Research Products

 

The BioPhysicalChemsitry Group@unica:

Selected Publications:

Siderophore receptors:

Bacterial porins and rules for antibiotics penetration:

  • Bodrenko, I.V., Salis, S., Acosta-Gutierrez, S. & Ceccarelli, M.  Diffusion of large particles through small pores: from entropic to enthalpic transport, J. Chem. Phys. 150, 211102 (2019) OPEN ACCESS (Download the PDF)
  • Acosta-Gutierrez, S. et al. Getting Drugs into Gram-Negative Bacteria: Rational Rules for Permeation through General Porins. ACS Infect. Dis. 4, 1487–1498 (2018).
  • Samanta, S. et al. Getting Drugs through Small Pores: Exploiting the Porins Pathway in Pseudomonas aeruginosa. ACS Infect. Dis. 4, 1519–1528 (2018).
  • , , , , , , and , Bacterial Outer Membrane Porins as Electrostatic Nanosieves: Exploring Transport Rules of Small Polar Molecules ACS Nano (2017) OPEN ACCESS (Download PDF)
  • Bodrenko, I. V., Wang, J., Salis, S., Winterhalter, M. & Ceccarelli, M. Sensing Single Molecule Penetration into Nanopores: Pushing the Time Resolution to the Diffusion Limit. ACS Sens 2, 1184–1190 (2017)
  • Pathania, M. et al. Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae. Structure (2018). doi:10.1016/j.str.2018.03.010

Intracellular channels:

  • Benkerrou, D. et al. A perspective on the modulation of plant and animal two pore channels (TPCs) by the flavonoid naringenin. Biophysical Chemistry 254, 106246 (2019), doi: 10.1016/j.bpc.2019.106246
  • Guardiani, C. et al. yVDAC2, the second mitochondrial porin isoform of Saccharomyces cerevisiae. Biochim Biophys Acta 1859, 270–279 (2019)
  • De Pinto, Matteo Ceccarelli, Mariano Andrea Scorciapino, G. M. I. S. A. M. M. C. V. et al. Folded Structure and Membrane Affinity of the N‐Terminal Domain of the Three Human Isoforms of the Mitochondrial Voltage- Dependent Anion-Selective Channel. ACS Omega 3, 11415–11425 (2018)

