Supporting Information
Triple mutated antibody scFv2F3 with high GPx activity: insights from MD, docking, MDFE, and MM-PBSA simulation
Quan Luo,*,a Chunqiu Zhang,a Lu Miao,a Dongmei Zhang,a Yushi Bai,a Chunxi Hou,a Junqiu Liu,[(],a Fei Yan,b Ying Mu,b Guimin Luob
aState Key Laboratory of Supramolecular Structure and Materials, Institute of Theoretical Chemistry, Jilin University, Changchun 130012, P. R. China.
bKey Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, Jilin University, Changchun, China.
Figure S1. Multiple sequence alignment of scFv-2F3 with template 1NQB, 1LMK, and 2GKI. The red, yellow, and grey boxes represent identical residues, conserved, and semi-conserved substitutions respectively. The complementarity determining regions (CDRs) are marked by magenta arrow, and the flexible linker (Gly4Ser)3 are marked by purple rectangular.
Figure S2. (a) 3D profiles of verified results of the scFv2F3 model. (b) Ramachandran plot of the preferred scFv2F3 model. The most favored regions are colored in red. Allowed, generously allowed, and disallowed regions are indicated as yellow, light yellow, and white regions, respectively.
The overall quality of scFv2F3 structure was examined by Profile-3D. The compatibility score of the refined model is 55.73, slightly higher than the expected score (53.30) of a valid protein, and the environment of each residue agrees well with that of known structures in the database as their compatibility score is positive (Fig. S2a). Procheck was used to calculate the backbone f, j torsion angles of scFv2F3 model. The percentage of residues within allowed regions in Ramachandran plot is 99% which indicate that the stereochemical quality of our model is reasonable (Fig. S2b).
Figure S3. (a) The total energy (red) and potential energy (black) of Model IV as a function of time during MD simulation. (b) Average RMSD of Cα atoms during the same MD simulation. Red: Model IV; Black: residue Trp29, Cys52, and Gln72.
Figure S4. Root mean square fluctuations (RMSFs) of backbone atoms (N, Cα, and C) averaged over the entire course of 10-ns MD trajectories of Model IV.
Figure S5. The results of molecular dynamics free energy simulation for the small model compound, using five quadrature points. (a) λ = 0.0, (b) λ = 0.11270, (c) λ = 0.50, (d) λ = 0.88729, (e) λ = 1.0.
Figure S6. The results of molecular dynamics free energy simulation for Model I, using five quadrature points. (a) λ = 0.0, (b) λ = 0.11270, (c) λ = 0.50, (d) λ = 0.88729 (e) λ = 1.0.
Figure S7. The results of molecular dynamics free energy simulation for Model II, using five quadrature points. (a) λ = 0.0, (b) λ = 0.11270, (c) λ = 0.50, (d) λ = 0.88729 (e) λ = 1.0.
Figure S8. The results of molecular dynamics free energy simulation for Model III, using five quadrature points. (a) λ = 0.0, (b) λ = 0.11270, (c) λ = 0.50, (d) λ = 0.88729 (e) λ = 1.0.
Figure S9. The results of molecular dynamics free energy simulation for Model IV, using five quadrature points. (a) λ = 0.0, (b) λ = 0.11270, (c) λ = 0.50, (d) λ = 0.88729 (e) λ = 1.0.
Table S1 The distance measurements in the active site of model and native GPxs.
Atom1 / Atom2 / GPx2 / GPx4 / GPx5 / Average Distance(Native GPx) / Model IV
Cys (S) / Trp (N) / 4.08 / 3.92 / 3.74 / 3.91 / 3.38
Cys (S) / Gln (O) / 3.29 / 3.33 / 4.34 / 3.65 / 3.19
Trp (N) / Gln (O) / 4.27 / 3.24 / 3.36 / 3.62 / 3.38
Arg(N) / Trp (N’) / 7.69 / 6.94 / 7.69 / 7.44 / 7.79
Arg(N) / Trp(O’) / 8.33 / 7.45 / 8.33 / 8.04 / 8.33
* Cys (S): The Sulfhydryl sulfur of Cys, Trp (N): The imino nitrogen of Trp, Gln (O): The amide oxygen of Gln, Trp (N’): The backbone nitrogen of Trp, Trp (O’): The backbone oxygen Trp, Arg(N): The guanidyl nitrogen of Arg.
[(]* Corresponding author, E-mail address: ;
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