Publications

Statistics

This graph shows the number of publications acknowledging support from the Action each year (to Feb 2019). The bars are coloured according to the number of COST Countries participating in each paper.

And this graph shows the number of publications by country (to Feb 2019), coloured by the number of collaborating countries on each paper.

2019

Validation and Applications of Protein–Ligand Docking Approaches Improved for Metalloligands with Multiple Vacant Sites, Giuseppe Sciortino, Eugenio Garribba, Jean-Didier Maréchal (2019) Inorg. Chem. 58 294-306

Zinc transporter 10 (ZnT10)-dependent extrusion of cellular Mn2+ is driven by an active Ca2+-coupled exchange, Moshe Levy, Nadav Elkoshi, Shiran Barber-Zucker, Eitan Hoch, Raz Zarivatch, Michal Hershfinkel and Israel Sekler (2019) Journal of Biological Chemistry e-pub ahead of print. doi: 10.1074/jbc.RA118.006816

Chemical rescue of H+ delivery in proton transfer mutants of reaction center of photosynthetic bacteria, Péter Maróti (2019) Biochimica et Biophysica Acta – Bioenergetics 1860 317-324.

Computational insight into the interaction of oxaliplatin with insulin, Giuseppe Sciortino, José-Emilio Sánchez-Aparicio, Jaime Rodríguez-Guerra Pedregal, Eugenio Garribba  and  Jean-Didier Maréchal (2019) Metallomics Advance Article doi:10.1039/C8MT00341F

2018

Directed Self-Assembly of Trimeric DNA-Bindingchiral Miniprotein Helicates, Jacobo Gómez-González, Diego G. Peña, Ghofrane Barka, Giuseppe Sciortino, Jean-Didier Maréchal, Miguel Veazquez López, M. Eugenio Vázquez (2018) Frint. Chem. 6 Article 520

In silico discovery of a Substituted 6-Methoxy-quinalidine with Leishmanicidal Activity in Leishmania infantum,
Strahinja Stevanović, Andrej Perdih, Milan Senćanski, Sanja Glišić, Margarida Duarte, Ana M. Tomás, Filipa V. Sena, Filipe M. Sousa, Manuela M. Pereira, Tom Solmajer (2018) Molecules 23 772

Dissecting the Forces that Dominate Dimerization of the Nucleotide Binding Domains of ABCB1, Dániel Szöllősi, Gergely Szakács, Peter Chiba, Thomas Stockner Biophysical Journal 114 331-342

Both reentrant loops of the sodium-coupled glutamate transporters contain molecular determinants of cation selectivity, Nechama Silverstein, Alaa Sliman, Thomas Stockner, Baruch I. Kanner (2018) Journal of Biological Chemistry 293 14200-14209

Fluorescence induction of photosynthetic bacteria, G. SIPKA, M. KIS, J.L. SMART, and P. MARÓTI, (2018) Photosyntetics 56 125-131

Directed Evolution of an Artificial Imine Reductase, Martina Hestericová, Dr. Tillman Heinisch, Lur Alonso‐Cotchico, Prof. Dr. Jean‐Didier Maréchal, Dr. Pietro Vidossich, Prof. Dr. Thomas R. Ward (2018) Angewandte Chemie Int. Ed. 130 1881-1886

Identification of the site of oxidase substrate binding in Scytalidium thermophilum catalase, Yonca Yuzugullu Karakus, Gunce Goc, Sinem Balci, Briony A. Yorke, Chi H. Trinh, Michael J. McPherson, Arwen R. Pearson (2018) Acta Crystallographica D74 979-985

Detection of a novel lysozyme monoclinic crystal form upon controlled relative humidity variation, A. Valmas, S. Logotheti, S. Saslis,  S. Fili, M. Spiliopoulou, D. Beckers, T. Degen, G. Nénert, A. N. Fitch, M. Calamiotou, F. Karavassili, I. Margiolaki (2018) Journal of Applied Crystallography 51 1671-1683

