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Molecular simulations of functional dynamics in biomolecular machines

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Functional dynamics plays an important role when biomolecular machines fulfill their functions. For example, transporter proteins transport their substrates across the membrane by changing their conformation between inward-open and outward-open conformations. Although it is difficult to directly simulate millisecond functional time of these biomolecular machines whose total atoms amount to several hundred thousand, we use techniques such as metadynamics or transition path sampling to uncover molecular mechanism of the functioning moments.

K. Okazaki, D. Wöhlert, J. Warnau, H. Jung, Ö. Yildiz, W. Kühlbrandt and G. Hummer, Nat. Commun. 10, 1742 (2019)
https://www.nature.com/articles/s41467-019-09739-0