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TitoloData di pubblicazioneAutoriTipoAbstract
Complexes formed by the siderophore-based monosulfactam antibiotic BAL30072 and their interaction with the outer membrane receptor PiuA of P. aeruginosa2019SCORCIAPINO, MARIANO ANDREA  ; MALLOCI, GIULIANO  ; SERRA, ILARIA  ; MILENKOVIC, STEFAN  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Diffusion of large particles through small pores: From entropic to enthalpic transport2019BODRENKO, IGOR  ; SALIS, SAMUELE  ; ACOSTA GUTIERREZ, SILVIA  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Glucose transport via the pseudomonad porin OprB: implications for the design of Trojan Horse anti-infectives2019ACOSTA GUTIERREZ, SILVIA  ; BODRENKO, IGOR  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
A perspective on the modulation of plant and animal two pore channels (TPCs) by the flavonoid naringenin2019BENKERROU, DEHBIA  ; MILENKOVIC, STEFAN  ; CECCARELLI, MATTEO  ; FILIPPINI, ALBERTO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
The complex of ferric-enterobactin with its transporter from Pseudomonas aeruginosa suggests a two-site model2019MILENKOVIC, STEFAN  ; MALLOCI, GIULIANO  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
yVDAC2, the second mitochondrial porin isoform of Saccharomyces cerevisiae2018BODRENKO, IGOR  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
Free energy calculations and molecular properties of substrate translocation through OccAB porins2018BENKERROU, DEHBIA  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Folded Structure and Membrane Affinity of the N-Terminal Domain of the Three Human Isoforms of the Mitochondrial Voltage-Dependent Anion-Selective Channel2018MANZO, GIORGIA  ; SERRA, ILARIA  ; CASU, MARIANO  ; CECCARELLI, MATTEO  ; SCORCIAPINO, MARIANO ANDREA  1 Contributo su Rivista::1.1 Articolo in rivista
Preacinetobactin not acinetobactin is essential for iron uptake by the BauA transporter of the pathogen Acinetobacter baumannii2018SERRA, ILARIA  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
Unusual Constriction Zones in the Major Porins OmpU and OmpT from Vibrio cholerae2018ACOSTA GUTIERREZ, SILVIA  ; WINTERHALTER, MATHIAS  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
Getting drugs into Gram-negative bacteria: Rational rules for permeation through general porins2018ACOSTA GUTIERREZ, SILVIA  ; BODRENKO, IGOR  ; WINTERHALTER, MATHIAS  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Getting drugs through small pores: Exploiting the porins pathway in Pseudomonas aeruginosa2018SAMANTA, SUSRUTA  ; BODRENKO, IGOR  ; ACOSTA GUTIERREZ, SILVIA  ; D'AGOSTINO, TOMMASO  ; WINTERHALTER, MATHIAS  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Effects of amphipathic profile regularization on structural order and interaction with membrane models of two highly cationic branched peptides with β-sheet propensity2018SERRA, ILARIA  ; CASU, MARIANO  ; CECCARELLI, MATTEO  ; RINALDI, ANDREA  ; SCORCIAPINO, MARIANO ANDREA  1 Contributo su Rivista::1.1 Articolo in rivista
Bacterial outer membrane porins as electrostatic nanosieves: exploring transport rules of small polar molecules2017ACOSTA GUTIERREZ, SILVIA  ; BODRENKO, IGOR  ; MALLOCI, GIULIANO  ; SCORCIAPINO, MARIANO ANDREA  ; WINTERHALTER, MATHIAS  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Porin flexibility in Providencia stuartii: Cell-surface-exposed loops L5 and L7 are markers of Providencia porin OmpPst12017D'AGOSTINO, TOMMASO  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
Sensing Single Molecule Penetration into Nanopores: Pushing the Time Resolution to the Diffusion Limit2017BODRENKO, IGOR  ; SALIS, SAMUELE  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
General method to determine the flux of charged molecules through nanopores applied to β-Lactamase inhibitors and OmpF2017PIRA, ALESSANDRO  ; SCORCIAPINO, MARIANO ANDREA  ; BODRENKO, IGOR  ; CECCARELLI, MATTEO  ; WINTERHALTER, MATHIAS  ; 1 Contributo su Rivista::1.1 Articolo in rivista
Towards In-Silica Screening of Molecule Permeation through Outer Membrane Channels in Gramm-Negative Bacteria2017BODRENKO, IGOR  ; ACOSTA GUTIERREZ, SILVIA  ; D'AGOSTINO, TOMMASO  ; SALIS, SAMUELE  ; SAMANTA, SUSRUTA  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.5 Abstract in rivista-
Filtering with the electric field: a story on protein channels electrostatics2017ACOSTA GUTIERREZ, SILVIA  ; MALLOCI, GIULIANO  ; BODRENKO, IGOR  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.5 Abstract in rivista-
How to get large drugs through small pores? Exploiting the porins pathway in Pseudomonas aeruginosa2017SAMANTA, SUSRUTA  ; D'AGOSTINO, TOMMASO  ; ACOSTA GUTIERREZ, SILVIA  ; SCORCIAPINO, MARIANO ANDREA  ; BODRENKO, IGOR  ; WINTERHALTER, MATHIAS  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.5 Abstract in rivista-
Investigation of siderophore-monobactam antibiotic derivatives: their iron(III)-complexes and binding to receptors2017SCORCIAPINO, MARIANO ANDREA  ; MALLOCI, GIULIANO  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.5 Abstract in rivista-
Rationalizing the permeation of polar antibiotics into Gram-negative bacteria2017SCORCIAPINO, MARIANO ANDREA  ; ACOSTA GUTIERREZ, SILVIA  ; BENKERROU, DEHBIA  ; D'AGOSTINO, TOMMASO  ; MALLOCI, GIULIANO  ; SAMANTA, SUSRUTA  ; BODRENKO, IGOR  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
The singular behavior of a b-type semi-synthetic two branched polypeptide: three-dimensional structure and mode of action2016SERRA, ILARIA  ; PIRA, ALESSANDRO  ; CECCARELLI, MATTEO  ; CASU, MARIANO  ; RINALDI, ANDREA  ; SCORCIAPINO, MARIANO ANDREA  1 Contributo su Rivista::1.1 Articolo in rivista
