Protein dynamics is a catch-all term referring to the conformational heterogeneity of folded protein structures. Weber described them as “screaming and kicking”. As is noted by (1), dynamics are described by 1) timescale, 2) amplitude, and 3) directionality, and they distinguish between fast and slow dynamics based on whether the energy barrier between the two sampled states exceed 1 kT.
Notes
- The variation among protein structures determined by X-ray-crystallography broadly reproduce the dynamics measured by NMR (2). They also fit NMR data better than ensembles folded using those NMR data.
- De novo designed proteins can also have conformational equilibria that are modified by point mutations (3).
- The free energy landscape model of protein dynamics was first proposed by (4).
Measurement
Related
1.
Henzler-Wildman K, Kern D. Dynamic personalities of proteins. Nature. 2007;450(7172):964–72. Available from: https://doi.org/10.1038/nature06522
2.
Best RB, Lindorff-Larsen K, DePristo MA, Vendruscolo M. Relation between native ensembles and experimental structures of proteins. Proceedings of the National Academy of Sciences. 2006;103(29):10901–6. Available from: https://doi.org/10.1073/pnas.0511156103
3.
Guo AB, Akpinaroglu D, Stephens CA, Grabe M, Smith CA, Kelly MJS, et al. Deep learning–guided design of dynamic proteins. Science. 2025;388(6749). Available from: https://doi.org/10.1126/science.adr7094
4.
Austin RH, Beeson KW, Eisenstein L, Frauenfelder H, Gunsalus IC. Dynamics of ligand binding to myoglobin. Biochemistry. 1975;14(24):5355–73. Available from: https://doi.org/10.1021/bi00695a021