Extension of the CHARMM Classical Drude Polarizable Force Field to N- and O-Linked Glycopeptides and Glycoproteins

Abstract

Molecular dynamic simulations are an effective tool to study complex molecular systems and are contingent upon the availability of an accurate and reliable molecular mechanics force field. The Drude polarizable force field, which allows for the explicit treatment of electronic polarization in a computationally efficient fashion, has been shown to reproduce experimental properties that were difficult or impossible to reproduce with the CHARMM additive force field, including peptide folding cooperativity, RNA hairpin structures, and DNA base flipping. Glycoproteins are essential components of glycoconjugate vaccines, antibodies, and many pharmaceutically important molecules, and an accurate polarizable force field that includes compatibility between the protein and carbohydrate aspect of the force field is essential to study these types of systems. In this work, we present an extension of the Drude polarizable force field to glycoproteins, including both N- and O-linked species. Parameter optimization focused on the dihedral terms using a reweighting protocol targeting NMR solution J-coupling data for model glycopeptides. Validation of the model include eight model glycopeptides and four glycoproteins with multiple N- and O-linked glycosylations. The new glycoprotein carbohydrate force field can be used in conjunction with the remainder of Drude polarizable force field through a variety of MD simulation programs including GROMACS, OPENMM, NAMD, and CHARMM and may be accessed through the Drude Prepper module in the CHARMM-GUI.

Figure 1.

Model compounds used in dihedral fitting of the O- and N-linkages. For O-linkage, an initial simple model compound based on THP-Thr/Ser without the hydroxyls on the hexopyranose ring was used (top of left panel) to perform the dihedral potential energy scans. Subsequently the full model compounds with the hydroxyls (bottom of left panel) were created based on conformations of the THP-based model compounds. Both α and β anomers of both the N- and O-glycan linkages were included explicitly in this study, therefore the linkages are represented with dotted line.

Figure 2.

Relative conformational energies of selected conformations of hexopyranose with N-acetyl substituted at C1 for both the α and β anomers. All the model compound conformations with relative QM energies below 12 kcal/mol are included. RMSE of Drude and additive C36 relative energies with respect to QM are included in parentheses shown in the inset.

Figure 3.

2D protein φ/ψ distribution of target data used during the O-linked dihedral fitting. The distribution is overlaid on the structure of the full O-linked Thr model compound (Figure 1, bottom left panel).

Figure 4.

Relative conformational energies of selected conformations of the hexopyranose monosaccharide linked to the Ser and Thr dipeptides for both the α and β anomers. All the model compound conformations with relative QM energies below 12 kcal/mol are included. RMSE of Drude and additive C36 relative energies with respect to QM are included in parentheses shown in the inset.

Figure 5.

³J_HαHβ vs φ (protein) distribution obtained from MD. ³J_HαHβ calculated based on eq 1 for every 1° form −180° to 180°. “QM” indicates the initial QM-based dihedral parameters.

Figure 6.

J-coupling values for the protein (φ) dihedral C-N-CA-C for the model compounds SER-BGLCNA and THR-BGLCNA. (A) and (C) represent the Drude FF results. (B) and (D) represent the additive C36 FF results. The results for the other six compounds are provided in the Supporting Information.

Figure 7.

J-coupling values for the dihedral HN-N-C2-H2 for the model compounds SER-BGLCNA and THR-BGLCNA. (A) and (C) represent the Drude FF results. (B) and (D) represent the additive C36 FF results. The results for the other four compounds are provided in the Supporting Information.

Figure 8.

J-coupling values for the dihedral N-CA-CB-OG for the model compounds SER-BGLCNA and THR-BGLCNA. (A) and (C) represent the Drude FF results. (B) and (D) represent the additive C36 FF results. With THR-BGLCNA experimental data is not available. The results for the other four compounds are provided in the Supporting Information.

Figure 9.

Boltzmann inverted glycosidic dihedral angle distributions associated with all the N-glycans from all four glycoproteins. A) C1-ND2-CG-CB vs. O5-C1-ND2-CG, B) ND2-CG-CB-CA vs. C1-ND2-CG-CB, and C) CG-CB-CA-N vs. ND2-CG-CB-CA. Black dots indicate the values of the dihedrals observed in crystallographic structures.

Figure 10.

Boltzmann inverted glycosidic dihedral angle distributions associated with all the O-glycans from all four glycoproteins. (A) C1-OG-CB-CA vs. O5-C1-OG-CB in Ser O-linkages, (B) OG-CB-CA-N vs. C1-OG-CB-CA in Ser O-linkages, (C) C1-OG1-CB-CA vs. O5-C1-OG1-CB in Thr O-linkages, and (D) OG1-CB-CA-N vs. C1-OG1-CB-CA in Thr O-linkages. Black dots indicate the values of dihedrals observed in crystallographic structures.

Figure 11.

Monosaccharide dipole moment analysis for the N-glycan of PDB code 1MYR at Asn265 (segment ID: CARB assigned by CHARMM-GUI, see Table 1). Changes in dipole moment across the simulation are shown on left. On right, the normalized probabilities of dipole moment are shown for each monosaccharide.