Biological macromolecules energy landscapes visualization

Abstract

The energy landscape approach has contributed significantly to the understanding of complex molecular systems such as the protein folding problem. In this scenario, minimalist and simplified models have played a fundamental role. This project will focus on biological macromolecules, in which we study the protein and chromatin energy landscape using simplified computational models and statistical physics approaches. The central idea is related to the visualization of the energy landscape exploring a method developed by our group at IBILCE-UNESP. This method, called Energy Landscape Visualization Method (ELViM), was aimed for visualization of the protein folding funnel, and presents great potential for detailing the molecular mechanisms by going beyond the one-dimensional representation. We will extend this methodology to be applied to more complex and challenging systems. The topics to be addressed are: (i) visualization of the energy landscape of proteins with no defined native structure, which are the intrinsically disordered proteins (IDPs); (ii) visualization of protein energy surfaces involving topological nodes and backtracking and (iii) study of chromatin. Alongside these specific objectives, long-term collaborative partnerships should also be developed. (AU)