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Is the Dynamics of a Folded Protein Similar to a Surface-Melted Inorganic Nanoparticle?



Jack F. Douglas, Esmael Haddadian1, Karl Freed, Hao Zhang


Karplus and coworkers have argued that proteins in their biologically active ‘native’ state should exhibit a dynamics similar to ‘surface-melted’ inorganic nanoparticles (NPs) because both types of NPs have a relatively dense, ordered, and immobile core surrounded by a interfacial region of relatively high mobility. Recent studies have indicated that this surface-melted state in NPs is actually a rather complex material state, intermediate between a solid and liquid, and it is then interesting to consider this analogy in some detail to probe its deeper significance and validity. In particular, simulations of pre-melted Ni NPs have indicated significant dynamic heterogeneity in the interfacial dynamics, and other features of glass-forming liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements having long range correlations (‘colored’ or ‘pink’ noise), and particle displacement events having a power-law scaling as found in earthquakes. Remarkably, we observe the same phenomena in molecular dynamics simulations of ubiquitin with explicit solvent where the extent of the collective motions within the protein is modulated by adjusting the liquid composition in water/glycerol mixtures.
Scientific Reports


ubiquitin, nanoparticles, molecular dynamics, string-like collective motion, glycerol-water solvent mixtures, protein quakes, colored noise


Douglas, J. , Haddadian1, E. , Freed, K. and Zhang, H. (2017), Is the Dynamics of a Folded Protein Similar to a Surface-Melted Inorganic Nanoparticle?, Scientific Reports (Accessed July 22, 2024)


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Created February 8, 2017, Updated April 23, 2020