Functional Protein Dynamics Directly from Sequences

The sequence correlations within a protein multiple sequence
alignment
are routinely being used to predict contacts within its structure,
but here we point out that these data can also be used to predict
a protein’s dynamics directly. The elastic network protein
dynamics models rely directly upon the contacts, and the normal modes
of motion are obtained from the decomposition of the inverse of the
contact map. To make the direct connection between sequence and dynamics,
it is necessary to apply coarse-graining to the structure at the level
of one point per amino acid, which has often been done, and protein
coarse-grained dynamics from elastic network models has been highly
successful, particularly in representing the large-scale motions of
proteins that usually relate closely to their functions. The interesting
implication of this is that it is not necessary to know the structure
itself to obtain its dynamics and instead to use the sequence information
directly to obtain the dynamics.