Research

General description

The group of Biomolecular Simulations study biological systems and processes using a variety of computational tools from the perspective of theoretical biophysics and biochemistry in close collaboration with several experimental groups around the world. Our focus is the characterization of properties and interactions between biological macromolecules such as proteins, nucleic acids and small ligands. Structural bioinformatics, comparative modelling, molecular dynamics simulations based on all-atoms potentials and simplified models are applied to the study and structural characterization different systems of biomedical relevance.

Specific research lines

Molecular modelization of HIV transcription complexes: We are modelling molecular adducts between viral and human proteins, which are crucial for the viral replication. This will provide new frameworks for the docking of specific antiviral compounds.

Coarse Grain Models: The simulation of large macromolecular complexes for biologically relevant times may require the use of simplified models to reduce the degree of complexity and computational cost of the simulations. We are developing new coarse grain models to use in molecular dynamics simulations of  nucleic acids macromolecules.

Simulation of structural and dynamic properties of biological membranes: Lipid “rafts” in plasma membranes are a challenging example of microdomain formation, lateral organization of membrane heterogeneities and specific membrane-protein interactions. We aim to study the structural and dynamics properties of a small “raft-like” domain inserted in a more “generic” phospholipid membrane by molecular dynamics simulations.

Modelling of the PKA-AKAP complexes: insights from structural bioinformatics: Cyclic adenosine monophosphate (cAMP) regulates a large number of cellular processes and its main effector enzyme is the cAMP-dependent protein kinase A (PKA), whose kinase activity is directly modulated by the binding of cAMP. Even though several different signalling pathways are controlled by the same  second messenger, signalling specificity is maintained in living cells by a mechanism based on compartmentalization into particular subcellular regions. Within this context, A-kinase anchoring proteins (AKAP) play a central role. In fact, AKAPs are scaffold proteins responsible for the intracellular localization of PKA, as they directly bind with nanomolar affinity to PKA and target to specific subcellular regions.