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Bacterial Immunity

We study the arms race between bacteria and their phage foes focusing on the molecular basis of prokaryotic anti-viral defence systems and viral countermeasures. To address it, we use a combination of bioinformatics, molecular biology, biochemistry and structural biology techniques. Understanding the dynamics of the interactions between these microorganisms has profound implications for phage-based therapies and the development of new biotechnological tools.

Publications 

      Note: first or co-first authorship underlined; corresponding or co-corresponding authorship with asterisk

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  • Knowing Our Enemy in the Antimicrobial Resistance Era: Dissecting the Molecular Basis of Bacterial Defense Systems

        Mario Martinez, Irene Rizzuto, Rafael Molina*

        International Journal of Molecular Sciences (2024) 25, 9, 4929

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  • Structural characterization of PaaX, the main repressor of the phenylacetate degradation pathway in Escherichia coli W: A novel fold of transcription regulator proteins

        Víctor M Hernández-Rocamora, Rafael Molina, Alejandra Alba, César Carrasco-López, Alzoray Rojas-Altuve, Santosh            Panjikar, Ana Medina, Isabel Usón, Carlos Alfonso, Beatriz Galán, Germán Rivas, Juan A Hermoso*, Jesús M Sanz*

        International Journal of Biological Macromolecules (2024) 254, 3, 127935

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  • Molecular basis of the final step of cell division in Streptococcus pneumoniae
    Siseth Martínez-Caballero, Céline Freton, Rafael Molina, Sergio G. Bartual, Virginie Gueguen-Chaignon, Chyslène Mercy, Federico Gago, Kiran V. Mahasenan, Ines G. Muñoz, Mijoon Lee, Dusan Hesek, Shahiar Mobashery, Juan A. Hermoso* and Chistophe Grangeasse*

       Cell Reports (2023) 42, 7, 112756

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  • Verification: model-free phasing with enhanced predicted models in ARCIMBOLDO_SHREDDER​
    Ana Medina, Elisabet Jiménez, Iracema Caballero, Albert Castellví, Josep Triviño Valls, Martin Alcorlo, Rafael Molina, Juan A. Hermoso, Massimo D. Sammito, Rafael Borges and Isabel Usón*

       Acta Crystallographica (2022) D78, 1-11

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  • Molecular basis of cyclic tetra-oligoadenylate processing by small standalone CRISPR-Cas ring nucleases
    Rafael Molina*, Ricardo Garcia-Martin, Blanca López-Méndez, Anne Louise Grøn Jensen, J Rafael Ciges-Tomas, Javier Marchena-Hurtado, Stefano Stella, Guillermo Montoya*

       Nucleic Acids Research (2022) 50 11199-11213

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  • Regulation of Lytic Machineries by the FtsEX Complex in the Bacterial Divisome

       Martin Alcorlo; Siseth Martinez-Caballero; Rafael Molina; Juan A. Hermoso*

       Macromolecular Protein Complexes IV. Subcellular Biochemistry (2022)

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  • Structural basis of cyclic oligoadenylate degradation by ancillary Type III CRISPR-Cas ring nucleases
    Rafael Molina*; Anne Louise Grøn Jensen; Javier Marchena Hurtado; Blanca Lopez Mendez; Stefano Stella; Guillermo Montoya*

       Nucleic Acids Research (2021) 49, 12577–12590

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  • Integrative structural biology of the penicillin-binding protein-1 from Staphylococcus aureus, an essential component of the divisome machinery
    Siseth Martinez Caballero; Kiran Mahasenan; Choon Kim; Rafael Molina; Rhona Fletzer; Mijoon Lee; Renee Bouley; Dusan Hesek; Jed Fisher; Ines Muñoz; Mayland Chang; Shahriar Mobashery*; Juan Hermoso*​

      Computational and Structural Biotechnology Journal (2021) 19, 5392-5405

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  • Crystal structure and pathophysiological role of the pneumococcal nucleoside-binding protein PnrA
    Mohammed R Abdullah; Maria T Batuecas; Franziska Jennert; Franziska Voß; Philipp Westhoff; Thomas P Kohler; Rafael Molina; Stephanie Hirschmann; Michael Lalk; Juan A Hermoso; Sven Hammerschmidt*

