Free energy change of polypeptides by Steered MD

Steered Molecular Dynamics (SMD) was used to analyze free energy changes associated with conformational changes in polypeptides. The distance between terminal atoms was controlled using a virtual particle, enabling evaluation of the energy difference between extended and helical states. This approach is expected to contribute to mechanical understanding of conformational changes and to biomaterial design.

Use Cases Highlights

Analysis of free energy changes along a reaction coordinate
Applicable to morphological changes of polymers

Analysis of free energy changes along a reaction coordinate

An alanine decamer was modeled as a polypeptide with the GAFF force field. The N-terminus was fixed, and a virtual particle was attached to the C-terminus for Steered MD (SMD) calculations by varying the terminal distance.

Model used in the calculation (alanine decamer). N-terminus fixed, C-terminus moved

Applicable to morphological changes of polymers

Free energy changes obtained from Steered Molecular Dynamics (SMD) are plotted against end-to-end distance. Similar results were obtained during elongation and contraction, and differences due to virtual particle velocity were also compared.

(Left) Free energy change between elongated and helical states of polypeptide. (Right) Free energy change when varying virtual particle velocity.

Reference

[1] S. Park, et al., “Free Energy Calculation from Steered Molecular Dynamics Simulations Using Jarzynski ’ s Equality,” J. Chem. Phys., 119, 3553, (2003).

Details of analysis

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