Computational study of secondary structure stability of peptide in solvents mixtures

• Grant number: 23/03308-8
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: April 01, 2023
• Status: Discontinued
• Field of knowledge: Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
• Principal Investigator: Leandro Martinez
• Grantee: Lucas Verona de Araujo
• Host Institution: Instituto de Química (IQ). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 13/08293-7 - CCES - Center for Computational Engineering and Sciences, AP.CEPID

Abstract

The structure of proteins and their folding mechanisms depend on the molecular environment, and are sensitive to small variations in temperature, pressure and the presence of organic molecules, known as co-solvents. TMAO and urea are two co-solvents whose effects on the stability of protein structures are well known, but the underlying molecular mechanisms are still not completely understood. In this project, we intend to introduce the student to molecular dynamics simulations, using enhanced sampling techniques, by studying the folding of peptides with different secondary structure elements (alpha-helices and beta-sheets) in aqueous solutions with co-solvents. The solvent effects will be analyzed using the minimum-distance distribution functions (MDDF) and the Kirkwood-Buff theory, seeking to compare the results obtained with the experimental parameters.