  During the last decade, network approaches became a powerful tool to describe
protein structure and dynamics. Here we review the links between disordered
proteins and the associated networks, and describe the consequences of local,
mesoscopic and global network disorder on changes in protein structure and
dynamics. We introduce a new classification of protein networks into
cumulus-type, i.e., those similar to puffy (white) clouds, and stratus-type,
i.e., those similar to flat, dense (dark) low-lying clouds, and relate these
network types to protein disorder dynamics and to differences in energy
transmission processes. In the first class, there is limited overlap between
the modules, which implies higher rigidity of the individual units; there the
conformational changes can be described by an energy transfer mechanism. In the
second class, the topology presents a compact structure with significant
overlap between the modules; there the conformational changes can be described
by multi-trajectories; that is, multiple highly populated pathways. We further
propose that disordered protein regions evolved to help other protein segments
reach rarely visited but functionally-related states. We also show the role of
disorder in spatial games of amino acids; highlight the effects of
intrinsically disordered proteins (IDPs) on cellular networks and list some
possible studies linking protein disorder and protein structure networks.

Molecular Networks;Disordered Systems and Neural Networks;Biological Physics