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Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy.

Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, McCammon JA - Proteins (2010)

Bottom Line: Y347, which demonstrates similar sampling patterns in the simulations of both force fields, is implicated as an important N1 residue that can "clamp" the ligand into a favorable binding pose.Free energy perturbation and thermodynamic integration calculations, using two different force fields, support the importance of Y347 and indicate a +3 to +5 kcal/mol change in the binding free energy of oseltamivir in the absence of calcium.With the important role of structure-based drug design for neuraminidase inhibitors and the growing literature on emerging strains and subtypes, inclusion of this calcium for active site stability is particularly crucial for computational efforts such as homology modeling, virtual screening, and free energy methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA. mlawrenz@ucsd.edu

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Y347 torsion changes during free energy calculations for the AMBER FF99SB ion-bound calculation (black, solid lines), AMBER FF99SB ion-free calculation with Y347 “in” starting structure (black, dashed), and with Y347 “out” starting structure (green, dashed); Also, GROMOS96 ion-bound simulations (red, solid lines) and GROMOS96 ion-free simulations (red, dashed).
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fig04: Y347 torsion changes during free energy calculations for the AMBER FF99SB ion-bound calculation (black, solid lines), AMBER FF99SB ion-free calculation with Y347 “in” starting structure (black, dashed), and with Y347 “out” starting structure (green, dashed); Also, GROMOS96 ion-bound simulations (red, solid lines) and GROMOS96 ion-free simulations (red, dashed).

Mentions: For comparison to the ion-bound FEP results (Table III) and to investigate the contribution of Y347 to the binding free energy, two sets of free energy calculations for the ion-free tetramer were carried out. The first calculation was initialized from a calcium-free structure selected after 5 ns of equilibration. During this equilibration period, Y347 had not yet flipped out of the pocket for three of the four monomers (see Supporting Information Fig. 2) and monitoring of the torsion throughout this calculation indicated 17% occurrence of the “out” Y347 state, compared to 6% in the calcium-bound simulation (black solid vs. black dashed in Fig. .4). Here, the free energy difference for the ion-bound and ion-free complexes is very small (Table III), which suggests that the AMBER FF99SB force field confers stability to other binding site residues and preserves an effective binding pose with oseltamivir. However, when cluster two (Table II) of the AMBER FF99SB ion-free MD simulations was selected as starting structure for each monomer in a second tetramer calculation, simulation time spent in the Y347 “out” conformation increased to 76% (green dashed line, Fig. .4). This increased destabilization of the active site framework gives more impact on the free energy of binding, with a +2.7 kcal/mol reduced favorability in ΔΔGbind. The change in results underscores both the influence of starting structure on sampling in free energy calculations, as well as the difficulty in achieving complete sampling using traditional MD methods.


Impact of calcium on N1 influenza neuraminidase dynamics and binding free energy.

Lawrenz M, Wereszczynski J, Amaro R, Walker R, Roitberg A, McCammon JA - Proteins (2010)

Y347 torsion changes during free energy calculations for the AMBER FF99SB ion-bound calculation (black, solid lines), AMBER FF99SB ion-free calculation with Y347 “in” starting structure (black, dashed), and with Y347 “out” starting structure (green, dashed); Also, GROMOS96 ion-bound simulations (red, solid lines) and GROMOS96 ion-free simulations (red, dashed).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2902668&req=5

fig04: Y347 torsion changes during free energy calculations for the AMBER FF99SB ion-bound calculation (black, solid lines), AMBER FF99SB ion-free calculation with Y347 “in” starting structure (black, dashed), and with Y347 “out” starting structure (green, dashed); Also, GROMOS96 ion-bound simulations (red, solid lines) and GROMOS96 ion-free simulations (red, dashed).
Mentions: For comparison to the ion-bound FEP results (Table III) and to investigate the contribution of Y347 to the binding free energy, two sets of free energy calculations for the ion-free tetramer were carried out. The first calculation was initialized from a calcium-free structure selected after 5 ns of equilibration. During this equilibration period, Y347 had not yet flipped out of the pocket for three of the four monomers (see Supporting Information Fig. 2) and monitoring of the torsion throughout this calculation indicated 17% occurrence of the “out” Y347 state, compared to 6% in the calcium-bound simulation (black solid vs. black dashed in Fig. .4). Here, the free energy difference for the ion-bound and ion-free complexes is very small (Table III), which suggests that the AMBER FF99SB force field confers stability to other binding site residues and preserves an effective binding pose with oseltamivir. However, when cluster two (Table II) of the AMBER FF99SB ion-free MD simulations was selected as starting structure for each monomer in a second tetramer calculation, simulation time spent in the Y347 “out” conformation increased to 76% (green dashed line, Fig. .4). This increased destabilization of the active site framework gives more impact on the free energy of binding, with a +2.7 kcal/mol reduced favorability in ΔΔGbind. The change in results underscores both the influence of starting structure on sampling in free energy calculations, as well as the difficulty in achieving complete sampling using traditional MD methods.

Bottom Line: Y347, which demonstrates similar sampling patterns in the simulations of both force fields, is implicated as an important N1 residue that can "clamp" the ligand into a favorable binding pose.Free energy perturbation and thermodynamic integration calculations, using two different force fields, support the importance of Y347 and indicate a +3 to +5 kcal/mol change in the binding free energy of oseltamivir in the absence of calcium.With the important role of structure-based drug design for neuraminidase inhibitors and the growing literature on emerging strains and subtypes, inclusion of this calcium for active site stability is particularly crucial for computational efforts such as homology modeling, virtual screening, and free energy methods.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA. mlawrenz@ucsd.edu

Show MeSH
Related in: MedlinePlus