IMIM - Institut Hospital del Mar d'Investigacions Mèdiques

Computational biochemistry and biophysics Jordi Villà-Freixa

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Computational biochemistry (Jordi Villà-Freixa)

The group of Computational biochemistry is currently lead by Jordi Villà i Freixa, associate professor at the Universitat Pompeu Fabra. The group was created in 2003, after the IP having spend several postdoctoral stages at the IMIM (Hospital del Mar Research Institut) and the departments of chemistry at the University of Minnesota and the University of Southern California.

The group, whose members are involved in a number of national and international projects ranging from the understanding of enzymatic reactivity at the atomic detail to building information systems useful to relate patients, clinicians and researchers, works on what we believe are the cornerstones of the role of a University-based research group:

  • Research: by using simulation techniques to understand the dynamical behavior of biological systems, at both molecular and systemic levels. The ultimate goal is to develop integrated multiscale models to explain specific but complex problems in the behaviour of biomolecules.
  • Technology Transfer: we have a strong interest in the translational aspects of bioinformatics research. Thus, the increasing interest in participating into the development of tools with real biomedical impact has lead us to promote the company start-up aScidea Computational Biology Solutions SL, which mission can be summarized in the democratization of acces to genomic information.
  • Teaching: as part of the University system, we coordinate or participate in the teaching of a number of undergraduate and graduate level courses in the Faculty of Health and Life Sciences, as well as have had an active role in external courses in a number of places.

Main research lines

1 . Biochemical Reactivity. In its origins, the group devoted its efforts to understand the effect of the different chemical groups in the protein-substrate interface and their influence in reactivity. The basic tools for this research are molecular dynamics simulations coupled to hybrid quantum mechanical/molecular mechanics approaches, in particular the simplified but extremely efficient EVB method developed by Warshel. Works on several biochemical systems during the postdoctoral stage at Warshel's lab have been followed by the work on the function of biomolecules, from enzymes to ion channels, how they move and fold and the way they interact.

2. Protein Folding and Conformational Changes. An active field of research in the group is the development of tools, and their implementation in our computer software Adun, for the exploration of the atomistic to coarse grain dynamical behaviour of biomolecules. This involves the study of new algorithms for the understanding of global movements in globular proteins or the use of coarse grain techniques to understand the dynamics supramolecular entities like the glycocalix structures. The ultimate goal of the group is to relate folding with protein interactions by using multiscale simulation schemas.

3. Molecular InteractionsElectrostatics plays an important role not only in reactivity but also in protein recognition and complex formation. We have investigated the effect of residue stability in the protein complex formation in several phosphate hydrolysis systems, and we try to find the link between reactivity and complex formation. This line of research represents the link between the microscopic to macroscopic research lines in the group, and it is expected to benefit from the multiscale research being performed in the framework of some projects the group is involved in.

4. Systems Biology. Both stochastic and deterministic modelling of biological networks is interesting for the group, and some new developments are being conducted in collaboration with Kevin Burrage. We are approaching fast integration of the stochastic modelling problem as a first step towards real multiscale modelling, joining all fields of interest in the grup. All developments are being ported to ByoDyn.

Fostered by the collaboration with the group of Berta Alsina at the UPF, the lab started to be interested in the modelling of cell fate specification and pattern formation during the early stages of development. The lab’s research in the field is assumed to get more significance in the upcoming years, as the tool ByoDyn, initially designed to answer simple questions in the specific problem we handled, has grown in several somehow unexpected and exciting directions, opening new possibilities for research in systems biology both at the deterministic and (lately) stochastic levels.

5. Biomedical Informatics. The realization that ICT is a desperate need to handle biomedical data and the only way to make sense of it in the current explosion of biomedical sciences, the group has put its experience in the development of such tools for the community. Taking profit of our expertise in the development of web-based systems we are contributing to the development of integrative tools in the field.

This trip has lead us to see virtually no boundaries to what one can answer using simulation techniques. Clearly an opportunity for exciting new fields of research of the dynamical behaviour of complex systems but also a warning for the need to find good descriptors of each and all types of individual interactions. A consensus between reductionist and complex views? maybe… keep tuned.

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