Soft material distributions in highly complex viral systems

• Grant number: 23/14353-4
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: December 01, 2023
• End date: November 30, 2025
• Field of knowledge: Physical Sciences and Mathematics - Chemistry - Physical-Chemistry
• Principal Investigator: Leandro Martinez
• Grantee: Camila Assis Tavares
• 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

This project aims to investigate the molecular architecture of viruses with focus on the distribution of solvents, lipids, ions, and other small molecules in the viral structures. Viral structures are known from macromolecular crystallography and Cryo-EM, but these experimental methods provide information mostly on the protein and nucleic acid distributions. Soft components such as lipid membranes, water, and other small molecules cannot be discriminated in atomic detail from these experimental techniques. Here, we will start from large-scale coarse-grained simulations of 5 complete viruses (Zika, Dengue type 2, Japanese Encephalitis, West Nile, and Tick-borne encephalitis viruses) performed by collaborators at the Institute Pasteur of Montevideo to obtain a detailed picture of the soft-material distributions and their specificities among different viruses. Each of these systems are challenging targets for any analysis of molecular distributions for their high structural complexity and size, comprising typically more than a million of particles, even in a coarse-grained representation. Specialized methods for the computation of the molecular structures are required and have been developed in the group of Prof. Leandro Martínez, supervisor of the project. Here, solvation structures will be studied using minimum-distance distribution functions, using the group's expertise, by means of the ComplexMixtures.jl package. These distribution functions allow the interpretation of the structure of complex solutions with many components automatically taking into consideration the shapes of the components of the system. Efficient implementations of the computation of these distributions and their decomposition in the contribution of specific chemical groups allow the visualization and understanding of macromolecular solvation in great detail. This project will bring a new view of the molecular interactions of the soft components of viral structures, providing insights into the function and structure of these important organisms.