Studies of energy landscapes of biological macromolecules

• Grant number: 19/22540-3
• Support Opportunities: Regular Research Grants
• Start date: May 01, 2020
• End date: November 30, 2022
• Field of knowledge: Physical Sciences and Mathematics - Physics
• Principal Investigator: Vitor Barbanti Pereira Leite
• Grantee: Vitor Barbanti Pereira Leite
• 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

Abstract

The approach of energy landscapes has significantly contributed to the understanding of complex molecular systems such as the protein folding problem. In this scenario, minimalist and simplified models have played a key role. This project will focus on biological macromolecules, in which we will study the energy landscape of proteins and RNAs using simplified computational models and statistical physics approaches. The central idea is related to the visualization of the energy landscapes, exploring a technique developed by our group at IBILCE-UNESP. This method called the Energy Landscape Visualization Method (ELViM). It is designed for visualization of the protein folding funnel and has excellent potential for detailing molecular mechanisms by going beyond one-dimensional representation. We will extend this methodology to apply to more complex and challenging systems. Topics to be addressed are: (i) visualization of energy landscapes of proteins without a defined native structure, which are intrinsically disordered proteins (IDPs); (ii) RNAs, which have multiple reference structures; and (iii) visualization of energy landscapes of proteins involving hierarchical folding or topological nodes. In parallel with these specific objectives, the methodologies developed and used by our group will be applied to problems involving collaborations outside IBILCE-UNESP, such as estrogen receptor, drug studies with applications in malaria treatment and forensic problems. (AU)

Scientific publications

(13)

(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)

CONTESSOTO, VINICIUS DE GODOI; RAMOS, FELIPE CARDOSO; DE MELO, RICARDO RODRIGUES; DE OLIVEIRA, VINICIUS MARTINS; SCARPASSA, JOSIANE ANIELE; DE SOUSA, AMANDA SILVA; ZANPHORLIN, LETICIA MARIA; SLADE, GABRIEL GOUVEA; PEREIRA LEITE, VITOR BARBANTI; RULLER, ROBERTO. lectrostatic interaction optimization improves catalytic rates and thermotolerance on xylanase. BIOPHYSICAL JOURNAL, v. 120, n. 11, p. 2172-2180, JUN 1 2021. (17/09662-7, 17/14253-9, 16/19766-1, 19/22540-3, 18/11614-3, 16/13998-8, 14/06862-7)

NGO, KHOA; DA SILVA, FERNANDO BRUNO; LEITE, VITOR B. P.; CONTESSOTO, VINICIUS G.; ONUCHIC, JOSE N.. Improving the Thermostability of Xylanase A from Bacillus subtilis by Combining Bioinformatics and Electrostatic Interactions Optimization. Journal of Physical Chemistry B, v. 125, n. 17, p. 4359-4367, MAY 6 2021. (16/19766-1, 19/22540-3, 14/06862-7, 16/13998-8, 17/09662-7)

MOURO, PAULO R.; SANCHES, MURILO N.; LEITE, VITOR B. P.; CHAHINE, JORGE. Exploring the Folding Mechanism of Dimeric Superoxide Dismutase. Journal of Physical Chemistry B, v. N/A, p. 12-pg., 2023-01-30. (21/15028-4, 19/22540-3)

CONTESSOTO, VINICIUS DE GODOI; RAMOS, FELIPE CARDOSO; DE MELO, RICARDO RODRIGUES; DE OLIVEIRA, VINICIUS MARTINS; SCARPASSA, JOSIANE ANIELE; DE SOUSA, AMANDA SILVA; ZANPHORLIN, LETICIA MARIA; SLADE, GABRIEL GOUVEA; PEREIRA LEITE, VITOR BARBANTI; RULLER, ROBERTO. Electrostatic interaction optimization improves catalytic rates and thermotolerance on xylanases. BIOPHYSICAL JOURNAL, v. 120, n. 11, p. 9-pg., 2021-06-01. (16/19766-1, 16/13998-8, 17/14253-9, 18/11614-3, 14/06862-7, 19/22540-3, 17/09662-7)

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., 2023-08-22. (21/15028-4, 19/22540-3, 23/02219-1)

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)

HERNANDEZ GONZALEZ, JORGE ENRIQUE; SALAS-SARDUY, EMIR; HERNANDEZ ALVAREZ, LILIAN; BARRETO GOMES, DIEGO ENRY; PASCUTTI, PEDRO GERALDO; OOSTENBRINK, CHRIS; LEITE, VITOR B. P.. In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. Journal of Computer-Aided Molecular Design, v. 35, n. 10, p. 1067-1079, OCT 2021. (16/24587-9, 20/10214-1, 16/19766-1, 18/03911-8, 19/22540-3)

RODRIGUES, CAIO H. P.; LEITE, VITOR B. P.; BRUNI, ALINE T.. Can NMR spectroscopy discriminate between NPS amphetamines and cathinones? An evaluation by in silico studies and chemometrics. CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, v. 210, MAR 15 2021. (19/22540-3, 16/19766-1)

CONTESSOTO, VINICIUS G.; FERREIRA, PAULO H. B.; CHAHINE, JORGE; LEITE, VITOR B. P.; OLIVEIRA, RONALDO J.. Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics. Journal of Physical Chemistry B, v. 125, n. 42, p. 11673-11686, OCT 28 2021. (16/13998-8, 19/22540-3, 16/19766-1)

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)

DA SILVA, FERNANDO BRUNO; DE OLIVEIRA, VINICIUS MARTINS; DE OLIVEIRA JUNIOR, ANTONIO BENTO; CONTESSOTO, VINICIUS DE GODOI; LEITE, VITOR B. P.. Processing of Composite Electrodes of Carbon Nanotube Fabrics and Inorganic Matrices via Rapid Joule Heating. Journal of Physical Chemistry B, v. N/A, p. 10-pg., 2023-02-01. (18/11614-3, 16/13998-8, 17/09662-7, 19/22540-3)

SINHORINI, LUIZ F. C.; RODRIGUES, CAIO H. P.; LEITE, VITOR B. P.; BRUNI, ALINE T.. Synthetic fentanyls evaluation and characterization by infrared spectroscopy employing in silico methods. COMPUTATIONAL AND THEORETICAL CHEMISTRY, v. 1204, OCT 2021. (16/19766-1, 19/22540-3)

DE OLIVEIRA, VINICIUS M.; DIAS, MARIELI M. G.; AVELINO, THAYNA M.; VIDEIRA, NATALIA B.; DA SILVA, FERNANDO B.; DORATIOTO, TABATA R.; WHITFORD, PAUL C.; LEITE, VITOR B. P.; FIGUEIRA, ANA CAROLINA M.. pH and the Breast Cancer Recurrent Mutation D538G Affect the Process of Activation of Estrogen Receptor alpha. BIOCHEMISTRY, v. 61, n. 6, p. 9-pg., 2022-02-21. (18/11614-3, 19/10274-7, 14/50739-5, 16/02348-2, 19/22540-3, 16/19766-1, 19/14465-1)