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Biological macromolecules energy landscapes visualization

Grant number: 18/18668-1
Support type:Scholarships abroad - Research
Effective date (Start): January 01, 2019
Effective date (End): June 30, 2019
Field of knowledge:Physical Sciences and Mathematics - Physics
Principal Investigator:Vitor Barbanti Pereira Leite
Grantee:Vitor Barbanti Pereira Leite
Host: José Nelson Onuchic
Home Institution: Instituto de Biociências, Letras e Ciências Exatas (IBILCE). Universidade Estadual Paulista (UNESP). Campus de São José do Rio Preto. São José do Rio Preto , SP, Brazil
Local de pesquisa : Rice University, United States  


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)

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)
YANG, HUAN; BANDARKAR, PRASAD; HORNE, RANSOM; LEITE, VITOR B. P.; CHAHINE, JORGE; WHITFORD, PAUL C. Diffusion of tRNA inside the ribosome is position-dependent. Journal of Chemical Physics, v. 151, n. 8 AUG 28 2019. Web of Science Citations: 0.

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