Study of atypical structures in the visualization of protein energy landscape

Abstract

The elucidation of functional mechanisms in proteins is a challenging issue of enormous relevance and important pathologies are associated with their dysfunctions. The energy landscape approach has contributed significantly to the understanding of biomolecular mechanisms, in which the approach to the problem of protein folding is its most notable success. Our group at IBILCE-UNESP has developed a technique for studying protein energy landscapes. This method, called Energy Landscape Visualization Method (ELViM), was designed to visualize the protein folding funnel and has great potential for detailing biomolecular mechanisms by going beyond the one-dimensional representation. Given a set of protein conformations, the method generates a two-dimensional representation of the energy landscape, which allows exploring the details of these systems. It so happens that when the projection is made in two-dimensional space, atypical configurations often occur that are significantly distant from all other points in the projection, which may lead to distorting the general picture of the representation. The current project aims to understand and characterize these atypical structures. Understanding these states will allow the introduction of filters for a better representation of these energy surfaces.