy A, Barcena-Uribarri I, Kleinekathöfer U, Benz R
Biophys J 113(4): 829-834
DOI:10.1016/j.bpj.2017.07.004

Conversion of OprO into an OprP-like Channel by Exchanging Key Residues in the Channel Constriction

JUB

2018

123

Schalk IJ
Clin Microbiol Infect 24(8): 801-802
DOI:10.1016/j.cmi.2018.03.037

Siderophore-antibiotic conjugates: exploiting iron uptake to deliver drugs into bacteria

CNRS

2018

122

Zomot E, Yardeni EH, Vargiu AV, Tam HK, Malloci G, Ramaswamy VK, Perach M, Ruggerone P, Pos KM, Bibi E
J Mol Biol 430(9): 1368-1385
DOI:10.1016/j.jmb.2018.02.026

A New Critical Conformational Determinant of Multidrug Efflux by an MFS Transporter

UNICA

2018

121

Masi M, Dumont E, Vergalli J, Pajovic J, Réfrégiers M, Pagès JM.
Res Microbiol. 2017 Dec 5. pii: S0923-2508(17)30197-3.
DOI:10.1016/j.resmic.2017.11.005

Fluorescence enlightens RND pump activity and the intrabacterial concentration of antibiotics

AMU, SYN

2018

120

Vargiu AV, Ramaswamy VK, Malloci G, Malvacio I, Atzori A, Ruggerone P
Res Microbiol, in press
DOI:10.1016/j.resmic.2017.12.001

Computer simulations of the activity of RND efflux pumps

UNICA

2018

119

Bolam DN, van den Berg B
Curr Opin Struct Biol 51: 35-43
DOI:10.1016/j.sbi.2018.03.001

TonB-dependent transport by the gut microbiota: novel aspects of an old problem

NEW

2018

118

Pathania M, Acosta-Gutierrez S, Bhamidimarri SP, Baslé A, Winterhalter M, Ceccarelli M, van den Berg B
Structure. 2018 May 1;26(5):708-721.e4. Epub 2018
DOI:10.1016/j.str.2018.03.010

Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae

JUB, UNICA, NEW

2018

117

Prajapati JD, Fernández Solano CJ, Winterhalter M, Kleinekathöfer U.
J Phys Chem B. 2018 Jan 6.
DOI:10.1021/acs.jpcb.7b12568

Enrofloxacin Permeation Pathways across the Porin OmpC.

JUB

2018

116

Lee J, Pothula KR, Kleinekathöfer U, Im W
J Phys Chem B, in press
DOI:10.1021/acs.jpcb.8b07109

Simulation Study of Occk5 Functional Properties in Pseudomonas aeruginosa Outer Membranes

JUB

2018

115

Perraud Q, Moynie L, Gasser V, Munier M, Godet J, Hoegy F, Mely Y, Mislin GLA, Naismith JH, Schalk IJ
ACS Chem Biol, in print
DOI:10.1021/acschembio.8b00543

A key role for the periplasmic PfeE esterase in iron acquisition via the siderophore Enterobactin in Pseudomonas aeruginosa

CNRS, USTAN

2018

114

Acosta-Gutierrez S, Ferrara L, Pathania M, Masi M, Wang J, Bodrenko I, Zahn M, Winterhalter M, Stavenger RA, Pages JM, Naismith JH, van den Berg B, Page M, Ceccarelli M.
ACS Infect Dis. 2018 Jul 2.
DOI:10.1021/acsinfecdis.8b00108

Getting drugs into Gram-negative bacteria: Rational rules for permeation through general porins.

JUB, GSK, AMU, USTAN, NEW, UNICA, BASILEA

2018

113

Samanta S, Bodrenko I, Acosta-Gutierrez S, D'Agostino T, Pathania M, Ghai I, Schleberger C, Bumann D, Wagner R, Winterhalter M, van den Berg B, Ceccarelli M
ACS Infect Dis. 2018 Jul 24
DOI:10.1021/acsinfecdis.8b00149

Getting drugs through small pores: exploiting the porins pathway in Pseudomonas aeruginosa

UNICA, JUB, NEW, UNIBAS, ION

2018

112

Julia Vergalli, Estelle Dumont, Jelena Pajovic´, Bertrand Cinquin, Laure Maigre, Muriel Masi, Matthieu Réfrégiers & Jean-Marie Pagès
nature protocols, VOL.13, NO.6
DOI:10.1038/nprot.2018.036

Spectrofluorimetric quantification of antibiotic drug concentration in bacterial cells for the characterization of translocation across bacterial membranes

AMU, SYN

2018

111

Anuwat Aunkham, Michael Zahn, Anusha Kesireddy, Karunakar Reddy Pothula, Albert Schulte, Arnaud Baslé, Ulrich Kleinekathöfer, Wipa Suginta & Bert van den Berg
Nature Communications 9, Article number: 220(2018)
DOI:10.1038/s41467-017-02523-y

Structural basis for chitin acquisition by marine Vibrio species

JUB, NEW

2018

110

Du D, Wang-Kan X, Neuberger A, van Veen HW, Pos KM, Piddock LJV, Luisi BF
Nat Rev Microbiol 16(9): 523-539
DOI:10.1038/s41579-018-0048-6

Multidrug efflux pumps: structure, function and regulation

GUF

2018

109

Benkerrou D, Ceccarelli M
Phys. Chem. Chem. Phys
DOI:10.1039/c7cp08299a

Free energy calculations and molecular properties of substrate translocation through OccAB porins