      Journal of Molecular Biology (2020) 338, 495–506

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  • Structural basis of CRISPR-Cas Type III prokaryotic defence systems.
    Rafael Molina; Nicholas Sofos; Guillermo Montoya*

      Current Opinion in Structural Biology (2020) 65, 119–129

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  • Structure of Csx1-cOA4 complex reveals the basis of RNA decay in Type III-B CRISPR-Cas
    Rafael Molina; Stefano Stella; Mingxia Feng; Nicholas Sofos; Vykintas Jauniskis; Irina Pozdnyakova; Blanca Lopez-Mendez; Qunxin She; Guillermo Montoya*

      Nature Communications (2019) 10, 4302

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  • Understanding the indirect DNA read-out specificity of I-CreI Meganuclease
    Jesus Prieto; Pilar Redondo; Blanca Lopez-Mendez; Marco D' Abramo; Nekane Merino; Francisco J. Blanco; Philippe Duchateau; Guillermo Montoya; Rafael Molina*

      Scientific Reports (2018) 8, 10286

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  • Three-dimensional structures of Lipoproteins from Streptococcus pneumoniae and Staphylococcus aureus
    Sergio Galan Bartual; Martin Alcorlo; Siseth Martinez-Caballero; Rafael Molina; Juan A. Hermoso*

      International Journal of Medical Microbiology (2018) 308, 692-704

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  • Structure and Dynamics of Mesophilic Variants from the Homing Endonuclease I-DmoI
    Josephine Alba; Maria J. Marcaida; Jesus Prieto; Guillermo Montoya; Rafael Molina*; Marco D'Abramo*

      Journal of Computer-Aided Molecular Design (2017) 31, 1063–1072

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  • X-ray Structure of Catenated Lytic Transglycosylase SltB1
    Teresa Dominguez-Gil; Rafael Molina; David Dik; Edward Spink; Shahriar Mobashery*; Juan A. Hermoso*

      Biochemistry (2017) 56, 6317–6320

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  • Carbohydrate Recognition and Lysis by Bacterial Peptidoglycan Hydrolases
    Martin Alcorlo; Siseth Martinez-Caballero; Rafael Molina; Juan A Hermoso*

      Current Opinion in Structural Biology (2017) 44, 87–100

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  • Conformational dynamics in penicillin-binding protein 2a of methicillin-resistant Staphylococcus aureus, allosteric communication network and enablement of catalysis
    Kiran V. Mahasenan; Rafael Molina; Renee Bouley; Maria T. Batuecas; Jed F. Fisher; Juan A. Hermoso; Mayland Chang; Shahriar Mobashery*

      Journal of the American Chemical Society (2017) 139, 2102–2110

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  • Effect of DNA on the Conformational Dynamics of the Endonucleases I-DmoI as provided by molecular dynamics simulations
    Alessandro Grottesi; Simone Cecconi; Rafael Molina; Marco D'Abramo*

      Biopolymers (2016). 105, 898–904

 

  • Renew or Die: The molecular mechanisms of peptidoglycan recycling and antibiotic resistance in Gram-negative pathogens
    Teresa Dominguez-Gil; Rafael Molina; Martin Alcorlo; Juan Hermoso*

      Drug Resistance Updates (2016) 28, 91-104

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  • Orthologous and Paralogous AmpD Peptidoglycan Amidases from Gram-Negative Bacteria
    Ivanna Rivera; Rafael Molina; Mijoon Lee; Juan A.Hermoso*

      Microbial Drug Resistance (2016) 22, 1-7

 

  • Structure of the I-SceI nuclease complexed with its dsDNA target and three catalytic metal ions
    Jesus Prieto; Pilar Redondo; Nekane Merino; Maider Villate; Guillermo Montoya; Francisco J. Blanco; Rafael Molina*

      Acta Crystallographica (2016) F72, 473 – 479

 

  • Key Players in I-DmoI Endonuclease Catalysis Revealed from Structure and Dynamics
    Rafael Molina; Neva Besker; Maria Jose Marcaida; Guillermo Montoya; Jesus Prieto; Marco D'Abramo*

