Propiedades físicas de las cápsides virales icosaédricas: modelos de potenciales de interacción y constantes de fuerza.

Abstract

Virology is a research field that needs physics to understand the behaviour of viruses, since there are a lot mechanisms that use thermodynamics, kinetics or electrostatics. These are some of the viral properties that we are going to study and explain. In this final degree work, we will start explaining the viruses in their fundamentals, introducing the capsids, the envelope of the viruses. We will consider only the case of the icosahedral viruses, since this geometrical form is the one that appears the most in nature. These capsids are formed by protein subunits, the capsomers. Icosahedral capsids are described by Caspar and Klug’s models, since they introduce the triangular number T, a very important parameter in virology. One of the most fastinating feature is the auto-assembly of viral capsids. This is a feature that we will explain via thermodynamics and kinetics. We will study as well the electrostatic interaction between the capsomers and the capsomers in the formed capsid through Poisson-Bolztmann’s equation. Another physical feature that we will study is the mechanical properties. Viruses endure external forces in their environment and the osmotic pressure that the genome applies to the capsid. That force can be measured and studied. The main focus of this work will be on the models that explain the interaction potential. First, we will explain the two different models that explain these interactions: Coarse-grained and All-atom. Then, we will explain our two-body interaction model, that is a Coarse-grained type, using trimers, a kind of triangular capsomers. Afterwards, we will introduce the variables that characterize the trimer orientation and the equilibrium conditions that fixes the privileged orientation of the trimers in order to form a capsid. Then, we will calculate the second derivative matrix of the interaction potential in order to calculate the force constants. Finally, we apply the equilibrium conditions to the matrix to obtain the force constants.