UNICA

2018

108

Ghai I, Bajaj H, Bafna JA, Damrany HAE, Winterhalter M, Wagner R
J Biol Chem
DOI:10.1074/jbc.ra117.000705

Ampicillin permeation across OmpF, the major outer membrane channel in E. coli

JUB, ION

2018

107

Ando T, Bhamidimarri SP, et al.
J. Phys. D: Appl. Phys, 116140
DOI:10.1088/1361-6463

The 2018 Correlative Microscopy Techniques Roadmap

JUB

2018

106

Molitor A, James CE, Fanning S, Pagès JM, Davin-Regli A.
J Med Microbiol. 2018 Jan 3.
DOI:10.1099/jmm.0.000667

Ram locus is a key regulator to trigger multidrug resistance in Enterobacter aerogenes

AMU, UCD

2018

105

Luscher A, Moynié L, Saint Auguste P, Bumann D, Mazza L, Pletzer D, Naismith JH, Köhler T.
Antimicrob Agents Chemother. 2018 Mar 19. pii: AAC.00097-18.
DOI:10.1128/aac.00097-18

The TonB-receptor repertoire of Pseudomonas aeruginosa for the uptake of siderophore-drug conjugates

USTAN, UNIBAS, JUB, UGE

2018

104

Abdali N, Younas F, Mafakheri S, Pothula KR, Kleinekathöfer U, Tauch A, Benz R
BMC Biochem 19(1): 3
DOI:10.1186/s12858-018-0093-9

Identification and characterization of smallest pore-forming protein in the cell wall of pathogenic Corynebacterium urealyticum DSM 7109

JUB

2018

103

Lome V, Brunel JM, Pagès J-M, Bolla JM.
Front Microbiol 9:204
DOI:10.3389/fmicb.2018.00204

Multiparametric Profiling for Identification of Chemosensitizers against Gram-Negative Bacteria

AMU

2018

102

Ferrer-Navarro M, Strehlitz A, Medina E, Vila J
Front. Microbiol 9: 928
DOI:10.3389/fmicb.2018.00928

Changed Expression of Cytoskeleton Proteins During Lung Injury in a Mouse Model of Streptococcus pneumoniae Infection

CRESIB

2018

101

Ramaswamy VK, Vargiu AV, Malloci G, Dreier J, Ruggerone P
Front Microbiol 9: 1144
DOI:10.3389/fmicb.2018.01144

Molecular Determinants of the Promiscuity of MexB and MexY Multidrug Transporters of Pseudomonas aeruginosa

UNICA

2018

100

Marie-Helene Nicolas-Chanoine, Noemie Mayer, Kathleen Guyot, Estelle Dumont, Jean-Marie Pagès
Front. Microbiol.
DOI:10.3389/fmicb.2018.01422

Interplay between membrane permeability and enzymatic barrier leads to antibiotic-dependent resistance in Klebsiella pneumoniae

AMU, APHP-BUH

2018

99

Hans Prochnow, Verena Fetz, Sven-Kevin Hotop, Mariel A. García-Rivera, Axel Heumann, and Mark Brönstrup
Anal. Chem., Article ASAP
DOI:10.1021/acs.analchem.8b03586

Subcellular Quantification of Uptake in Gram-Negative Bacteria

JUB

2018

98

Tanzir Ahmed, Sander van den Driesche, Martin Oellers, Roland Hemmler, Karsten Gall, Satya Prathyusha Bhamidimarri, Mathias Winterhalter, Richard Wagner, Michael J. Vellekoop
Multidisciplinary Digital Publishing Institute Proceedings 2 ( 2018), 920
DOI:10.3390/proceedings2130920

Fast Formation of Lipid Bilayer Membranes for Simultaneous Analysis of Molecular Transport Using Parylene Coated Chips

JUB, ION

2018

97

Alessia Gilardi; Satya P Bhamidimarri; Mark Brönstrup; Ursula Bilitewski; Ravi K Marreddy; Klaas M Pos; Lorraine Benier; Philip Gribbon; Mathias Winterhalter; Björn Windshügel
Biochimica et Biophysica Acta (BBA) - General Subjects
DOI:10.1016/j.bbagen.2017.07.014

Biophysical characterization of E. coli TolC interaction with the known blocker hexaamminecobalt

IME-SP, JUB, GUF

2017

96

Ishan Ghai, Mathias Winterhalter, Richard Wagner
Biochemical and Biophysical Research Communications. Volume 484, Issue 1, 26 February 2017, Pages 51–55
DOI:10.1016/j.bbrc.2017.01.076

Probing transport of charged ß-lactamase inhibitors through OmpC, a membrane channel from E. coli

JUB, ION

2017

95

Naresh Niranjan Dhanasekar, Soumeya Aliouane, Mathias Winterhalter, Jean-Marie Pagès, Jean-Michel Bolla
Biochemistry and Biophysics Reports
DOI:10.1016/j.bbrep.2017.06.007

Peptide translocation across MOMP, the major outer membrane channel from Campylobacter jejuni

JUB, AMU

2017

94

Paulen A, Hoegy F, Roche B, Schalk IJ, Mislin GLA
Bioorg Med Chem Lett. 2017 Nov 1;27(21):4867-4870
DOI:10.1016/j.bmcl.2017.09.039

