The origins
The CBBL is currently lead by Jordi Villà i Freixa, associate professor at the UVic-UCC. The origin of the lab is traced back to the period 2003-2012, when it started with the same name at the Department of Experimental and Health Sciences of the Universitat Pompeu Fabra, in Barcelona.
Within the CBBL we use simulation techniques to do our best to understand the dynamical behavior of biological systems (see the ResearcherID link for Jordi Villà-Freixa’s publications or our lab’s repository of publications). These systems are explored at the molecular but also at the systemic level, following several fields of research. The ultimate goal is to develop integrated multiscale models to explain specific but complex problems in the behavior of biomolecules.
CBBL research lines
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 and free energy calculations, in particular the simplified but extremely efficient EVB method developed by Arieh Warshel. Works on several biochemical systems during the postdoctoral stage at Warshel’s lab have been followed by the increasing interest of the group on the biochemistry of selenoproteins, on the electrostatic effects on the reactivity of phosphate hydrolysis proteins, the conductivity of ion channels, or the effect of post-translational modifications in enzyme reactivity, among others.
Molecular modelling, Protein Folding and Conformational Changes
An active field of research in the group is the development of tools and their implementation for the exploration of the atomistic to coarse grain dynamical behavior 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 of supramolecular entities. The ultimate goal of the group is to relate folding with protein interactions by using multiscale simulaton schemas.
Molecular Interactions
Electrostatics 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.
Dynamical networks simulation
Both stochastic and deterministic modelling of biological networks is interesting for the group, and some new developments have been conducted in collaboration with Kevin Burrage and others. All developments have been ported to
The ultimate goal of the lab is to integrate multiple levels of understanding of biological problems, bringing new ideas into the biomedical and biotechnological fields.
This trip has shown to push forward the boundaries to what one can answer using simulation techniques. Clearly an opportunity for exciting new fields of research of the dynamical behavior 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.