Evidence of functional deficits at the single muscle fiber level in experimentally-induced renal insufficiency, Georgia I. Mitrou, Giorgos K. Sakkas, Konstantina P. Poulianiti, Aggeliki Karioti, Konstantinos Tepetes, Grigorios Christodoulidis, Giannis Giakas, Ioannis Stefanidis, Michael A. Geeves, Yiannis Koutedakis, Christina Karatzaferi (2018) Journal of Biomechanics 82 259-265

SwitCCh: Metal‐Site Design for Controlling the Assembly of a Coiled‐Coil Homodimer, Jana Aupič, Fabio Lapenta, Roman Jerala (2018) ChemBioChem 19 2453-2457

Photocage-initiated time-resolved solution X-ray scattering investigation of protein dimerization Inokentijs Josts, Stephan Niebling, Yunyun Gao, Matteo Levantino, Henning Tidow, Diana Monteiro (2018) IUCrJ 5 667-672

Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study, Björn Hellenkamp,Sonja Schmid, Olga Doroshenko, Oleg Opanasyuk, Ralf Kühnemuth, Soheila Rezaei Adariani, Benjamin Ambrose, Mikayel Aznauryan, Anders Barth, Victoria Birkedal, Mark E. Bowen, Hongtao Chen, Thorben Cordes, Tobias Eilert, Carel Fijen, Christian Gebhardt, Markus Götz, Giorgos Gouridis, Enrico Gratton, Taekjip Ha, Pengyu Hao, Christian A. Hanke, Andreas Hartmann, Jelle Hendrix, Lasse L. Hildebrandt, Verena Hirschfeld, Johannes Hohlbein, Boyang Hua, Christian G. Hübner, Eleni Kallis, Achillefs N. Kapanidis, Jae-Yeol Kim, Georg Krainer, Don C. Lamb, Nam Ki Lee, Edward A. Lemke, Brié Levesque, Marcia Levitus, James J. McCann, Nikolaus Naredi-Rainer, Daniel Nettels, Thuy Ngo, Ruoyi Qiu, Nicole C. Robb, Carlheinz Röcker, Hugo Sanabria, Michael Schlierf, Tim Schröder, Benjamin Schuler, Henning Seidel, Lisa Streit, Johann Thurn, Philip Tinnefeld, Swati Tyagi, Niels Vandenberk, Andrés Manuel Vera, Keith R. Weninger, Bettina Wünsch, Inna S. Yanez-Orozco, Jens Michaelis, Claus A. M. Seidel, Timothy D. Craggs, Thorsten Hugel (2018) Nature Methods 15 669-676

Dopamine transporter oligomerization involves the scaffold domain, but spares the bundle domain, Kumaresan Jayaraman, Alex N. Morley, Daniel Szöllősi, Tsjerk A. Wassenaar, Harald H. Sitte, Thomas Stockner (2018) PLOS Computational Biology 14 e1006229

Structural basis for energy transduction by respiratory alternative complex III. Sousa, J. S., Calisto, F., Langer, J. D., Mills, D. J., Refojo, P. N., Teixeira, M., Kühlbrandt, W., Vonck, J., Pereira, M. M. (2018).  Nature communications, 9, 1728. doi:10.1038/s41467-018-04141-8

Decoding Surface Interaction of VIVO Metallodrug Candidates with Lysozyme Giuseppe Sciortino, Daniele Sanna, Valeria Ugone, Agustí Lledós, Jean-Didier Maréchal, Eugenio Garribba (2018) Inorganic Chemistry 57 (8), 4456-4469 DOI: 10.1021/acs.inorgchem.8b00134

Coiled coil protein origami: from modular design principles towards biotechnological applications, Fabio Lapenta, Jana Aupič, Žiga Strmšek, Roman Jerala (2018) Chem. Soc. Rev. 47 3530-3542

PyChimera: use UCSF Chimera modules in any Python 2.7 project, Jaime Rodríguez-Guerra Pedregal, Jean-Didier Maréchal; , Bioinformatics, 34,  1784–1785