Synthesis of conjugates between oxazolidinone antibiotics and a pyochelin analogue

CNRS

2017

93

Giuliano Malloci, Giovanni Serra, Andrea Bosin, Attilio Vittorio Vargiu, Paolo Ruggerone
Biophysical Journal Volume 112, Issue 3, Supplement 1, 3 February 2017, Pages 493a–494a
DOI:10.1016/j.bpj.2016.11.2671

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

UNICA

2017

92

Schuster S, Vavra M, Schweigger TM, Rossen JWA, Matsumura Y, Kern WV
Int J Antimicrob Agents. 2017 Jul 6. pii: S0924-8579(17)30252-2.
DOI:10.1016/j.ijantimicag.2017.03.023

Contribution of AcrAB-TolC to multidrug resistance in an Escherichia coli sequence type 131 isolate

UKL-FR

2017

91

Que-Tien Tran, Laure Maigre, Tommaso D'Agostino, Matteo Ceccarelli, Mathias Winterhalter, Jean-Marie Pagès, Anne Davin-Regli
Res Microbiol. 2017 May 30. pii: S0923-2508(17)30111-0
DOI:10.1016/j.resmic.2017.05.003

Porin flexibility in Providencia stuartii: cell-surface-exposed loops L5 and L7 are markers of Providencia porin OmpPst1

JUB, UNICA, AMU

2017

90

Prajapati JD, Fernández Solano CJ, Winterhalter M, Kleinekathöfer U.
J Chem Theory Comput. 2017 Aug 17.
DOI:10.1021/acs.jctc.7b00467

Characterization of Ciprofloxacin Permeation Pathways across the Porin OmpC using Metadynamics and a String Method

JUB

2017

89

Pothula, Karunakar; Dhanasekar, Naresh; Lamichhane, Usha; Younas, Farhan; Pletzer, Daniel; Benz, Roland; Winterhalter, Mathias; Kleinekathöfer, Ulrich
J. Phys. Chem. B, 2017, 121 (12), pp 2614–2621
DOI:10.1021/acs.jpcb.7b01787

A Single Residue Acts as Gate in OccK Channels

JUB

2017

88

Ghai, Ishan; Pira, Alessandro; Scorciapino, Mariano; Bodrenko, Igor; Benier, Lorraine; Ceccarelli, Matteo; Winterhalter, Mathias; Wagner, Richard
The Journal of Physical Chemistry Letters
DOI:10.1021/acs.jpclett.7b00062

A General Method to Determine the Flux of Charged Molecules Through Nanopores Applied to ß-Lactamase Inhibitors and OmpF

JUB, UNICA, ION

2017

87

Neveshkin, Alexander; Citak, Funda; Ball, Vincent; Winterhalter, Mathias
Langmuir. 2017 Jul 25;33(29):7256-7262
DOI:10.1021/acs.langmuir.7b01959

Polydopamine coating to stabilize free standing lipid bilayer for channel sensing

JUB

2017

86

Soundararajan G, Bhamidimarri SP, Winterhalter M.
ACS Chem Biol. 2017 Jun 16;12(6):1656-1664
DOI:10.1021/acschembio.6b01150

Understanding carbapenem translocation through OccD3 (OpdP) of Pseudomonas aeruginosa.

JUB

2017

85

Bajaj H, Acosta Gutierrez S, Bodrenko I, Malloci G, Scorciapino MA, Winterhalter M, Ceccarelli M.
ACS Nano. 2017 11:5465-5473
DOI:10.1021/acsnano.6b08613

Bacterial Outer Membrane Porins as Electrostatic Nanosieves: Exploring Transport Rules of Small Polar Molecules

UNICA, JUB

2017

84

Bodrenko, Igor; Wang, Jiajun; Salis, Samuele; Winterhalter, Mathias; Ceccarelli, Matteo
ACS Sens. 2017 Aug 25;2(8):1184-1190.
DOI:10.1021/acssensors.7b00311

Sensing Single Molecule Penetration into Nanopores: Pushing the Time Resolution to the Diffusion Limit

UNICA, NAN, JUB

2017

83

Glenwright AJ, Pothula KR, Bhamidimarri SP, Chorev DS, Baslé A, Firbank SJ, Zheng H, Robinson CV, Winterhalter M, Kleinekathöfer U, Bolam DN, van den Berg B.
Nature
DOI:10.1038/nature20828

Structural basis for nutrient acquisition by dominant members of the human gut microbiota.

JUB, NEW

2017

82

Muriel Masi, Matthieu Refregiers, Klaas M. Pos, Jean-Marie Pages
Nature Microbiology
DOI:10.1038/nmicrobiol.2017.1

Mechanisms of envelope permeability and antibiotic efflux in Gram-negative bacteria

AMU, SYN, GUF

2017

81

Abellón-Ruiz J, Kaptan SS, Baslé A, Claudi B, Bumann D, Kleinekathöfer U, van den Berg B.
Nat Microbiol. 2017 Oct 16.
DOI:10.1038/s41564-017-0046-x

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

NEW, UNIBAS, JUB

2017

80

A. Allam, L. Maigre, J. Vergalli, E. Dumont, B. Cinquin, R. Alves de Souza, E. Pinet, N. Smith, J-P. Herbeuval, M. Réfregiers, I. Artaud, J-M. Pagès
Scientific Reports 7, Article number: 986
DOI:10.1038/s41598-017-00945-8

