Chapter 2: Molecular Dynamics Simulations: Principles and Applications for the Study of Membrane Proteins

The plasma membrane is responsible for the maintenance of the correct chemical composition in cells, separating harmful substances from key biochemical processes required for basic human function. Membrane proteins are responsible for communication and transport phenomena across the membrane, facilitating a dynamic relationship between the cell interior and exterior despite the physical blockade. How these proteins function on a molecular level, however, remains largely unresolved. A fuller understanding is steadily emerging due to the increasing availability of three-dimensional structures of membrane proteins, in combination with computational methodologies such as molecular dynamics simulations. In this chapter, we present the key principles and considerations of performing molecular dynamics simulations in the context of membrane proteins, highlighting the leading applications in this field.