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Understanding functional mechanisms of proteins and RNAs through energy landscapes


The energy landscape approach has contributed significantly to the understanding of complex molecular systems, such as the problem of protein folding. This project will focus on the study of energy landscapes of proteins and RNAs using coarse-grained models and statistical physics approaches. The central idea is related to the visualization of the energy surface using the Energy Landscape Visualization Method (ELViM), which is a method developed by our group at IBILCE-UNESP. The ELViM was designed for visualization of the protein folding funnel and has great potential for detailing molecular mechanisms by going beyond the unidimensional representation. We will apply this methodology to complex and challenging biomolecular systems. The topics to be addressed in this project are: (i) Study of energy landscape of proteins with no defined native structure, which are intrinsically disordered proteins (IDPs); (ii) Proteins with singular folding, such as fold-switching, which have more than one native structure, and repeat proteins that present hierarchical folding; (iii) Studies of riboswitch and RNA fragments; (iv) Study of the mechanism of action of peptides on membranes with antimicrobial and anticancer potential. In addition to advancing the understanding of these complex biomolecules, this project also aims to make ELViM widely available as a server on the internet. (AU)

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Scientific publications
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
VIEGAS, RAFAEL G.; SANCHES, MURILO N.; CHEN, ALAN A. A.; PAULOVICH, FERNANDO V.; GARCIA, ANGEL E.; LEITE, VITOR B. P.. Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 63, n. 17, p. 9-pg., . (21/15028-4, 19/22540-3, 23/02219-1)

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