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Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS.

Kutzner C, Czub J, Grubmüller H - J Chem Theory Comput (2011)

Bottom Line: In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation.A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package.Application to the molecular motor F(1)-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

View Article: PubMed Central - PubMed

Affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

ABSTRACT
We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the molecular motor F(1)-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

No MeSH data available.


Time evolution of the angular position of the γ rotor computed as the best-fit angle with respect to the γ longest principal axis for the F1 motor enforced to rotate in the synthesis direction using Viso (A) and Vflex2 (B).
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fig8: Time evolution of the angular position of the γ rotor computed as the best-fit angle with respect to the γ longest principal axis for the F1 motor enforced to rotate in the synthesis direction using Viso (A) and Vflex2 (B).

Mentions: Because for the flexible potentials the local rotation axis adapts dynamically, it is interesting to monitor the evolution of the F1 rotor angle θ also with respect to a variable axis. Figure 8 shows the time dependence of θ computed in the same manner as previously but now with the instantaneous (longest) principal axis of the γ subunit used as the reference axis. Significantly smoother variation of θ with time is seen in Figure 8 compared to using a fixed symmetry axis (Figure 6B,C). This result illustrates the ability of the flexible methods to adapt the rotation geometry to the structure and conformational changes of the stator.


Keep It Flexible: Driving Macromolecular Rotary Motions in Atomistic Simulations with GROMACS.

Kutzner C, Czub J, Grubmüller H - J Chem Theory Comput (2011)

Time evolution of the angular position of the γ rotor computed as the best-fit angle with respect to the γ longest principal axis for the F1 motor enforced to rotate in the synthesis direction using Viso (A) and Vflex2 (B).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3091370&req=5

fig8: Time evolution of the angular position of the γ rotor computed as the best-fit angle with respect to the γ longest principal axis for the F1 motor enforced to rotate in the synthesis direction using Viso (A) and Vflex2 (B).
Mentions: Because for the flexible potentials the local rotation axis adapts dynamically, it is interesting to monitor the evolution of the F1 rotor angle θ also with respect to a variable axis. Figure 8 shows the time dependence of θ computed in the same manner as previously but now with the instantaneous (longest) principal axis of the γ subunit used as the reference axis. Significantly smoother variation of θ with time is seen in Figure 8 compared to using a fixed symmetry axis (Figure 6B,C). This result illustrates the ability of the flexible methods to adapt the rotation geometry to the structure and conformational changes of the stator.

Bottom Line: In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation.A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package.Application to the molecular motor F(1)-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

View Article: PubMed Central - PubMed

Affiliation: Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.

ABSTRACT
We describe a versatile method to enforce the rotation of subsets of atoms, e.g., a protein subunit, in molecular dynamics (MD) simulations. In particular, we introduce a "flexible axis" technique that allows realistic flexible adaptions of both the rotary subunit as well as the local rotation axis during the simulation. A variety of useful rotation potentials were implemented for the GROMACS 4.5 MD package. Application to the molecular motor F(1)-ATP synthase demonstrates the advantages of the flexible axis approach over the established fixed axis rotation technique.

No MeSH data available.