Biological macromolecules energy landscapes visualization

• Grant number: 18/18668-1
• Support Opportunities: Scholarships abroad - Research
• Start date: January 01, 2019
• End date: June 30, 2019
• Field of knowledge: Physical Sciences and Mathematics - Physics
• Principal Investigator: Vitor Barbanti Pereira Leite
• Grantee: Vitor Barbanti Pereira Leite
• Host Investigator: José Nelson Onuchic
• Host 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
• Institution abroad: Rice University, United States

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)

Scientific publications

(8)

(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. (16/19766-1, 14/50739-5, 18/18668-1)

DE OLIVEIRA, VINICIUS M.; CAETANO, DANIEL L. Z.; DA SILVA, FERNANDO B.; MOURO, PAULO R.; DE OLIVEIRA, JR., ANTONIO B.; DE CARVALHO, SIDNEY J.; LEITE, VITOR B. P.. pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 16, n. 1, p. 765-772, JAN 2020. (16/19766-1, 18/18668-1, 18/11614-3, 18/01841-2)

OLIVEIRA, JR., ANTONIO B.; YANG, HUAN; WHITFORD, PAUL C.; LEITE, VITOR B. P.. Distinguishing Biomolecular Pathways and Metastable States. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 15, n. 11, p. 6482-6490, NOV 2019. (16/19766-1, 14/50739-5, 18/18668-1)

SANCHES, MURILO N.; KNAPP, KAITLIN; OLIVEIRA, ANTONIO B.; WOLYNES, PETER G.; ONUCHIC, JOSE N.; LEITE, VITOR B. P.. Examining the Ensembles of Amyloid-beta Monomer Variants and Their Propensities to Form Fibers Using an Energy Landscape Visualization Method. Journal of Physical Chemistry B, DEC 2021. (18/18668-1, 19/22540-3)

DA SILVA, FERNANDO B.; DE OLIVEIRA, VINICIUS M.; SANCHES, MURILO N.; CONTESSOTO, VINICIUS G.; LEITE, VITOR B. P.. Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions. JOURNAL OF CHEMICAL INFORMATION AND MODELING, v. 60, n. 2, p. 982-988, FEB 2020. (16/19766-1, 16/13998-8, 17/09662-7, 17/25130-5, 18/11614-3, 18/18668-1)

MOURO, PAULO R.; POVINELLI, ANA P. R.; LEITE, VITOR B. P.; CHAHINE, JORGE. Exploring Folding Aspects of Monomeric Superoxide Dismutase. Journal of Physical Chemistry B, v. 124, n. 4, p. 650-661, JAN 30 2020. (16/19766-1, 18/18668-1)

OLIVEIRA, JR., ANTONIO B.; LIN, XINGCHENG; KULKARNI, PRAKASH; ONUCHIC, JOSE N.; ROY, SUSMITA; LEITE, VITOR B. P.. Exploring Energy Landscapes of Intrinsically Disordered Proteins: Insights into Functional Mechanisms. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, v. 17, n. 5, p. 3178-3187, MAY 11 2021. (16/01343-7, 19/22540-3, 18/18668-1)

DODERO-ROJAS, ESTEBAN; FERREIRA, LUIZA G.; LEITE, VITOR B. P.; ONUCHIC, JOSE N.; CONTESSOTO, VINICIUS G.. Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro. PLoS One, v. 15, n. 1, JAN 28 2020. (17/09662-7, 18/18668-1, 16/13998-8)