A comparative study between Poisson-Boltzmann equation and molecular dynamics simulations in the description of protein systems

• Grant number: 19/13774-0
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: August 01, 2019
• End date: July 31, 2020
• Field of knowledge: Engineering - Chemical Engineering
• Principal Investigator: Luís Fernando Mercier Franco
• Grantee: Ana Laura Ramos Romano
• Host Institution: Faculdade de Engenharia Química (FEQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil

Abstract

Proteins are one of the basic molecular systems in the configuration of biological systems. The modeling of protein systems is, however, quite challenging for several intrinsic characteristics of these systems, such as molecular size, structural complexity, presence of charges in the chain, and the interaction with the medium. The most traditional approach for the calculation of the electrostatic potential on the surface of proteins is by numerically solving the Poisson-Boltzmann equation. Two major limitations in this approach, however, preclude a more precise description: the consideration that the solvent is a continuous medium and the use of the crystallographic structure of the protein in a static manner disregarding the interaction with the medium. In this project, we will use a more robust strategy that overcomes these limitations: molecular dynamics simulations. This computational technique allows us to calculate the electrostatic potential at the surface of the protein considering the interaction with the molecules of the solvent and the ions dissolved in the solvent. Therefore, we intend to better understand the limitations of the application of the Poisson-Boltzmann equation in systems containing proteins.