Structural and Computational BiologyStructural biology of protein & nucleic acid complexes and molecular machines

Structural biology of protein & nucleic acid complexes and molecular machines
Group Leader

Professor (IBMB-CSIC)

+34 93 40 34951

Our research focuses on the three-dimensional structure of proteins, nucleic acids and their complexes with the aim to further our understanding of several essential mechanisms in the cell. We use a number of molecular biology and structural biology techniques, with a focus on X-ray diffraction crystallography. Our approach usually starts with the cloning of relevant genes and the expression and purification of the encoded proteins. Proteins, nucleic acids and their complexes are then crystallized and analysed by X-ray diffraction, using synchrotron radiation. The final outcome is a detailed 3D view of the molecular structures at atomic resolution.

We examine systems related to horizontal gene transfer which involve the DNA translocation across the cell membranes. In addition, we address the regulatory mechanisms of gene expression and the control mechanisms of DNA replication. We also study unique DNA structures, like DNA junctions, and novel drugs that target DNA.

DNA replication control. Plasmids are extra-chromosomal DNA molecules that replicate autonomously. In pathogenic bacteria, plasmids may carry antibiotic resistance genes. Plasmid replication is controlled by gene products encoded in the plasmid itself. In collaboration with Manuel Espinosa and Gloria del Solar (CIB-CSIC), we are currently studying this system in streptococcal plasmids.

Horizontal gene transfer. Conjugation is the main route for horizontal gene transfer in bacteria and is responsible for the spread of antibiotic resistance. During conjugation, plasmid DNA is processed and transported across cell membranes between cells. The relaxosome is a protein-DNA complex formed by several proteins and a DNA segment called the Origin of Transfer. The transport complex is a transmembrane multiprotein assembly. In collaboration with Fernando de la Cruz (U. of Cantabria), we are examining this system in E. coli plasmid R388.

DNA packaging in viruses. Portal proteins or connectors are large multimeric proteins involved in DNA packaging into viral capsids. With the help of other proteins, they translocate the DNA through one vertex of the capsid. We are currently analysing various connectors and other related DNA packaging proteins, in collaboration with José L. Carrsacosa and José María Valpuesta (CNB-CSIC).

Transcription regulation. We study several transcription factors and their complexes with other proteins and DNA promoter regions. In collaboration with Margarita Salas (CBM-CSIC), in bacteriophage φ29 we examine the transcriptional regulator p4 that functions as a switch between early and late gene expression during the infection cycle. In E.coli, we address the PhoB transcriptional activator, a response regulator of the two-component signal transduction system that controls the expression of more than 40 genes related to phosphate assimilation.

DNA structure and drug-DNA interactions. Unique DNA structures, such as four-way and three-way junctions related to DNA recombination and other processes, are being structurally analysed. Novel DNA-binding drugs that target these peculiar structures and other sequence-specific drugs are also under study.

Viral replication machinery. Within the Structural Genomics European Consortium VIZIER, the replication enzymes and ancillary proteins of human pathogenic RNA virus are currently being structurally characterized. The final aim is to provide tools for the discovery of new antiviral agents.

Protein complexes, epigenetic regulation of gene expression and cancer. As a partner of the European Consortium 3D-REPERTOIRE and coordinator of the Spanish Structural Genomics Consortium GENES, our group studies several protein complexes and molecular machines, some of which are related to the epigenetic control of gene expression. Targets for anticancer therapy are among the proteins currently being analysed.

