Publications  (first or co-first authorship underlined; corresponding or co-corresponding authorship with asterisk)
Rafael Molina Monterrubio

Regulation of Lytic Machineries by the FtsEX Complex in the Bacterial Divisome
Martin Alcorlo; Siseth Martinez-Caballero; Rafael Molina; Juan A. Hermoso*
in:  Macromolecular Protein Complexes IV. Subcellular Biochemistry, vol 99. Springer, Cham. (2022),
Eds.: Harris, J.R., Marles-Wright, J.  (doi: 10.1007/978-3-031-00793-4_9)

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  
(doi: 10.1093/nar/gkab1130)

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  
(doi: 10.1016/j.csbj.2021.09.018)

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  (doi: 10.1016/j.jmb.2020.11.022)

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  (doi: 10.1016/

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  (doi: 10.1038/s41467-019-12244-z)

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   (doi: 10.1038/s41598-018-28599-0)

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  (doi: 10.1016/j.ijmm.2017.10.003)

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   (doi: 10.1007/s10822-017-0087-5)

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
  (doi: 10.1021/acs.biochem.7b00932)

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  (doi: 10.1016/

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  (doi: 10.1021/jacs.6b12565)

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  (doi: 10.1002/bip.22933)

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  (doi: 10.1016/j.drup.2016.07.002)

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  (doi: 01/06/2016. 10.1089/mdr.2016.0083)

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  (doi: 10.1107/S2053230X16007512)

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  (doi: 10.1021/acschembio.5b00730)

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  (doi: 10.1074/jbc.M115.678342)

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  (doi:  10.1074/jbc.M115.658666)

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  (doi:

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  (doi: 10.1038/nsmb.2932)

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  (doi: 10.1107/S1399004714011183)

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  (doi: 10.1107/S1399004714005483)

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  (doi: 10.1107/S2053230X1400065X)

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  (doi: 10.1107/S2053230X13033037)

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  (doi: 10.1107/S0907444913016429)

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  (doi: 10.1107/S1744309112038857)

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  (doi: 10.1074/jbc.M112.379966)

Molecular scissors for in situ cellular repair
Jesus Prieto; Rafael Molina; Guillermo Montoya*
Critical Reviews in Biochemistry and Molecular Biology (2012) 47, 207-221  (doi: 10.3109/10409238.2011.652358)

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  (doi: 10.1093/nar/gks320)

Meganucleases and Their Biomedical Applications
Rafael Molina; Guillermo Montoya; Jesus Prieto*
Encyclopedia of Life Sciences (2011) John Wiley & Sons, Ltd  (doi: 10.1002/9780470015902.a0023179)

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  (doi: 10.1107/S1744309110006718)

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  (doi: 10.1107/S0907444909017958)

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  (doi: 10.1038/embor.2008.245)

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  (doi: 10.1093/protein/gzn034)

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  (doi:10.1016/

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  (doi:

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  (doi: 10.1107/S1744309107035865)

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  (doi: 10.1111/j.1742-4658.2005.04849.x)

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  (doi: 10.1016/j.jmb.2004.03.003)