Monte Carlo modeling of transport processes in the cell membrane

• Grant number: 17/16910-7
• Support Opportunities: Scholarships in Brazil - Master
• Start date: December 01, 2017
• End date: June 30, 2019
• Field of knowledge: Physical Sciences and Mathematics - Physics - General Physics
• Principal Investigator: Adriano Mesquita Alencar
• Grantee: Yan Borges Barreto
• Host Institution: Instituto de Física (IF). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated research grant: 13/17368-0 - Cardiovascular genomics: mechanisms & novel therapeutics - CVGen mech2ther, AP.TEM
• Associated scholarship(s): 18/11904-1 - Monte Carlo modeling of ion transport in sodium-calcium exchanger, BE.EP.MS

Abstract

The main objective of this project is to study the dynamics of the transport processes through the cell membrane. This will be done through the development of statistical mechanics models for the systems composed by proteins which perform the transport of solutes. In this project, we will study two of these proteins, viz. lactose permease, which performs the transport of lactose through the cell membrane; and the cardiac sodium-calcium exchanger NCX1, which performs the intracellular regulation of sodium and calcium in cardiomyocytes.In the case of permease, our model will be able to answer some questions that remain open in the literature, such as the reason why the protonation is important for the binding of sugar. The answers for that questions will be important steps towards fully understanding the operating mechanism of permease. In the case of NCX1, the interest lies in the fact that, in experiments performed by our group, pulsating living cells of cardiomyocytes regulated through a calcium flux are adhered to a substrate in order to measure mechanical properties of these cells. These measurements are part of a FAPESP thematic project (2013/17368-0) whose aim is the regeneration of the heart. In the two cases, we will use the Markov chains Monte Carlo method for modeling the dynamics of transport of the solutes. This method has been consecrated in modeling of biological systems in statistical mechanics, being that our group already has experience with it. Finally, once we have modeled these two transport proteins, we hope we can extract some general informations concerning the transport process in membranes. (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)

BARRETO, YAN B.; RODRIGUES, MATHEUS L.; ALENCAR, ADRIANO M.. Transport cycle of Escherichia coli lactose permease in a nonhomogeneous random walk model. Physical Review E, v. 99, n. 5, MAY 22 2019. (17/16910-7)

BARRETO, YAN B.; RODRIGUES, MATHEUS L.; ALENCAR, ADRIANO M.. Transport cycle of Escherichia coli lactose permease in a nonhomogeneous random walk model. PHYSICAL REVIEW E, v. 99, n. 5, p. 5-pg., 2019-05-22. (17/16910-7)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

BARRETO, Yan Borges. Statistical mechanical modeling of transport processes across the cell membrane. 2019. Master's Dissertation - Universidade de São Paulo (USP). Instituto de Física (IF/SBI) São Paulo.