Microspectrofluorimetry to dissect the permeation of ceftazidime in Gram-negative bacteria

AMU, SYN

2017

79

Bialek-Davenet S, Mayer N, Vergalli J, Duprilot M, Brisse S, Pagès JM, Nicolas-Chanoine MH
Sci Rep. 2017 Jul 27;7(1):6722.
DOI:10.1038/s41598-017-06503-6

In-vivo loss of carbapenem resistance by extensively drug-resistant Klebsiella pneumoniae during treatment via porin expression modification

AMU, APHP-BUH

2017

78

Ramaswamy, V. K., Vargiu, A. V., Malloci, G., Dreier, J., & Ruggerone, P.
Sci Rep 7(1): 8075
DOI:10.1038/s41598-017-08747-8

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

BASILEA, UNICA

2017

77

Vergalli J, Dumont E, Cinquin B, Maigre L, Pajovic J, Bacqué E, Mourez M, Réfregiers M, Pagès J-M
Sci. Reports 7: 9821
DOI:10.1038/s41598-017-08775-4

Fluoroquinolone structure and translocation flux across bacterial membrane

AMU, SYN, SARD

2017

76

Ramaswamy, V. K., Cacciotto, P., Malloci, G., Vargiu, A. V., & Ruggerone, P.
Essays in Biochemistry, 61(1), 141–156
DOI:10.1042/ebc20160065

Computational modelling of efflux pumps and their inhibitors

UNICA

2017

75

Pagès J-M
Biol Aujourdhui 211(2): 149-154
DOI:10.1051/jbio/2017020

Antibiotic transport and membrane permeability: new insights to fight bacterial resistance

AMU

2017

74

Mariano Andrea Scorciapino, Silvia Acosta-Gutierrez, Dehbia Benkerrou, Tommaso D’Agostino, Giuliano Malloci, Susruta Samanta, Igor Bodrenko, Matteo Ceccarelli
Journal of Physics: Condensed Matter 1–16
DOI:10.1088/1361-648x/aa543b

Rationalizing the permeation of polar antibiotics into Gram-negative bacteria

UNICA

2017

73

Moynie L, Luscher A, Rolo D, Pletzer D, Tortajada A, Weingart H, Braun Y, Page MG, Naismith JH, Köhler T
Antimicrob Agents Chemother 61(4): e02531-16
DOI:10.1128/aac.02531-16

Structure and Function of the PiuA and PirA Siderophore-Drug Receptors from Pseudomonas aeruginosa and Acinetobacter baumannii

USTAN, JUB, BASILEA, UGE, UNIBAS, NEW

2017

72

Wu A, Tymoszuk P, Haschka D, Heeke S, Dichtl S, Petzer V, Seifert M, Hilbe R, Sopper S, Talasz H, Bumann D, Lass-Flörl C, Theurl I, Zhang K, Weiss G
Infect Immun 85: e00418-17
DOI:10.1128/iai.00418-17

Salmonella utilizes zinc to subvert anti-microbial host defense of macrophages via modulation of NF-kB signaling

UNIBAS, NAN

2017

71

Davin-Regli A, Masi M, Bialek S, Nicolas-Chanoine MH, Pagès JM
In: Li XZ., Elkins C., Zgurskaya H. (eds) Efflux-Mediated Antimicrobial Resistance in Bacteria (Adis, Cham), 281-306
DOI:10.1007/978-3-319-39658-3_11

Antimicrobial Drug Efflux Pumps in Enterobacter and Klebsiella

AMU

2016

70

Ramaswamy VK, Cacciotto P, Malloci G, Ruggerone P, Vargiu AV.
In: Li XZ., Elkins C., Zgurskaya H. (eds) Efflux-Mediated Antimicrobial Resistance in Bacteria (Adis, Cham), 797-831.
DOI:10.1007/978-3-319-39658-3_30

Multidrug Efflux Pumps and Their Inhibitors Characterized by Computational Modeling

UNICA

2016

69

Pletzer D, Braun Y, Weingart H. A. van Leeuwenhoek.
2016 109(6):737-53.
DOI:10.1007/s10482-016-0675-8

Swarming motility is modulated by expression of the putative xenosiderophore transporter SppR-SppABCD in Pseudomonas aeruginosa PA14.

JUB

2016

68

K. R. Pothula, C. J. Solano and U. Kleinekathöfer
Biochimica et Biophysica Acta (BBA) – Biomembranes
DOI:10.1016/j.bbamem.2015.12.020

Simulations of outer membrane channels and their permeability

JUB

2016

67

Tommaso D’Agostino, Samuele Salis, and Matteo Ceccarelli
BBA-Biomembranes 2016
DOI:10.1016/j.bbamem.2016.01.004

A Kinetic Model for Molecular Diffusion through Pores

UNICA

2016

66

Kinana AD, Vargiu AV, Nikaido H
Biochem Biophys Res Commun 480(4): 552-557
DOI:10.1016/j.bbrc.2016.10.083

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

UNICA

2016

65

P. Bhamidimarri, J. D. Prajapati, B. van den Berg, M. Winterhalter and U. Kleinekathöfer
Biophys. J. 110, 600–611
DOI:10.1016/j.bpj.2015.12.027

Role of Electroosmosis in the Permeation of Neutral Molecules: CymA and Cyclodextrin as an Example