Characterization of mercury(II)-induced inhibition of photochemistry in the reaction center of photosynthetic bacteria, Gábor Sipka, Mariann Kis, Péter Maróti (2018) Photosynthesis Research 136 379-392

The dual role of MamB in magnetosome membrane assembly and magnetite biomineralization, René Uebe, Noa Keren‐Khadmy, Natalie Zeytuni, Emanuel Katzmann, Yotam Navon, Geula Davidov, Ronit Bitton, Jürgen M. Plitzko, Dirk Schüler, Raz Zarivach (2018) Molecular Microbiology 107 542-557

A Single Mutation is Sufficient to Modify the Metal Selectivity and Specificity of a Eukaryotic Manganese Superoxide Dismutase to Encompass Iron, Thérèse Hunter, Rosalin Bonett, Anthony Sacco, Marita Vella, Paul‐Michael Sultana, Chi H. Trinh, Hava B. R. Fadia, Tomasz Borowski, Rebeca Garcia‐Fandiño, Thomas Stockner, Gary J. Hunter (2018) Chemistry: A European Journal 24 5303-5308

Photoprotection in intact cells of photosynthetic bacteria: quenching of bacteriochlorophyll fluorescence by carotenoid triplets Gábor Sipka, Péter Maróti Photosynthesis Research (2018) 136 17-30

Prediction of the interaction of metallic moieties with proteins: An update for protein‐ligand docking techniques, Giuseppe Sciortino, Jaime Rodríguez‐Guerra Pedregal, Agustí Lledós, Eugenio Garribba, Jean‐Didier Maréchal Journal of Computational Chemistry (2018) 39 42-51

2017

Design of coiled-coil protein-origami cages that self-assemble in vitro and in vivo, Ajasja Ljubetič, Fabio Lapenta, Helena Gradišar, Igor Drobnak, Jana Aupič, Žiga Strmšek, Duško Lainšček, Iva Hafner-Bratkovič, Andreja Majerle, Nuša Krivec, Mojca Benčina, Tomaž Pisanski, Tanja Ćirković Veličković, Adam Round, José María Carazo, Roberto Melero, Roman Jerala (2017) Nature Biotechnology 35 1094-1101

Dynamics of P-type ATPase transport revealed by single-molecule FRET, Mateusz Dyla, Daniel S. Terry, Magnus Kjaergaard, Thomas L.-M. Sørensen, Jacob Lauwring Andersen, Jens P. Andersen, Charlotte Rohde Knudsen, Roger B. Altman, Poul Nissen, Scott C. Blanchard (2017) Nature 551 346-351

Computational approaches for deciphering the equilibrium and kinetic properties of iron transport proteins, H. Abdizadeh, A. R. Atilgan, C. Atilgan, B. Dedeoglu (2017) Metallomics 9 1512-1533

Functional responses of uremic single skeletal muscle fibers to redox imbalances, GI Mitrou, KP Poulianiti, Y Koutedakis, AZ Jamurtas, MD Maridaki, I Stefanidis, GK Sakkas, and C Karatzaferi (2017) Hippokratia 21 3

Design of an enantioselective artificial metallo-hydratase enzyme containing an unnatural metal-binding amino acid, Ivana Drienovská, Lur Alonso-Cotchico, Pietro Vidossich, Agustí Lledós, Jean-Didier Maréchal, Gerard Roelfes (2017) Chem. Sci. 8 7228-7235

Modulators of actin-myosin dissociation: basis for muscle type differences in contraction during fatigue, Christina Karatzaferi, Nancy Adamek, Michael A. Geeves (2017) Am J Physiol Cell Physiol 313 C644-C654

Transition metal binding selectivity in proteins and its correlation with the phylogenomic classification of the cation diffusion facilitator protein family, Shiran Barber-Zucker, Boaz Shaanan, Raz Zarivach (2017) Nature Scientific Reports 7 16381

