CCB Seminar: Vitor Leite, Ph.D.

Speaker: Vitor Leite, Ph.D. (São Paulo University) 

Title: From Multidimensional Challenges to Intuitive Insights in Biomolecular Landscapes 

Abstract: Understanding the dynamic behavior of biomolecules involves navigating vast, high-dimensional energy landscapes that emerge from molecular dynamics simulations. The complexity of these landscapes, shaped by countless degrees of freedom, poses significant analytical challenges. Traditional methods often rely on predefined reaction coordinates or linear projections, which can obscure critical details and limit interpretability. The Energy Landscape Visualization Method (ELViM) overcomes these challenges by employing a multidimensional projection approach that preserves key structural relationships without requiring predefined metrics. This seminar discusses ELViM’s methodology and its application to two complex biomolecular systems: the SAM-II riboswitch and histone proteins. In the SAM-II riboswitch, ELViM elucidates the role of Mg²⁺ ions in stabilizing RNA folding transitions, uncovering essential structural intermediates and transition states critical for biological function. For histones, ELViM reveals how post-translational modifications alter the energy landscape and conformational heterogeneity, shedding light on their roles in chromatin dynamics. By providing intuitive, low-dimensional visualizations of intricate energy landscapes, ELViM offers a transformative lens for understanding biomolecular structure and dynamics, enabling insights that are otherwise inaccessible through conventional techniques.