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Research Programmes

Structural & Computational Biology

Biomolecular NMR: Structure and dynamics of proteins and protein complexes

mpons

Miquel Pons

Principal Investigator
Professor (Organic Chemistry Dept. - UB)

Office Tel : +34 93 403 46 83 // +34 93 403 92 54
Lab Tel : +34 93 403 46 77 // +34 93 403 71 32
e-mail : miquel.ponsirbbarcelona.org

Background

Non-constitutive protein-protein interactions often play a crucial role in regulatory processes. These interactions tend to be weak and give rise to a dynamic interactome: the association state of a protein or its interacting partners change in response to environmental stimuli and modulate biological responses. The inherent plasticity of these systems constitutes a challenge for their structural characterization but makes them attractive targets for modulation using small molecules. A flexible, highly interdisciplinary approach is required to address these challenges.

NMR provides structural and dynamic information at atomic level of complex systems, including isolated proteins, protein complexes and ligand-protein complexes in solution, and constitutes the focus of our research activity. We complement NMR with several other biophysical techniques, such as fluorescence anisotropy, circular dichroism, calorimetry, analytical ultracentrifugation, small angle X-ray scattering (SAXS) and tools of molecular biology, chemistry and computation.

Research Interests

We perform structural studies of dynamic biomolecular systems involved in protein-protein or protein-ligand interactions, with special emphasis on nuclear magnetic resonance methods. Particular effort is devoted to the development of the NMR methodology required to address the above challenges and to the development of small molecules as tools to modulate protein-protein interactions and as reporters for the study of very large macromolecular systems.

Research Lines

I. Self-association of low molecular weight phosphatases

Our group, in collaboration with Prof. García de la Torre (U. Murcia), has made a significant contribution to the development and application of methods to predict NMR relaxation rates and residual dipolar couplings from three-dimensional structures of globular proteins. These methods provide cross-validation between structures determined in crystals and NMR observations, and highlight dynamic processes that occur in solution, including inter-domain motions or weak protein-protein interactions. Moreover, they have allowed the identification of tetramers formed by a low molecular weight protein tyrosine phosphatase. Low molecular weight phosphatases participate in signal transduction processes by competing with kinases but their regulation is not well understood. Tetramer formation by low molecular weight phosphatases indicates a regulation mechanism for signal transduction under the prevalent crowding conditions of cellular cytoplasm that would be the supramolecular equivalent of a proenzyme. We use 15N NMR relaxation measurements along with 129Xe chemical shifts to characterize the effect of solution conditions on the oligomerization of low molecular weight phosphatases. In addition, using structural information, we also perform screenings to identify small molecule inhibitors.

    Collaborations:
  • Prof. García de la Torre (Universidad de Múrcia)
  • Dr. Michael Akke (Lund University)
  • Dr. Eike Brunner (Universität Regensburg)

II. Structural studies of nucleoid-associated proteins of the Hha/H-NS family
(J. García)

The H-NS/Hha system is involved in the regulation of bacterial gene expression in response to environmental changes such as temperature and ionic strength. H-NS has a DNA-binding domain and additional domains responsible for dimerization and oligomerization. Hha was discovered by Prof. Antonio Juarez’s group at the University of Barcelona Although Hha lacks a DNA-binding domain, it interacts with H-NS and modulates its effects. We have recently demonstrated that Hha shows conformational plasticity that is affected by its binding to H-NS fragments or by temperature. This observation strengthens the hypothesis that Hha or its interaction with H-NS acts as a sensor for temperature and ionic strength regulation of H-NS-regulated gene expression. Several essential residues for the interaction of H-NS and Hha have recently been identified by our group.

    Collaborations:
  • Prof. Antonio Juarez (University of Barcelona)

III. Ligand screening by combination of NMR and high-throughput computational docking

Our group produces high-throughput docking protocols, based on the Autodock programme, with an improved genetic algorithm, an optimized conversion from 1D to 3D representations of ligands and a novel similarity-based genetic selection algorithm to search large databases. A very efficient similarity measure (LINGOSim) that is directly applicable to 1D representations has been developed for this purpose. This protocol is complemented by a new, extremely rapid method (> 120,000 compounds/second) to predict solubility and logP values to facilitate the selection of the most promising candidates for NMR screening. These methods can be used for the initial search for drug candidates or for the development of small molecule tools for biomedical research. Our team works in close collaboration with the combinatorial chemistry groups at the IRB Barcelona.

    Collaborations:
  • Dr. Michael Thormann (Morphochem A.G., München)
  • Prof. Fernando Albericio (IRB Barcelona-PCB)
  • Dr. Miriam Royo ( Combinatorial Chemistry. PCB)
  • Prof. Antonio F. Tiburcio (University of Barcelona)

IV. Protein stability and the origin of the Hofmeister effect
(O. Millet)

Protein-water interaction at protein surfaces affects protein stability and is perturbed either by surface mutations or by the addition of ions. A thermodynamic analysis indicates a common origin for both effects and provides both an explanation and a possible quantification of the Hofmeister effect.

V. Large-scale motions: naturally disordered proteins and domain motions
(P. Bernadó)

Large-scale motions, such as those occurring in domain motion or in unfolded proteins, require a dynamic description of structures through statistical models and tools that are sensitive to average properties. Hydrodynamic and shape calculations and the generation of conformational ensembles are used to analyze experimental data obtained by NMR or SAXS.

Funding

This group receives financial support from the following sources:

  • Ministerio de Educación y Ciencia (Spanish Ministry of Science and Education)
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Research Directory

Core facilities and Services Directory

  • Generalitat de catalunya
  • Generalitat de catalunya. Salut
  • Universidad de Barcelona
  • Parc cientific

Institute for Research in Biomedicine (IRB Barcelona)
Parc Científic de Barcelona
C/ Baldiri Reixac 10
08028 Barcelona - Spain
Tel: (+34)93 403 7111 | Fax: +34 93 403 7114
infoarrobairbbarcelona.org