Exploiting the porin pathway for polar compound delivery into Gram-negative bacteria2016SCORCIAPINO, MARIANO ANDREA  ; D'AGOSTINO, TOMMASO  ; ACOSTA GUTIERREZ, SILVIA  ; MALLOCI, GIULIANO  ; BODRENKO, IGOR  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Macroscopic electric field inside water-filled biological nanopores2016ACOSTA GUTIERREZ, SILVIA  ; BODRENKO, IGOR  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Internal electric field of Gram- unspecific porins directs the choreography of antibiotic translocation2016SCORCIAPINO, MARIANO ANDREA  ; D'AGOSTINO, TOMMASO  ; ACOSTA GUTIERREZ, SILVIA  ; BODRENKO, IGOR  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.5 Abstract in rivista-
Water-based screening of antibiotics permeability2016ACOSTA GUTIERREZ, SILVIA  ; SCORCIAPINO, MARIANO ANDREA  ; BODRENKO, IGOR  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.5 Abstract in rivista-
A kinetic model for molecular diffusion through pores2016D'AGOSTINO, TOMMASO  ; SALIS, SAMUELE  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
VDAC3 as a sensor of oxidative state of the intermembrane space of mitochondria: the putative role of cysteine residue modifications2016GUARDIANI, CARLO  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
Molecular Basis of Filtering Carbapenems by Porins from β-Lactam-resistant Clinical Strains of Escherichia coli2016SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
A computational study of ion current modulation in hVDAC3 induced by disulfide bonds2016GUARDIANI, CARLO  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Unexpected modifications of cysteines in VDAC3: indication that VDAC3 may signal the mitochondrial intermembrane redox state2016GUARDIANI, CARLO  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.5 Abstract in rivista-
Can modification of VDAC(s) cysteine residues act as a sensor of oxidative state of the intermembrane space of mitochondria?2016GUARDIANI, CARLO  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.5 Abstract in rivista-
MOMP from Campylobacter jejuni Is a Trimer of 18-Stranded β-Barrel Monomers with a Ca(2+) Ion Bound at the Constriction Zone2016ACOSTA GUTIERREZ, SILVIA  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
A database of force-field parameters, dynamics, and properties of antimicrobial compounds2015MALLOCI, GIULIANO  ; VARGIU, ATTILIO VITTORIO  ; SERRA, GIOVANNI  ; BOSIN, ANDREA  ; RUGGERONE, PAOLO  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Molecular basis of substrate translocation through the outer membrane channel OprD of Pseudomonas aeruginosa2015SAMANTA, SUSRUTA  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Small-molecule transport by CarO, an abundant eight-stranded β-barrel outer membrane protein from Acinetobacter baumannii2015D'AGOSTINO, TOMMASO  ; CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
Physical methods to quantify small antibiotic molecules uptake into Gram-negative bacteria2015CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Filtering with electric field: the case of E. coli porins2015ACOSTA GUTIERREZ, SILVIA  ; SCORCIAPINO, MARIANO ANDREA  ; BODRENKO, IGOR  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Analysis of fast channel blockage: revealing substrate binding in the microsecond range2015BODRENKO, IGOR  ; RUGGERONE, PAOLO  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
The N-Terminal peptides of the three human isoforms of the mitochondrial voltage-dependent anion channel have different helical propensities2015GUARDIANI, CARLO  ; SCORCIAPINO, MARIANO ANDREA  ; AMODEO, GIUSEPPE FEDERICO  ; GRDADOLNIK, JOZE  ; CECCARELLI, MATTEO  ; CASU, MARIANO  1 Contributo su Rivista::1.1 Articolo in rivista
Charged residues distribution modulates selectivity of the open state of human isoforms of the voltage dependent anion-selective channel2014AMODEO, GIUSEPPE FEDERICO  ; SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Transport of Antibiotics through the Substrate Specific OprD Channel of Pseudomonas Aeruginosa2014CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista-
Antibiotic Transport through Porins2014CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista-
Role of Antibiotic Side Chains in Uptake Through OmpPst1 Channel from Providencia Stuartii2014CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista-
The open state of human VDAC isoforms compared through MD simulations2014SCORCIAPINO, MARIANO ANDREA  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.5 Abstract in rivista-
The Gating Mechanism of the Human Aquaporin 5 Revealed by Molecular Dynamics Simulations2013CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
Different molecular mechanisms of inhibition of bovine viral diarrhea virus and hepatitis C virus RNA-dependent RNA polymerases by a novel benzimidazole2013VARGIU, ATTILIO VITTORIO  ; CECCARELLI, MATTEO  ; RUGGERONE, PAOLO  ; BLOIS, SYLVAIN SERGE DANIEL  ; GILIBERTI, GABRIELE  ; 1 Contributo su Rivista::1.1 Articolo in rivista
Deletion of β-strands 9 and 10 converts VDAC1 voltage dependence in an asymmetrical process2013CECCARELLI, MATTEO  ; 1 Contributo su Rivista::1.1 Articolo in rivista
Structure-Function Paradigm in Human Myoglobin: How a Single-Residue Substitution Affects NO Reactivity at Low pO(2)2013SCORCIAPINO, MARIANO ANDREA  ; CASU, MARIANO  ; CECCARELLI, MATTEO  1 Contributo su Rivista::1.1 Articolo in rivista
   
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