Fig 1.
Glycoprotein simulation workflow.
Flowchart describing the overall procedure used to simulate glycoproteins.
Fig 2.
Inputs and results of homology modelling of BChE.
Homology model performed using Modeller 9.16 [20]. AChE and BChE are homologically similar, but their residues indices do not map one to one. Only AChE residues within the tetramerization domain (BChE residues 530–574, AChE residues 540–584) were used as model inputs. The active site SER198 is shown in purple, with the reader oriented directly above the gorge of the active site. The N terminus is at the right, and the C terminus at the left in all images. Green glow indicates residues used as inputs in the model.
Table 1.
Simulated BChE glycoforms and their corresponding glycan distribution.
Fig 3.
CFG cartoon representations of the proglycan abbreviations created with GlycanBuilder [35]. Blue squares are N–acetylglucosamine, green circles are mannose, yellow circles are galactose, and magenta diamonds are N-Acetylneuraminic acid. Linkages and anomeric centers are labeled.
Fig 4.
Initial and final conformations.
Initial (top) and final (bottom) conformations of the simulated human (left) and glycan 241 (–) (right) glycoforms. Images are oriented such that the reader is viewing directly into the active site gorge. Glycans are labeled in the top left image by color. An asterisk denotes a monosialylated glycan. The active site SER198 is colored in pink.
Fig 5.
Core backbone residues (5–529) atomic RMSD over 100 ns from the initial conformation (left) and the final conformation (right) for the human and glycan 241 (-) simulations. of BChE.
Fig 6.
Glycan and protein conformational dihedral angles.
Glycan conformational dihedral angles ϕg, ψg, and ωg of α1-6 dimannose (left) and protein conformational dihedral angles ϕp, ψp, and ωp of dialanine (right). Glycan linkages only contain an ωg when the linkage occurs on the terminal carbon; otherwise, the linkage only contains ϕg and ψg.
Fig 7.
Dynamics of conformational dihedral angle ϕg.
MSAD (left column), MAD (middle column) and AACF (right column) of the ϕg (top row) and ϕp (bottom row) of the human and glycan 241 (–) BChE glycoform. MSAD is displayed in log–log plots, while MAD and AACF are displayed in semi–log plots. The first and third quartiles of the MSAD are shown in colored dashed lines, and a representative diffusive line is shown in a black dashed line. A power law fit from τ = 0–2 ns of the AACF is shown in a dashed line, and a linear fit from τ = 20–60 ns is also shown in a dashed line.
Fig 8.
MSAD of three representative glycans combining all ϕ, ψ and ω conformational dihedral angles in the Human and Glycan (–) glycoforms. Glycan 455 represents a lower bound, 57 represents a higher bound, and 17 represent a central glycan. The asterisk on Glycan 17 indicates a monosialilated glycan.
Table 2.
Anomalous diffusion parameters α and Dα for all glycan conformational dihedral angles categorized by glycan.
Table 3.
Anomalous diffusion parameters α and Dα for all glycan and protein conformational dihedral angles categorized by conformational dihedral angle.
Fig 9.
Active site cavity images of the simulated BChE glycoforms. The human cavity at t = 0 ns (top left) is representative of the glycan 241 (–) cavity at t = 0 ns. The glycan 241 (–) cavity at t = 100 ns (bottom left) is representative of the glycan 241 (+) cavity at t = 100 ns. Cavities were generated using VOIDOO [18]. The cavity surface shown represents the surface accessible to the center of a probe of radius 1.4 Å. Protein residues lining the entrance are opaque, with select residues in licorice representation. ASP70, THR284 and PRO285 are enlarged, as their grouped center of mass distance distance is used to represent gorge accessibility. Glycan 241 is the only glycan shown, and is colored according to Fig 3.
Fig 10.
Center of mass distance between ASP70 and combined residues THR284 and PRO285. These residues are located at the top of the active site gorge, and characterize the opening and closing of the gorge.
Fig 11.
100 ns, 1000 frame secondary structure overlays of human (left) and glycan 241 (–) (right) BChE glycoforms. α–helices are colored in gray, β–sheets in red, 310–helices in orange, coil in white and turn in cyan. The active site SER198 is colored in green.
Fig 12.
Tetramerization domain radius of gyration.
Radius of gyration along the longest principal component of the BChE tetramerization domain, residues 530–574.