Fig 1.
Three-dimensional structure of monomeric β1 subunit (ATP1B1) and β2 subunit (ATP1B2).
A) 3D structure of the β1 subunit monomer including its glycosylations. B) Ramachandran plot of the β1 subunit monomer where it can be seen that only 1% of the residues of the proteins are included in the disallowed regions. C) 3D structure of the β2 subunit monomer including its glycosylations. D) Ramachandran plot of the β2 subunit monomer where it can be seen that none of the residues of the proteins are included in the disallowed regions. The extracellular domains of the β1 and β2 subunits depicted in A and C are with the N-terminal (residues 63 and 70) colored in yellow and the C-terminal (residues 303 and 289) in green. The distinctive alpha-helix of the β-subunits is localized in the bottom. For relative orientation to the alpha subunits, see S7 Fig.
Fig 2.
Dimeric 3D structure of β1 subunit and β2 subunit in trans orientation.
A) Dimeric structure of . B) Dimeric structure of β2 − β2. For both cases Chain A is colored in purple and Chain B is colored in blue. Glycosylations are marked in balls and sticks.
Fig 3.
Structural Analysis of ATP1B1 and ATP1B2 dimers: A) Root mean square deviation analysis (RMSD) of the dimers β1 and β2.
A) Root mean square deviation analysis (RMSD) of the dimers β1 and β2 . Root mean square fluctuation (RMSF) analysis of the alpha carbons of the dimers (B) and β2 − β2 (C).
Fig 4.
Interfaces at ATP1B1 and ATP1B2 dimers.
Graphical representation of the protein interfaces at β1 and β2 dimers in different snapshots obtained from the MD simulations using PDBSUM server. (*) Residues that appear in all conformations are marked as hot spots.
Fig 5.
Multiple sequence alignment of ATP1B1 and ATP1B2.
A multiple alignment is shown (ATP1B1 Human (P05026), ATP1B1 Dog (P06583), and ATP1B2 Human (P14415). Yellow Arrows: Hot Spots residues of human ATP1B1. Red arrows: Hot spots residues of human ATP1B2. Orange box: Dog Sequence 1 from ref. 15 and Green box: dog Sequence 2 from ref. 16.
Fig 6.
Constant hydrogen-bonds in β1 and β2 dimers.
Distance between atoms (Asn226A:HD21-Thr264B:OG1) for β1 and (Asn220A:ND2-Thr155B:O) for β2 were calculated along the trajectories using Carma Software.
Table 1.
Glycan-protein interactions of ATP1B1 (β1 dimer).
Table 2.
Glycan-protein interactions of ATP1B2 (β2 dimer).
Table 3.
MM-PBSA calculation of ATP1B1 (β1) and ATP1B2 (β2) dimeric complexes.
Fig 7.
Free energy landscapes considering the first two principal components of and β2 − β2 dimers.
Fig 8.
Motion associated with PC1 and PC2.
Chain A goes from red in the N-terminus to white in the C-terminus while chain B goes from white in the N-terminus to blue in the C-terminus. Green tubes show the motion associated with the principal components.