JUB, NEW

2016

64

Allam A, Maigre L, Alves de Sousa R, Dumont E, Vergalli J, Pagès J-M, Artaud I.
Eur J Med Chem. 2016 Oct 25. pii: S0223-5234(16)30916-3.
DOI:10.1016/j.ejmech.2016.10.054

New amphiphilic neamine conjugates bearing a metal binding motif active against MDR E. aerogenes Gram-negative bacteria

AMU, SYN

2016

63

I Lytvynenko, S Brill, C Oswald, KM Pos
J Mol Biol, Volume 428, Issue 3, 644–657
DOI:10.1016/j.jmb.2015.12.006

Molecular basis of polyspecificity of the Small Multidrug Resistance Efflux Pump AbeS from Acinetobacter baumannii

GUF

2016

62

Luana G M Ferrara, Gregor D Wallat, Lucile Moynié, Naresh Niranjan Dhanasekar, Mathias Winterhalter, Jean-Michel Bolla, Soumeya Aliouane, Jean-Marie Pagès, Silvia Acosta-Gutiérrez, Matteo Ceccarelli, James H Naismith
Journal of Molecular Biology 428, no. 22 (November 6, 2016): 4528–43.
DOI:10.1016/j.jmb.2016.09.021

MOMP From Campylobacter Jejuni Is a Trimer of 18-Stranded ß-Barrel Monomers with a Ca(2+) Ion Bound at the Constriction Zone.

NEW, JUB, AMU, UNICA

2016

61

Ferrer-Navarro M, Balleste-Delpierre C, Vila J, Fabrega A
J Proteomics 146: 141-7
DOI:10.1016/j.jprot.2016.06.032

Characterization of the outer membrane subproteome of the virulent strain Salmonella Typhimurium SL1344

CRESIB

2016

60

Zahn M, Bhamidimarri SP, Baslé A, Winterhalter M, van den Berg B.
Structure. (2016) 24:221-31
DOI:10.1016/j.str.2015.12.009

Structural Insights into Outer Membrane Permeability of Acinetobacter baumannii

NEW, JUB

2016

59

Solano CJF, Pothula KR, Prajapati JD, De Biase PM, Noskov SY, Kleinekathöfer U
J Chem Theory Comput 12(5): 2401-17
DOI:10.1021/acs.jctc.5b01196

BROMOCEA Code: An Improved Grand Canonical Monte Carlo/Brownian Dynamics Algorithm Including Explicit Atoms

JUB

2016

58

Daury L, Orange F, Taveau JC, Verchère A, Monlezun L, Gounou C, Marreddy RK, Picard M, Broutin I, Pos KM, Lambert O
Nat Commun 7: 10731
DOI:10.1038/ncomms10731

Tripartite assembly of RND multidrug efflux pumps

GUF

2016

57

Oswald, C., Tam, H-K., Pos, K. M.
Nat. Commun. 7: 13819
DOI:10.1038/ncomms13819

Transport of lipophilic carboxylates is mediated by transmembrane helix 2 in multidrug transporter AcrB

GUF

2016

56

Acosta Gutierrez S, Bodrenko I, Scorciapino MA, Ceccarelli M
Phys Chem Chem Phys 18(13): 8855-64
DOI:10.1039/c5cp07902k

Macroscopic electric field inside water-filled biological nanopores

UNICA

2016

55

Kinana AD, Vargiu AV, May T, Nikaido H
Proc Natl Acad Sci USA 113(5): 1405-10
DOI:10.1073/pnas.1525143113

Aminoacyl ß-naphthylamides as substrates and modulators of AcrB multidrug efflux pump

UNICA

2016

54

Arunmanee W, Pathania M, Solovyova AS, Le Brun AP, Ridley H, Basle A, van den Berg B, Lakey JH
Proc Natl Acad Sci U S A 113(34): E5034-43
DOI:10.1073/pnas.1602382113

Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis

NEW

2016

53

Sjuts H, Vargiu AV, Kwasny SM, Nguyen ST, Kim HS, Ding X, Ornik AR1, Ruggerone P, Bowlin TL, Nikaido H, Pos KM, Opperman TJ
Proc Natl Acad Sci USA 113(13): 3509-14
DOI:10.1073/pnas.1602472113

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

UNICA, GUF

2016

52

Harsha Bajaj, Mariano A. Scorciapino, Lucile Moynie, Malcolm G. P. Page, James H. Naismith, Matteo Ceccarelli, and Mathias Winterhalter
J. Biol. Chem. 291 (2016) 2837-47
DOI:10.1074/jbc.m115.690156

Molecular Basis of Filtering Carbapenems by Porins from ß-Lactam-resistant Clinical Strains of Escherichia coli

JUB, UNICA, USTAN, BASILEA

2016

51

Kostyanev, T; Bonten, M; O'Brien, S; Steel, H; Ross, S; François, B; Tacconelli, E; Winterhalter, M; Stavenger, R; Karlén, A; Harbarth, S; Hackett, J; Jafri, H; Cuong, V; MacGowan, A; Witschi, A; Angyalosi, G; Elborn, S; deWinter, R; Goossens, H
J. Antimicrob. Chemother. 71 (2): 290-295
DOI:10.1093/jac/dkv339

The Innovative Medicines Initiative's New Drugs for Bad Bugs programme – European public-private partnerships for the development of new strategies to tackle antibiotic resistance

