Dynamics of protein cavities associated with protein fluctuations and
conformational plasticity is essential for their biological function.
NMR ensembles, Molecular Dynamics (MD) simulations combined with
Principal Component Analysis (PCA), and Normal Mode Analysis (NMA)
provide appropriate frameworks to explore functionally relevant protein
dynamics and cavity changes relationships. Within this context, we have
developed ANA (Analysis of Null Areas), an efficient method to calculate
cavity volumes. ANA is based on a combination of algorithms that
guarantees its robustness against numerical differentiations. This is a
unique feature with respect to other methods. Herein, we test ANA as a
biophysical and bioinformatic method to analyze different structural and
dynamics properties of cavities. In order to address this task, we have
developed an updated and improved version of ANA that expands it use to
quantify changes in cavity features, like volume and flexibility, due to
protein structural distortions performed on predefined biologically
relevant directions, e.g, directions of largest contribution to protein
fluctuations (PCA modes) obtained by MD simulations or ensembles of NMR
structures, collective NMA modes or any other direction of motion
associated with specific conformational changes. A web page has been
developed and its facilities are explained in detail, making the
software available to all users. Firstly, we show that ANA can be useful
to explore gradual changes of cavity volume and flexibility associated
with protein ligand binding. Secondly, we perform a comparison study of
the extent of variability between protein backbone structural
distortions, and changes in cavity volumes and flexibilities evaluated
for an ensemble of NMR active and inactive conformers of the epidermal
growth factor receptor (EGFR) structures. Finally, we compare changes in
size and flexibility between sets of NMR structures for different
homologous chains of dynein.