Dengue virus 3 NS5 methyltransferase domain: expression, purification, crystallization and first structural data from microcrystalline specimens, Alexandros Valmas, Stavroula Fili, Nikos Nikolopoulos, Maria Spiliopoulou, Magdalini Christopoulou, Fotini Karavassili, Christos Kosinas, Konstantinos Bastalias, Eleftheria Rosmaraki, Julie Lichiére, Andrew Fitch, , Detlef Beckers, Thomas Degen, Nicolas Papageorgiou, Bruno Canard, Bruno Coutard, Irene Margiolaki (2017) Zeitschrift für Kristallographie 233 DOI:10.1515/zkri-2017-2091

Metal-Dependent DNA Recognition and Cell Internalization of Designed, Basic Peptides Soraya Learte-Aymamí, Natalia Curado, Jéssica Rodríguez, M. Eugenio Vázquez, and José L. Mascareñas Journal of the American Chemical Society 2017 139 (45), 16188-16193 DOI: 10.1021/jacs.7b07422

Elucidation of Binding Site and Chiral Specificity of Oxidovanadium Drugs with Lysozyme through Theoretical Calculations, Giuseppe Sciortino, Daniele Sanna, Valeria Ugone, Giovanni Micera, Agustí Lledós, Jean-Didier Maréchal, and Eugenio Garribba (2017) Inorganic Chemistry 56 12938-12951, DOI: 10.1021/acs.inorgchem.7b01732

The biophysics of a critical phenomenon: colonization and sedimentation of the photosynthetic bacteria Rubrivivax gelatinosus, Mariann Kis, Gábor Sipka, Ferhan Ayaydin, Péter Maróti (2017) European Biophysical Journal doi: 10.1007/s00249-017-1236-4

GaudiMM: A modular multi-objective platform for molecular modeling, Jaime Rodríguez-Guerra Pedregal, Giuseppe Sciortino, Jordi Gausp, Martí Municoy, Jean-Didier Maréchal (2017) Journal of Computational Chemistry, DOI:10.1002/jcc.24847

Modulation of coiled-coil dimer stability through surface residues while preserving pairing specificity Igor Drobnak, Helena Gradišar, Ajasja Ljubeti, Estera Merljak & Roman Jerala (2017) Journal of the American Chemical Society, in press

Stoichiometry and kinetics of mercury uptake by photosynthetic bacteria Mariann Kis, Gábor Sipka & Peter Maróti (2017) Photosynthesis Research 132 197-209

X-ray radiation damage to biological macromolecules: further insights Elspeth F Garman & Martin Weik (2017) Journal of Synchrotron Radiation 24 1-6

2016

Structure and Function of Bacterial Cytochrome c Oxidases, Joseph A. Lyon, Florian Hilber, Martin Caffrey (2016) In: Cramer W., Kallas T. (eds) Cytochrome Complexes: Evolution, Structures, Energy Transduction, and Signaling. Advances in Photosynthesis and Respiration (Including Bioenergy and Related Processes), vol 41 Springer, Dordrecht. pp 307-329

Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems, Mykola Dimura, Thomas O Peulen, Christian A Hanke, Aiswaria Prakash, Holger Gohlke, Claus AM Seidel (2016) Current Opinion in Structural Biology 40 163-185

Cyclo-lib: a database of computational molecular dynamics simulations of cyclodextrins, Edgar Mixcoha, Roberto Rosende, Rebeca Garcia-Fandino, Ángel Piñeiro (2016) Bioinformatics 32 3371-3373

Bioelectrochemical monitoring of soluble guanylate cyclase inhibition by the natural β-carboline canthin-6-one Antonio Doménech-Carbó, Regina Rodrigo, Jean-Didier Maréchal, Erwan Poupon, Alain Fournet, Bruno Figadère, Gerardo Cebrián-Torrejón (2016) Journal of Molecular Structure e-pub ahead of print DOI: 10.1016/j.molstruc.2016.12.016

A look into the biochemistry of magnetosome biosynthesis in magnetotactic bacteria Shiran Barber-Zucker & Raz Zavirach (2016) ACS Chem. Biol. e-pub ahead of print DOI: 10.1021/acschembio.6b01000