GSK, JUB

2016

50

Gasser V, Baco E, Cunrath O, August PS, Perraud Q, Zill N, Schleberger C, Schmidt A, Paulen A, Bumann D, Mislin GL, Schalk IJ.
Environ Microbiol. 2016 Mar;18(3):819-32.
DOI:10.1111/1462-2920.13199

Catechol siderophores repress the pyochelin pathway and activate the enterobactin pathway in Pseudomonas aeruginosa: an opportunity for siderophore-antibiotic conjugates development

CNRS, UNIBAS

2016

49

Schuster S, Vavra M, Kern W
Antimicrob Agent Chemother
DOI:10.1128/aac.00314-16

Evidence of a substrate discriminating entrance channel in the lower porter domain of the multidrug resistance efflux pump AcrB

UKL-FR

2016

48

Bohnert JA, Schuster S, Kern WV, Karcz T, Olejarz A, Kaczor A, Handzlik J, Kiec-Kononowicz K
Antimicrob Agents Chemother 60(4): 1974-83
DOI:10.1128/aac.01995-15

Novel Piperazine Arylideneimidazolones Inhibit the AcrAB-TolC Pump in Escherichia coli and Simultaneously Act as Fluorescent Membrane Probes in a Combined Real-Time Influx and Efflux Assay

UKL-FR

2016

47

Charles Auffray, Rudi Balling, Inês Barroso, et.al.
Genome Medicine 20168:71
DOI:10.1186/s13073-016-0323-y

Making sense of big data in health research: Towards a European Union action plan

IME-SP

2016

46

Vargiu AV, Pos KM, Poole K, Nikaido H
Front Microbiol 7: 833
DOI:10.3389/fmicb.2016.00833

Editorial: Bad Bugs in the XXIst Century: Resistance Mediated by Multi-Drug Efflux Pumps in Gram-Negative Bacteria

UNICA, GUF

2016

45

Malloci G, Serra G, Bosin A, Vargiu AV
Computation 4: 5
DOI:10.3390/computation4010005

Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin As A Test Case

UNICA

2016

44

Scorciapino, M. A. et al.
Future Med Chem 8, 1047–1062 (2016).
DOI:10.4155/fmc-2016-0038

Exploiting the porin pathway for polar compound delivery into Gram-negative bacteria.

UNICA

2016

43

Vaas LAI, Witt G, Windshügel B, Bosin A, Serra G, Bruengger A, Winterhalter M, Gribbon P, Levy-Petelinkar CJ, Kohler M
PeerJ Computer Science 2:e83
DOI:10.7717/peerj-cs.83

Electronic laboratory notebooks in a public-private-partnership

IME-SP, UNICA, JUB, BASILEA, GSK, UGE

2016

42

N. Modi, S. Ganguly, I. Bárcena-Uribarri, R. Benz, B. van den Berg and U. Kleinekathöfer
Biophys. J. 109, 1429–1438
DOI:10.1016/j.bpj.2015.07.035

Structure, Dynamics, and Substrate Specificity of the OprO Porin from Pseudomonas aeruginosa

JUB, NEW

2015

41

Isabella, Vincent M.; Campbell, Arthur J.; Manchester, John; et al.
CHEMISTRY & BIOLOGY 22: 535-547
DOI:10.1016/j.chembiol.2015.03.018

Toward the Rational Design of Carbapenem Uptake in Pseudomonas aeruginosa

AZ

2015

40

Vila-Farres X, Lopez-Rojas R, Pachon-Ibanez ME, Teixido M, Pachon J, Vila J, Giralt E
Eur J Med Chem 101: 34-40
DOI:10.1016/j.ejmech.2015.06.016

Sequence-activity relationship, and mechanism of action of mastoparan analogues against extended-drug resistant Acinetobacter baumannii

CRESIB

2015

39

Winterhalter M, Ceccarelli M
Eur J Pharm Biopharm. 95, 63-7
DOI:10.1016/j.ejpb.2015.05.006

Physical methods to quantify small antibiotic molecules uptake into Gram-negative bacteria

JUB, UNICA

2015

38

Zahn M, D'Agostino T, Eren E, Baslé A, Ceccarelli M, van den Berg B.
J Mol Biol. 427:2329-39
DOI:10.1016/j.jmb.2015.03.016

Small-Molecule Transport by CarO, an Abundant Eight-Stranded ß-Barrel Outer Membrane Protein from Acinetobacter baumannii

UNICA, NEW

2015

37

Du, D., van Veen, H.W., Murakami, S., Pos, K. M. and Luisi, B.
Curr. Opinion Struc. Biol. 33: 76-91
DOI:10.1016/j.sbi.2015.07.015

Structure, mechanism and cooperation of bacterial multidrug efflux transporters

GUF

2015

36

Zhou Y, Joubran C, Miller-Vedam L, Vincent I, Nayar A, Tentarelli S, Miller A
Anal. Chem., 87 (7), pp 3579–3584
DOI:10.1021/ac504880r

Thinking Outside the "Bug": A Unique Assay To Measure Intracellular Drug Penetration in Gram-Negative Bacteria

AZ

2015

35

Acosta-Gutierrez S, Scorciapino M, Mariano A, Bodrenko I, and Matteo Ceccarelli
J. Phys. Chem. Lett., 6 (10), pp 1807–1812
DOI:10.1021/acs.jpclett.5b00612

