Mutations in the Ankyrin Repeat Domain of the Human TRPV4 Protein Affect
Binding of ATP: a Combined Molecular Dynamics and Network Analysis Study
Abstract
Molecular dynamics (MD) simulations and residue interaction network
analyses were carried out to investigate how some mutations on the human
TRPV4 ankyrin repeating domain (ARD) change the ATP-binding strengths.
Contact residue interaction networks (RINs) generated from the MD
simulation trajectories are connected graphs with the ATP nodes having
high importance. Besides four ATP-binding residues identified in early
researches, extra ATP-binding residues are found for the wild type and
mutant human TRPV4 ARDs based on the contact RIN results. Analyses of
the first neighbor lists of the ATP nodes in contact RINs, and
visualization of the average structures help to locate two distinct
ATP-binding areas for different groups of mutants, with the wild type,
K197R, R269H, V342F mutants in the first group, and E183K, E278K and
R232C in the second. Further dihedral angle analyses, PCA analyses and
mutation-site first-neighbor analyses demonstrate that the mutations
usually cause remote interaction changes to the mutation sites, alter
the collaborative behaviors of different domains of the human TRPV4 ARD,
and eventually affect the ATP-binding strengths.