Using normal modes analysis to characterize the flexibility of protein

Protein 3D structures are tightly related to protein functions. There are withal missing links
between protein structure and function and studies have shown that protein dynamics is one of
them.

The transport of compounds of various sizes through cell membranes is partly ensured by
transmembrane proteins, such as channels or carriers. Their 3D structure is often characterized by
an opening providing a route through which ions or small molecules will be traveling. During the
transport process these tunnels may change geometry, adjusting their access and permeability to
regulate the protein’s function. These structural changes are happening on time scales that are
often too long to be captured by molecular dynamics simulations.
In the talk I will discuss our approach to these complex problems.

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