Filtering with Electric Field: The Case of E. coli Porins

UNICA

2015

34

Niraj Modi, Ivan Barcena Uribarri, Manjeet Bains, Roland Benz, Robert Hancock, Ulrich Kleinekathoefer
ACS Chemical Biology 10: 441-51
DOI:10.1021/cb500399j

Tuning the affinity of anion binding sites in porin channels with negatively charged residues: Molecular details for OprP

JUB

2015

33

Cama J, Bajaj H, Pagliara S, Maier T, Braun Y, Winterhalter M, Keyser UF.
J. Am. Chem. Soc., 137, 13836–13843
DOI:10.1021/jacs.5b08960

Quantification of Fluoroquinolone Uptake through the Outer Membrane Channel OmpF of Escherichia coli

JUB

2015

32

Gutsmann T, Heimburg T, Keyser U, Mahendran KR, Winterhalter M.
Nat Protoc. 10:188-98
DOI:10.1038/nprot.2015.003

Protein reconstitution into freestanding planar lipid membranes for electrophysiological characterization

JUB

2015

31

Van den Berg B, Prathyusha Bhamidimarri S, Winterhalter M
Sci. Report, 5, 11927
DOI:10.1038/srep11927

Crystal structure of a COG4313 outer membrane channel

NEW, JUB

2015

30

B. Cinquin, L. Maigre, E. Pinet, J. Chevalier, R. A. Stavenger, S. Mills, M. Réfregiers and J.-M. Pagès
Sci. Rep. 5:17968
DOI:10.1038/srep17968

Microspectrometric insights on the uptake of antibiotics at the single bacterial cell level

AMU, SYN, GSK, AZ

2015

29

Bodrenko I, Bajaj H, Ruggerone P, Winterhalter M, Ceccarelli M.
Analyst. 140:4820-7
DOI:10.1039/c4an02293a

Analysis of fast channel blockage: revealing substrate binding in the microsecond range

UNICA, JUB

2015

28

Weichbrodt C, Bajaj H, Baaken G, Wang J, Guinot S, Kreir M, Behrends JC, Winterhalter M, Fertig N.
Analyst. 140:4874-81
DOI:10.1039/c4an02335h

Antibiotic translocation through porins studied in planar lipid bilayers using parallel platforms

NAN, JUB

2015

27

Pothula KR, Kleinekathöfer U
Analyst 140(14): 4855-64
DOI:10.1039/c5an00036j

Theoretical analysis of ion conductance and gating transitions in the OpdK (OccK1) channel

JUB

2015

26

Samanta S, Scorciapino MA, Ceccarelli M
Physical Chemistry Chemical Physics : PCCP 17: 23867–76
DOI:10.1039/c5cp02844b

Molecular Basis of Substrate Translocation Through the Outer Membrane Channel OprD of Pseudomonas Aeruginosa.

UNICA

2015

25

Paulen A, Gasser V, Hoegy F, Perraud Q, Pesset B, Schalk IJ, Mislin GL
Org Biomol Chem 13(47): 11567-79
DOI:10.1039/c5ob01859e

Synthesis and antibiotic activity of oxazolidinone-catechol conjugates against Pseudomonas aeruginosa

CNRS

2015

24

Vaulont S, Schalk IJ
Med Sci (Paris) 31(8-9): 756-63
DOI:10.1051/medsci/20153108014

Roles of bacterial and mammalian siderophores in host-pathogen interactions

CNRS

2015

23

van den Berg B, Prathyusha Bhamidimarri S, Dahyabhai Prajapati J, Kleinekathöfer U, Winterhalter M.
Proc Natl Acad Sci U S A. 112:E2991-9
DOI:10.1073/pnas.1424835112

Outer-membrane translocation of bulky small molecules by passive diffusion

JUB, NEW

2015

22

Périamé M, Philippe N, Condell O, Fanning S, Pagès JM, Davin-Regli A
Lett Appl Microbiol.
DOI:10.1111/lam.12435

Phenotypic changes contributing to Enterobacter gergoviae biocide resistance

AMU, UCD, JUB

2015

21

Pletzer D, Braun Y, Dubiley S, Lafon C, Köhler T, Page MGP, Mourez M, Severinov K, Weingart H
J Bacteriol 197:2217–222
DOI:10.1128/jb.00234-15

The Pseudomonas aeruginosa PA14 ABC Transporter NppA1A2BCD Is Required for Uptake of Peptidyl Nucleoside Antibiotics

JUB, UGE, BASILEA, SARD

2015

20

Schulz R, Vargiu AV, Ruggerone P, Kleinekathöfer U.
Biomed Res Int. 487298
DOI:10.1155/2015/487298

Computational study of correlated domain motions in the AcrB efflux transporter

UNICA, JUB

2015

19

Philippe N, Maigre L, Santini S, Pinet E, Claverie JM, Davin-Regli A, Pagès JM, Masi M
PLOS ONE. 2015 Sep 23;10(9):e0138828
DOI:10.1371/journal.pone.0138828

In vivo evolution of bacterial resistance in two cases of Enterobacter aerogenes infections during treatment with imipenem

AMU, JUB

2015

18

Benz R., Jones M.D., Younas F., Maier E., Modi N., Mentele R., Lottspeich F., Kleinekathöfer U., and Smit J.
PLoS One
DOI:10.1371/journal.pone.0143557

OmpW of Caulobacter crescentus functions as an outer membrane channel for cations

