"Baila Morena: The Choreography of Proteins Under a Computational Microscope"

Abstract:

This seminar introduces computational methods in biomolecular dynamics and engineering with a focus on atomistic modeling and molecular dynamics simulations. These techniques allow us to explore the conformational space of biological macromolecules, their structure-function relationships, and how they respond to perturbations, such as mutations, at an atomic level. Proteins are not static structures; they move, shift, fold, and interact in intricate and purposeful ways. In this talk, I’ll use computational tools to explore the choreography of proteins in action. We will explore everything from the adaptive light-harvesting systems of plants and diatoms to the unpredictable behavior of intrinsically disordered proteins, and how their molecular motion can be harnessed for engineering applications in medicine and sustainability. Three case studies will illustrate the power and versatility of molecular simulations:

1. Photosynthetic organisms, such as higher plants and diatoms, have antenna complexes that can switch dynamically between efficient light harvesting and robust photoprotective states. Diatoms, which account for approximately 20% of global primary production, thrive in highly variable light environments on the ocean surface. Despite their ecological importance, the atomistic mechanisms behind this switch remain elusive. Understanding and engineering this molecular adaptation could lead to increased biomass production for biofuels and nutrients.

2. Intrinsically Disordered Proteins (IDPs): Nearly 70% of proteins contain at least one intrinsically disordered region (IDR), and approximately 20% are predominantly disordered, exhibiting flexible structures that play essential roles in regulation, signaling, and membrane interaction. This seminar will highlight how computational tools can be used to study the dynamic behavior and biological interactions of IDPs.

3. Nucleases enable targeted DNA editing guided by RNAs (sgRNAs). The seminar will provide insights into the conformational dynamics of these effector proteins and discuss mutation strategies aimed at enhancing editing efficiency and delivery into target cells.

Together, these case studies demonstrate how molecular simulations can reveal hidden aspects of biological complexes and guide their rational engineering.

Bio:

Dr. Vangelis Daskalakis is an Assistant Professor in the Department of Chemical Engineering at the University of Patras, Greece (since Sept 2023), and a Visiting Faculty Member at the Foundation for Research and Technology – Hellas (FORTH/ICE-HT) since Mar 2025. With a strong academic trajectory and extensive interdisciplinary experience, Dr. Daskalakis works at the intersection of biomolecular engineering, computational biophysics, and structural biology. He holds a Ph.D. in Computational Biophysical Chemistry and an M.Sc. in Theoretical Chemistry from the University of Crete, where he also completed his undergraduate studies in Chemistry. Before joining the University of Patras, he served as an Associate and Assistant Professor at the Cyprus University of Technology and conducted postdoctoral research at the Barcelona Supercomputing Center. Dr. Daskalakis leads the Biomolecular Dynamics & Engineering Lab, where three Ph.D candidates and one post-doctoral researcher work with focus on the molecular-level understanding of biological systems using high-performance computing (HPC). His work integrates molecular dynamics simulations with ab initio quantum methods and bioinformatics tools to investigate the structure–function relationships in proteins and complex biomolecular assemblies. His main areas of interest include photosynthetic light-harvesting complexes, transmembrane transporter proteins, and genome-editing effectors such as CRISPR-Cas and Fanzor systems. He has coordinated or contributed to over 20 competitive research projects funded by the European Commission, national research agencies, and major HPC initiatives, including Horizon Europe, PRACE, and EuroHPC JU. He has published more than 50 peer-reviewed articles in high-impact journals such as JACS and PNAS, with significant contributions to the understanding of (down) regulatory mechanisms in photosynthesis. Beyond his research, Dr. Daskalakis is an experienced and dedicated educator. He has taught courses in scientific programming, computational biology, molecular dynamics, biochemistry, and thermodynamics at both undergraduate and postgraduate levels. He is passionate about knowledge-sharing and actively supports interdisciplinary engagement among early-career scientists, especially in the rapidly advancing fields of computational life sciences and biomolecular engineering.