WG1: Macromolecular interactions in signaling pathways

The main objective of WG1 is to elucidate the protein-protein interactions and dynamics that give rise to signal transduction at the molecular-level, with emphasis on how modulation of these interactions generates specificity in transmembrane receptor-mediated signal transduction. Together with the other work groups, WG1 contributes molecular-level detail to the holistic map of signal transduction developed by the Action.

Specifically, WG1 focuses on the structural basis for molecular interactions among signaling proteins using high-resolution methods (e.g. X-ray crystallography, NMR, cryo-electron microscopy), on the dynamic interactions among signaling proteins using time-resolved methods (e.g. NMR, EPR, single molecule FRET, super-resolution microscopy), and on the analysis of different aspects of these interactions using computational approaches.

Additional goals include identifying key features in protein structure and dynamics that are shared among signaling proteins or those that determine interaction specificity, examining how kinetics of molecular interactions influence signaling, studying the interplay between subcellular localization and protein-protein interactions, or investigating how genetic variations perturb or modulate such interactions.

WG2: Biological roles of signal transduction

The main objective of WG2 is to connect the molecular interactions in signal transduction and their subcellular localization to the cellular response. The biological importance of molecular interactions in signal transduction can only be understood within the context of the living cell and (patho) physiological state of an organism.

Experts in WG2 will define and characterize signaling pathways for different cell types and physiological systems (e.g. neurobiology, cardiovascular, cancer, and immunity) with respect to receptor type, which cytosolic effectors are involved, and which downstream signaling pathways are affected. WG2 will investigate how the location and timing of macromolecular interactions affects the signaling outcome, using high-resolution and time-resolved cell imaging methods. Experts in WG2 will characterize chemical modulators of signal transduction, identify new protein targets for structure/function analysis, test efficacy of ligands in cell-based assays and animal models, with the goal of bringing these compounds towards clinical trials (translational medicine).

This activity will identify new model biological systems and new therapeutic targets since signaling pathways must be defined in order to understand how disease results from imbalances in signal transduction.

WG3: Molecular Modulators of Signal Transduction

The basic objective of WG3 is the design and optimization of molecules that interact with components of the signal transduction cascade. The design of functionally-selective ligands will be possible through information about relevant receptor conformations or residues provided by WG1 and WG2. WG3 works closely with WG4 (advanced technologies and methods) to develop chemical probes to be used to investigate cell signalling mechanisms (cf. WG1 and WG2) and to facilitate high-resolution structural analysis of GPCR complexes.

We are specifically focusing on the design, synthesis and characterisation of molecular modulators, including small molecules, peptides and peptidomimetics that target specific proteins, protein conformations or signalling pathways. These tools might help understanding the molecular mechanism of signal transduction cascade that supports developing functionally selective therapeutics.

WG4: Advanced Methodologies and Technologies

The primary objective of WG4 is to promote advanced methodologies and technologies within the Action and to coordinate sharing through collaboration.

We are particularly focused on cutting-edge approaches that can help achieve the aims of the Action, as well as re-purposing of existing methodologies and technologies from other fields of biomedical research. Structured in 3 major branches, Biological & Biophysical, Computational and Chemical methods, the WG will also establish best practice principles for the application of commonly used methodologies across groups within and beyond the Action.

These emerging approaches will support WG1, WG2, and WG3 in achieving their goals and will be highlighted through the bi-annual WG meetings, training schools and STSMs.

WG5: Public web resources

WG5 will integrate and avail experimental data emanating from the Action and global field. This will disseminate results widely and sustainable, and inspire and equip the most valuable new studies to expand the coverage of receptors targets and pathways within the field. So far, work on the follow resources have been initiated:

WG5 will integrate and avail experimental data emanating from the Action and global field. This will disseminate results widely and sustainable, and inspire and equip the most valuable new studies to expand the coverage of receptors targets and pathways within the field. So far, work on the follow resources have been initiated:

01. Biased ligands in a database of reference probes.

02. An atlas of pathway physiological/therapeutic effects to inform the development of functionally selective probes/drugs.

03. A database of molecular dynamics trajectories to investigate the role of receptor dynamics in ligand-receptor activation and signal transduction.

04. Reference structures and sequence alignments, for GPCRs, G proteins and arrestins.

05. Data-driven tools to design new experiments, such as in vitro mutations to elucidate molecular mechanisms of chemical probes on signalling protein machineries

As the community and data grows, further online data and tools will be tailored together with the research community to define additional joint development-data generation projects and to raise the funding needed.

REFERENCES

01. Flock, T., Hauser, A.S., Lund, N., Gloriam, D.E., Balaji, S. and Babu, M.M. (2017) Selectivity determinants of GPCR-G-protein binding. Nature, 545, 317-322.

02. Pandy-Szekeres, G., Munk, C., Tsonkov, T.M., Mordalski, S., Harpsoe, K., Hauser, A.S., Bojarski, A.J. and Gloriam, D.E. (2018) GPCRdb in 2018: adding GPCR structure models and ligands. Nucleic Acids Res, 46, D440-D446.

03. Harding, S.D., Sharman, J.L., Faccenda, E., Southan, C., Pawson, A.J., Ireland, S., Gray, A.J.G., Bruce, L., Alexander, S.P.H., Anderton, S., Bryant, C., Davenport, A.P., Doerig, C., Fabbro, D., Levi-Schaffer, F., Spedding, M. and Davies, J.A. (2017) The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY. Nucleic Acids Res., gkx1121-gkx1121.

04. Bento, A.P., Gaulton, A., Hersey, A., Bellis, L.J., Chambers, J., Davies, M., Krüger, F.A., Light, Y., Mak, L., McGlinchey, S., Nowotka, M., Papadatos, G., Santos, R. and Overington, J.P. (2014) The ChEMBL bioactivity database: an update. Nucleic Acids Res., 42, D1083-1090.

05. Isberg, V., de Graaf, C., Bortolato, A., Cherezov, V., Katritch, V., Marshall, F.H., Mordalski, S., Pin, J.P., Stevens, R.C., Vriend, G. and Gloriam, D.E. (2015) Generic GPCR residue numbers – aligning topology maps while minding the gaps. Trends Pharmacol. Sci., 36, 22-31.