The Environment Shapes the Inner Vestibule of LeuT Azmat Sohail, Kumaresan Jayaraman, Santhoshkannan Venkatesan, Kamil Gotfryd, Markus Daerr, Ulrik Gether, Claus J. Loland, Klaus T. Wanner, Michael Freissmuth, Harald H. Sitte, Walter Sandtner, Thomas Stockner (2016) PLOS Comp. Biol. DOI:10.1371/journal.pcbi.1005197

Ruthenation of Non‐stacked Guanines in DNA G‐Quadruplex Structures: Enhancement of c‐MYC Expression Jéssica Rodríguez, Jesús Mosquera, José R. Couceiro, M. Eugenio Vázquez & José L. Mascareñas (2016) Angewandte Chemie Int. Ed. 128 15844-15847

Coxsackievirus B3 protease 3C: expression, purification, crystallization and preliminary structural insights S. Fili, A. Valmas, M. Christopoulou, M. Spiliopoulou, N. Nikolopoulos, J. Lichière, S. Logotheti, F. Karavassili, E. Rosmaraki, A. Fitch, J. Wright, D. Beckers, T. Degen, G. Nénert, R. Hilgenfeld, N. Papageorgiou, B. Canard, B. Coutard and I. Margiolaki (2016) Acta Cryst. F72 877-884

Self-assembling a,g-cyclic peptides that generate cavities with tunable properties Nuria Rodriguez-Vazquez, Rebeca Garcıa-Fandino, Manuel Amorın and Juan R. Granja (2016) Chem. Sci., 7 183-187.

A designed DNA binding motif that recognizes extended sites and spans two adjacent major grooves Jessica Rodrıguez, Jesus Mosquera, Rebeca Garcıa-Fandino, M. Eugenio Vazquez and Jose L. Mascarenhas (2016) Chem. Sci., 7 3298-3303.

Predicting long term cooperativity and specific modulators of receptor interactions in human transferrin from dynamics within a single micro state Haleh Abdizadeh, Canan Atilgan (2016) Phys. Chem. Chem. Phys18 7916-7926.

Lipid Bilayer Membrane Perturbation by Embedded Nanopores: A Simulation Study Rebeca Garcia-Fandiño, Ángel Piñeiro, Jemma L. Trick, and Mark S. P. Sansom (2016) ACS Nano10  3693–3701.

Membrane transporters studied by EPR spectroscopy: structure determination and elucidation of functional dynamics, Anna Mullen, Jenny Hall, Janika Diegel, Isa Hassan, Adam Fey, Fraser MacMillan (2016) Biochemical Society Transactions, 44 905-915.

Optimization of the classical method for nucleation and growth of rhombohedral insulin crystals by pH titration and screening  F.V. Hodzhaoglu, M. Conejero-Muriel, I.L. Dimitrov, J.A. Gavin (2016) Bulgarian Chemical Comunications, 48,  A, 29-37.

Nickel-Promoted Recognition of Long DNA Sites by Designed Peptide Derivatives  Jessica Rodrıguez, Jesus Mosquera,  M. Eugenio Vazquez and Jose L. Mascarenhas (2016) Chem. Eur. J., 22, 13474-13477.

Disease-Homologous Mutation in the Cation Diffusion Facilitator Protein MamM Causes Single-Domain Structural Loss and Signifies Its Importance  Shiran Barber-Zucker , René Uebe , Geula Davidov, Yotam Navon, Dror Sherf, Jordan H. Chill, Itamar Kass, Ronit Bitton, Dirk Schüler, Raz Zarivach (2016) Scientific Reports 6 31933.