      ACS Chemical Biology (2016) 11, 1401–1407

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  • Crystal structure of the homing endonuclease I-CvuI provides a new template for genome modification
    Rafael Molina; Pilar Redondo; Blanca Lopez-Mendez; Maider Villate; Nekane Merino; Francisco Blanco; Julien Valton; Silvestre Grizot; Phillippe Duchateau; Jesus Prieto; Guillermo Montoya*

      Journal of Biological Chemistry (2015) 290, 28727–28736

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  • Engineering a Nickase on the Homing Endonuclease I-DmoI Scaffold
    Rafael Molina; Maria Jose Marcaida; Pilar Redondo; Marco Marenchino; Phillippe Duchateau; Marco D'Abramo; Guillermo Montoya*; Jesus Prieto*

      Journal of Biological Chemistry (2015) 290, 18534–18544

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  • Structure of p15PAF–PCNA complex and implications for clamp sliding during DNA replication and repair
    Alfredo De Biasio; Alain Ibañez de Opakua; Gulnahar Mortuza; Rafael Molina; Tiago Cordeiro; Francisco Castillo; Maider Villate; Nekane Merino; Sandra Delgado; David Gil Carton; Irene Luque; Tammo Diercks; Pau Benadó; Guillermo Montoya; Francisco Blanco*

      Nature Communications (2015) 6, 1–12

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  • Visualizing phosphodiester-bond hydrolysis by an endonuclease
    Rafael Molina; Stefano Stella; Pilar Redondo; Hansel Gomez; Maria Jose Marcaida; Modesto Orozco; Jesus Prieto; Guillermo Montoya*

      Nature Structural & Molecular Biology (2015) 22, 65–72

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  • BuD, a helix–loop–helix DNA-binding domain for genome modification
    Stefano Stella; Rafael Molina; Blanca Lopez-Mendez; Alexandre Juillerat; Claudia Bertonati; Fayza Daboussi; Ramon Campos-Olivas; Phillippe Duchateau; Guillermo Montoya*

      Acta Crystallographica (2014) D70, 2042-2052

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  • A complement to the modern crystallographer’s toolbox: caged gadolinium complexes with versatile binding modes
    Meike Stelter; Rafael Molina; Sandra Jeudy; Richard Kahn; Chantal Abergel; Juan Antonio Hermoso*

      Acta Crystallographica (2014) D70, 1506-1516

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  • Crystallization and preliminary X-ray diffraction analysis of the homing endonuclease I-CvuI from Chlorella vulgaris in complex with its target DNA
    Pilar Redondo; Nekane Merino; Maider Villate; Francisco J. Blanco; Guillermo Montoya; Rafael Molina*

      Acta Crystallographica (2014) F70, 256-259

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  • Expression, purification, crystallization and preliminary X-ray diffraction analysis of the novel modular DNA-binding protein BurrH in its apo form and in complex with its target DNA
    Stefano Stella; Rafael Molina; Claudia Bertonati; Alexandre Juillerat; Guillermo Montoya*

      Acta Crystallographica (2013) F70, 87-91

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  • The crystal structure of AvrBs3-DNA complex provides new insight into the initial thymine recognition mechanism
    Stefano Stella; Rafael Molina; Igor Yefimenko; Jesus Prieto; George Silva; Claudia Bertonati; Alexandre Juillerat;Philippe Duchateau; Guillermo Montoya*

      Acta Crystallographica (2013) D69, 1707-1716

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  • Expression, purification, crystallization and preliminary X-ray diffraction analysis of the dihydroorotase domain of human CAD
    Nada Lallous; Araceli Grande-García; Rafael Molina; Santiago Ramon-Maiques*

      Acta Crystallographica (2012) F68, 1341–1345

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  • 5’-Cytosine-Phosphoguanine (CpG) Methylation Impacts the Activity of Natural and Engineered Meganucleases
    Julien Valton; Fayza Daboussi; S Leduc; Rafael Molina; Pilar Redondo; Rachel Macmaster; Guillermo Montoya; Philippe Duchateau*

      Journal of Biological Chemistry (2012). 287, 30139–30150

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  • Molecular scissors for in situ cellular repair
    Jesus Prieto; Rafael Molina; Guillermo Montoya*

