DIPC Community Seminar: A personal perspective on simulations of biomolecules: challenges and opportunities

DIPC Community Seminar

The simulation of biomolecules has emerged as a powerful tool in elucidating the intricate dynamics and functions of biological systems. Molecular dynamics simulations, utilizing classical and quantum mechanics principles, provide insights into biomolecular structures, interactions, and conformational changes at atomic resolution. Advancements in computational techniques and hardware have facilitated the simulation of increasingly large and complex biomolecular systems, enabling researchers to explore phenomena such as protein folding, ligand binding, enzymatic reactions, and membrane dynamics with unprecedented detail. In the present talk, I will review some of the challenges and opportunities that simulation of biosystems provides to understand biochemical processes. I will focus on the problematic case of intrinsically disordered peptides (IDP), which have gained paramount importance due to their involvement in various diseases. Understanding how different factors, such as the specific sequence, the presence of metals, or chemical modifications of the IDP, induce secondary structure in these disordered systems is essential for comprehending their roles in biological processes. Multi-level computational modeling is a fundamental tool for investigating IDPs, providing insights into their conformation landscape and structural ensembles accessible at different conditions. The talk will also introduce recent work conducted by the group in this area, showcasing examples of induction of secondary structure in IDPs through different examples. Our results show that the concept of configurational ensemble and entropy are critical to give a proper description of the behavior of these systems and their biological activity.