JUB

2015

17

Müller R. T., Pos K. M.
Biol Chem. 396(9-10):1083-9
DOI:10.1515/hsz-2015-0150

The assembly and disassembly of the AcrAB-TolC three-component multidrug efflux pump

GUF

2015

16

Davin-Regli A, Pagès JM
Front Microbiol 6:392
DOI:10.3389/fmicb.2015.00392

Enterobacter aerogenes and Enterobacter cloacae; versatile bacterial pathogens confronting antibiotic treatment

AMU

2015

15

Anes J, McCusker MP, Fanning S, Martins M
Front Microbiol 6: 587
DOI:10.3389/fmicb.2015.00587

The ins and outs of RND efflux pumps in Escherichia coli

UCD

2015

14

Dreier J and Ruggerone P
Front Microbiol 6: 660
DOI:10.3389/fmicb.2015.00660

Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa

BASILEA, UNICA

2015

13

Malloci, G.; Vargiu, A.V.; Serra, G.; Bosin, A.; Ruggerone, P.; Ceccarelli, M.
Molecules 2015, 20, 13997-14021
DOI:10.3390/molecules200813997

A Database of Force-Field Parameters, Dynamics, and Properties of Antimicrobial Compounds

UNICA

2015

12

Cha, H., Pos KM
In: Krämer R., Ziegler C. (eds) Membrane Transport Mechanism. Springer Series in Biophysics, vol 17. Springer, Berlin, Heidelberg Chapter 9: 207-232
DOI:10.1007/978-3-642-53839-1_9

Cooperative transport mechanism and proton-coupling in the multidrug efflux transporter complex AcrAB-TolC. Membrane Transport Mechanism – 3D structure and beyond

GUF

2014

11

G.L.A. Mislin and I.J. Schalk
Metallomics 6, 408-420
DOI:10.1039/c3mt00359k

Siderophore-dependent iron uptake systems as gates for antibiotic Trojan horse strategies against Pseudomonas aeruginosa

CNRS

2014

10

Baco E, Hoegy F, Schalk IJ, Mislin GL
Org Biomol Chem 12(5): 749-57
DOI:10.1039/c3ob41990h

Diphenyl-benzo[1,3]dioxole-4-carboxylic acid pentafluorophenyl ester: a convenient catechol precursor in the synthesis of siderophore vectors suitable for antibiotic Trojan horse strategies

CNRS

2014

9

Bialek-Davenet S, Lavigne JP, Guyot K, Mayer N, Tournebize R, Brisse S, Leflon-Guibout V, Nicolas-Chanoine MH.
J. Antimicrob. Chemother.
DOI:10.1093/jac/dku340

Differential contribution of AcrAB and OqxAB efflux pumps to multidrug resistance and virulence in Klebsiella pneumonia

APHP-BUH

2014

8

Cunrath O, Gasser V, Hoegy F, Reimmann C, Guillon L, Schalk IJ.
Env. Microbiology 2014
DOI:10.1111/1462-2920.12544

A cell biological view of siderophore Pyochelin iron uptake pathway in Pseudomonas aeruginosa

CNRS

2014

7

Stavenger RA, Winterhalter M
Sci. Transl. Med. 6:228ed7
DOI:10.1126/scitranslmed.3008605

TRANSLOCATION project: how to get good drugs into bad bugs

JUB, GSK

2014

6

Cha, H., Müller, RT, Pos, KM
Antimicrob. Agents Chemother. 58:4767-4772
DOI:10.1128/aac.02733-13

Switch-loop flexibility affects transport of large drugs by the promiscuous AcrB multidrug efflux transporter

GUF

2014

5

Daniel Pletzer, Corinne Lafon, Yvonne Braun, Thilo Köhler, Malcolm G. P. Page, Michael Mourez, Helge Weingart
PLOS ONE
DOI:10.1371/journal.pone.0111311

High-Throughput Screening of Dipeptide Utilization Mediated by the ABC Transporter DppBCDF and its Substrate-binding Proteins DppA1-A5 in Pseudomonas aeruginosa

JUB, UGE, BASILEA, SARD

2014

4

Eicher, T, Seeger, MA, Anselmi, C, Zhou, W, Brandstätter, L, Verrey, F, Diederichs, K, Faraldo-Gómez, JD, Pos, KM
eLife 3:e03145
DOI:10.7554/eLife.03145

Coupling of remote alternating-access transport mechanisms for protons and substrates in the multidrug efflux pump

GUF

2014

3

N. Modi, I. Bárcena-Uribarri, M. Bains, R. Benz, R.E.W. Hancock, and U. Kleinekathöfer
Biochemistry 52, 5522-5532
DOI:10.1021/bi400522b

Role of the central arginine R133 towards the ion selectivity of the phosphate specific channel OprP: effects of charge and solvation

JUB

2013

2

J. Lu, N. Modi, and U. Kleinekathöfer
J. Phys. Chem. B, 117 (50), pp 15966–15975
DOI:10.1021/jp408495v

Simulation of Ion Transport Through an N-acetylneuraminic Acid-inducible Membrane Channel: From Understanding to Engineering

JUB

2013

1

P. Ruggerone, S. Murakami, K. M. Pos, and A.V. Vargiu
Curr. Top. Med. Chem. 13, 3079-3100
DOI:10.2174/15680266113136660220

RND Efflux Pumps: Structural Information Translated Into Function And Inhibition Mechanisms

UNICA, GUF

2013