      Critical Reviews in Biochemistry and Molecular Biology (2012) 47, 207-221

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  • Non-specific protein-DNA interactions control I-CreI target binding and cleavage
    Rafael Molina; Pilar Redondo; Stefano Stella; Marco Marenchino; Marco D'Abramo; Francesco Gervasio; Jean Charles Epinat; Julien Valton; Philippe Duchateau; Jesus Prieto; Guillermo Montoya*

      Nucleic Acids Research (2012) 40, 6936–6945

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  • Meganucleases and Their Biomedical Applications
    Rafael Molina; Guillermo Montoya; Jesus Prieto*

      Encyclopedia of Life Sciences (2011) John Wiley & Sons, Ltd

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  • Crystallization and preliminary crystallographic analysis of the catalytic module of endolysin Cp-7, a phage infecting Streptococcus pneumoniae
    Noella Silva-Martin; Rafael Molina; Ivan Angulo; Jose Miguel Mancheño; Pedro Garcia; Juan Antonio Hermoso*

      Acta Crystallographica (2010) F66, 670-673

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  • Characterization of gadolinium complexes for SAD phasing in Macromolecular Crystallography: application to CbpF
    Rafael Molina; Meike Stelter; Richard Kahn*; Juan A. Hermoso*

      Acta Crystallographica (2009) D65, 823–831

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  • Crystal Structure of CbpF, a Bifunctional Choline-Binding Protein and Autolysis Regulator from Streptococcus pneumoniae
    Rafael Molina; Ana Gonzalez; Meike Stelter; Inmaculada Perez-Dorado; Richard Kahn; Maria Morales; Susana Campuzano; Nuria E. Campillo; Shahriar Mobashery; Jose Luis Garcia; Pedro Garcia; Juan A. Hermoso*

      EMBO Reports (2009). 10, 246–251

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  • A one-pot, simple methodology for cassette randomisation and recombination for focused directed evolution
    Aurelio Hidalgo; Anna Schließmann; Rafael Molina; Juan A. Hermoso; Uwe T. Bornscheuer*

      Protein Engineering, Design & Selection (PEDS) (2008) 21, 567–576

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  • Tuning of the FMN binding and oxido-reduction properties by neighboring side chains in Anabaena flavodoxin
    Susana Frago; Guillermina Goñi; Beatriz Herguedas; Jose Ramon Peregrina; Ana Serrano; Inmaculada Perez-Dorado; Rafael Molina; Carlos Gomez-Moreno; Juan Antonio Hermoso; Marta Martinez-Julvez; Stephen G Mayhew; Milagros Medina*

      Archives of Biochemistry and Biophysics (2007) 467, 206-217

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  • Enhancement of the Stability of a Prolipase from Rhizopus oryzae toward Aldehydes by Saturation Mutagenesis
    Mirella Di Lorenzo; Aurelio Hidalgo; Rafael Molina; Juan A. Hermoso; Domenico Pirozzi; Uwe T. Bornscheuer*

      Applied and Environmental Microbiology (2007) 73(22), 7291-7299

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  • Crystallization and preliminary X-ray diffraction studies of choline-binding protein F from Streptococcus pneumoniae
    Rafael Molina; Ana Gonzalez; Miriam Moscoso; Pedro Garcia; Meike Stelter; Richard Kahn; Juan A. Hermoso*

      Acta Crystallographica (2007) F63, 742-745

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  • Probing the determinants of substrate specificity of feruloyl esterase, AnFaeA, from Aspergillus niger
    Craig. B Faulds; Rafael Molina; Ramon Gonzalez; F Husband; Natalie Juge; Julia Sanz-Aparicio; Juan A. Hermoso*

      FEBS Journal (2005) 272, 4362–4371

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  • The crystal structure of feruloyl esterase A from Aspergillus Niger suggests evolutive functional convergence in feruloyl esterase family
    Juan A. Hermoso; Julia Sanz-Aparicio; Rafael Molina; Natalie Juge; Ramon Gonzalez; Craig B. Faulds*

      Journal of Molecular Biology (2004) 338, 495–506

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