Pluta R, Boer DR, Lorenzo-Díaz F, Russi S, Gómez H, Fernández-López C, Pérez-Luque R, Orozco M, Espinosa M and Coll M.
P Natl Acad Sci Usa, 114 (32), E6526-E653 (2017)
Boer DR, Ruiz-Masó JA, Rueda M, Petoukhov MV, Machón C, Svergun DI, Orozco M, del Solar G and Coll M.
Sci Rep, 6 20915 (2016)
Boer DR, Freire-Rios A, van den Berg WA, Saaki T, Manfield IW, Kepinski S, López-Vidrieo I, Franco-Zorrilla JM, de Vries SC, Solano R, Weijers D and Coll M.
Cell, 156 (3), 577-89 (2014)
Rubio-Cosials A, Sidow JF, Jiménez-Menéndez N, Fernández-Millán P, Montoya J, Jacobs HT, Coll M, Bernadó P and Solà M.
Nat Struct Mol Biol, 18 (11), 1281-9 (2011)
Blanco AG, Canals A, Bernués J, Solà M and Coll M.
Embo J, 30 3776-3785 (2011)
Nadal M, Mas PJ, Blanco AG, Arnan C, Solà M, Hart DJ and Coll M.
P Natl Acad Sci Usa, 107 (37), 16078-83 (2010)
Jiménez-Menéndez N, Fernández-Millán P, Rubio-Cosials A, Arnan C, Montoya J, Jacobs HT, Bernadó P, Coll M, Usón I and Solà M.
Nat Struct Mol Biol, 17 (7), 891-3 (2010)
Boer DR, Ruíz-Masó JA, López-Blanco JR, Blanco AG, Vives-Llàcer M, Chacón P, Usón I, Gomis-Rüth FX, Espinosa M, Llorca O, del Solar G and Coll M.
Embo J, 28 (11), 1666-78 (2009)
Oleksy A, Blanco AG, Boer R, Usón I, Aymamí J, Rodger A, Hannon MJ and Coll M.
Angew Chem Int Edit, 45 (8), 1227-31 (2006)
Badia D, Camacho A, Pérez-Lago L, Escandón C, Salas M and Coll M
Mol Cell, 22 73-81 (2006)
Guasch A, Lucas M, Moncalián G, Cabezas M, Pérez-Luque R, Gomis-Rüth FX, de la Cruz F and Coll M.
Nat Struct Mol Biol, 10 (12), 1002-10 (2003)
Gomis-Rüth FX, Moncalián G, Pérez-Luque R, González A, Cabezón E, de la Cruz F and Coll M.
Nature, 409 (6820), 637-41 (2001)
Ortiz-Lombardía M, González A, Eritja R, Aymamí J, Azorín F and Coll M.
Nat Struct Mol Biol, 6 (10), 913-7 (1999)

This group receives financial support from the following sources:

  • European Union
  • Ministerio de Educación y Ciencia (Spanish Ministry of Science & Education)
  • Ministerio de Industria, Turismo y Comercio (Spanish Ministry of Industry, Tourism and Trade)
  • Generalitat de Catalunya (Government of Catalonia)
  • Fundació La Marató de TV3 ("La Marató TV3" Foundation)

Group news & mentions

<p>3D structure of the protein relaxase bound to a DNA fragment. The histidine residue that performs the DNA nicking, is shown in blue (bottom right) (Radoslaw Pluta, IRB Barcelon</p>
11 Sep 2017

The radio programme of RNE Laboratorio de Jal has referred to

<p>3D structure of the protein relaxase bound to a DNA fragment. The histidine residue that performs the DNA nicking, is shown in blue (bottom right) (Radoslaw Pluta, IRB Barcelon</p>
26 Jul 2017

Antibiotic resistance of the bacterium Staphylococcus aureus is responsible for 11,300 deaths a year in the United States alone—a figure that corresponds to half of all deaths caused by Gr

2 Dec 2014

Excelenciencia.org has published an article that includes statements made by Manuel Palacín after the “Transporters and other Molecular Machines” conference, part of Barcelona Biomed Conferences, w

Upcoming events

27 Sep
Aula Fèlix Serratosa, Parc Científic de Barcelona
Speaker:
Speaker: Cristina Pujades, Ph.D. Group Leader of the Department of Experimental and Health Sciences, University Pompeu Fabra, PRBB, Barcelona, Spain.
05 Oct
Thurday, October 5, Aula Fèlix Serratosa
Speaker:
Alberto López, director of the Fulbright Commission and Patricia de la Hoz, Communication and documentation manager
19 Oct
Aula Fèlix Serratosa, Parc Científic de Barcelona
Speaker:
Kristian Pietras, Ph.D. Lund University, Dept of Laboratory Medicine, Division of Translational Cancer Research, Medicon Village Lund, Sweden