Rapid Electron Transfer within the III-IV Supercomplex in Corynebacterium glutamicum Simone Graf, Olga Fedotovskaya, Wei-Chun Kao, Carola Hunte, Pia Ädelroth, Michael Bott, Christoph von Ballmoos & Peter Brzezinski (2016) Scientific Reports 6 34098

Induction and anisotropy of fluorescence of reaction center from photosynthetic bacterium Rhodobacter sphaeroides. Sipka G, Maróti P. (2015) Photosynthesis Research, 127 61-68

2015

Refinement of the Central Steps of Substrate Transport by the Aspartate Transporter GltPh: Elucidating the Role of the Na2 Sodium Binding Site Venkatesan SK, Saha K, Sohail A, Sandtner W, Freissmuth M, Ecker GF, Sitte HH, Stockner TS. (2015) PLOS Computational Biology 11 e1004551

Molecular dynamics simulations for designing biomimetic pores based on internally functionalized self-assembling α,γ-peptide nanotubes. Calvelo M, Vázquez S, García-Fandiño R. (2015) Physical Chemistry Chemical Physics, 17, 28586-28601

Using synchrotrons and XFELs for time-resolved X-ray crystallography and solution scattering experiments on biomolecules. Levantino M, Yorke BA, Monteiro DC, Cammarata M, Pearson AR. (2015) Current Opinion in Structural Biology 35 41-48

Human insulin polymorphism upon ligand binding and pH variation: the case of 4-ethylresorcinol. Fili S, Valmas A, Norrman M, Schluckebier G, Beckers D, Degen T, Wright J, Fitch A, Gozzo F, Giannopoulou AE, Karavassili F, Margiolaki I. (2015) IUCr Journal 2 534-544

Type-II NADH:quinone oxidoreductase from Staphylococcus aureus has two distinct binding sites and is rate limited by quinone reduction. Sena FV, Batista AP, Catarino T, Brito JA, Archer M, Viertler M, Madl T, Eurico J. Cabrita EJ, Pereira MP. (2015) Molecular Microbiology 98 272-288

 Investigating the dynamic nature of the ABC transporters: ABCB1 and MsbA as examples for the potential synergies of MD theory and EPR applications. Stockner T, Mullen A, MacMillan F. (2015) Biochemical Society Transactions 43 1023-1032

Fluorescence-Labeled Bis-benzamidines as Fluorogenic DNA Minor-Groove Binders: Photophysics and Binding Dynamics. Bordello J, Sánchez MI, Vázquez ME, Mascareñas JL, Al-Soufi W, Novo M. (2015) Chemistry- a European Journal 21 1609-1619

Purple non-sulfur photosynthetic bacteria monitor environmental stresses. Kis M, Sipka G, Asztalos E, Rázga Z, Maróti P. (2015) Journal of Photochemistry and Photobiology B: Biology 151 110-117

The rate of second electron transfer to QB in bacterial reaction center of impaired proton delivery shows hydrogen-isotope effect. Maróti A, Wraight CA, Maróti P. Biochimica et Biophysica Acta 1847 223-230

Novel crystalline phase and first-order phase transitions of human insulin complexed with two distinct phenol derivatives. Valmas A, Magiouf K, Fili S, Norrman M, Schluckebier G, Beckers D, Degen T, Wright J, Fitch A, Gozzo F, Giannopoulou AE, Karavassili F, Margiolaki I. (2015) Acta Crystallographica D71 819-828

Protonated Rhodosemiquinone at the QB Binding Site of the M265IT Mutant Reaction Center of Photosynthetic Bacterium Rhodobacter sphaeroides. Maróti A, Wraight CA, Maróti P. (2015) Biochemistry 54 2095-2103

Fluorescence relaxation in intact cells of photosynthetic bacteria: donor and acceptor side limitations of reopening of the reaction center. Asztalos E, Sipka G, Maróti P. (2015) Photosynthetic Research 124 31-44

Stigmatellin Probes the Electrostatic Potential in the QB Site of the Photosynthetic Reaction Center. Gerencsér L, Boros B, Derrien V, Hanson, DK, Wraight CA, Sebban P, Maróti P. (2015) Biophysical Journal 108 379-394

2014

Assembly of photosynthetic apparatus in Rhodobacter sphaeroides as revealed by functional assessments at different growth phases and in synchronized and greening cells. Kis M, Asztalos G, Sipka G, Maróti P. (2014) Photosynthetic Research 122 261-273