Figure 1.
General reaction catalyzed by the NSTs.
Figure 2.
Interactions of N-sulfotransferase domain in NST1 bound to PAPS and PAP with the heparan disaccharide, as predicted by AutoDock.
The disaccharide is shown as blue sticks, with sulfate as yellow and amide atoms as pink; PAPS and PAP are shown as green sticks with sulfate as yellow or phosphate as orange. Key reaction residues for enzyme function are shown as gray sticks.
Table 1.
N-sulfotransferase 1 and mutants docking energies and hydrogen bond distances.
Figure 3.
All-atom root-mean-square deviation (RMSD) of the protein, plotted against the 50 ns MD simulation time, for the systems containing (A) the NST alone and for the (B) NST/PAPS, (C) NST/PAPS/α-GlcN-(1→4)-GlcA and (D) NST/PAP/α-GlcNS-(1→4)-GlcA complexes.
Black, NST-1; Green, Lys614Ala; Blue, His716Ala, Red, Lys833Ala.
Figure 4.
Per residue interaction energies between NST sidechain residues and sulfate in both PAPS and disaccharide models.
Figure 5.
CαRMSF of the first eigenvector as a function of residue number.
Black, NST; green, NSTLys614Ala; blue, NSTHis716Ala; red, NSTLys833Ala. A, N-sulfotransferase domain (NST) alone; B, NST-PAPS systems; C, NST-PAPS-GlcN-GlcA; D, NST-PAP-GlcNS-GlcA.
Table 2.
Cosine Content of the First Three Eigenvectors.
Figure 6.
Effect of mutated residues in structural conformational changes.
Computational dynamic analysis of NST is shown as cyan Cα trace in each model. Porcupine plots showing the direction and amplitude of conformational changes between PAPS/GlcN-GlcA and PAP/GlcNS-GlcA states represented by the first eigenvector of the principal mode Cα atoms calculated from the 50 ns simulation. The orientation of the blue cone indicates the direction of motion of the atom, and its length is proportional to the amplitude of the motion. Predicted binding residues are shown: yellow, Lys614; green, His716; and purple, Lys833. Right column: principal component analysis of combined MD trajectory of NST/PAPS/GlcN-GlcA and NST/PAP/GlcNS-GlcA and mutants. Projection of the MD trajectories on the first eigenvector of the covariance matrix of Cα atoms. Black, projections of the first 50 ns of the combined trajectory NST-PAPS-GlcN-GlcA; red, projections of the 50 of the combined trajectory NST-PAP-GlcNS-GlcA. N-sulfotransferase domain and Lys614, His716 and Lys833 are represented in figures A-D.
Figure 7.
Radial distribution functions.
g(r), centered on the side chain atoms of the residues involved in sulfate transfer to the oxygen atoms of modeled water of the eight complexes: Black, Sulfonate Oγ solvation; red, Lys614 Nγ solvation; green, His716 NHτ solvation, blue, Lys833 Nγ solvation; yellow, glycan NH2 solvation.