Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles.
Molecular dynamics simulations of ubiquitin in water/glycerol solutions are used to test the suggestion by Karplus and coworkers that proteins in their biologically active state should exhibit a dynamics similar to 'surface-melted' inorganic nanoparticles (NPs). Motivated by recent studies indicating that surface-melted inorganic NPs are in a 'glassy' state that is an intermediate dynamical state between a solid and liquid, we probe the validity and significance of this proposed analogy. In particular, atomistic simulations of ubiquitin in solution based on CHARMM36 force field and pre-melted Ni NPs (Voter-Chen Embedded Atom Method potential) indicate a common dynamic heterogeneity, along with other features of glass-forming (GF) liquids such as collective atomic motion in the form of string-like atomic displacements, potential energy fluctuations and particle displacements with long range correlations ('colored' or 'pink' noise), and particle displacement events having a power law scaling in magnitude, as found in earthquakes. On the other hand, we find the dynamics of ubiquitin to be even more like a polycrystalline material in which the α-helix and β-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the α-helix and β-sheet domains.
Biological Sciences Collegiate Division, University of Chicago, Chicago, IL 60637, USA.
Esmael J
EJ
Haddadian
Department of Chemical and Materials Engineering, University of Alberta, Alberta, T6G 1H9 Canada.
Hao
H
Zhang
Department of Chemistry, James Franck Institute, and Computation Institute, University of Chicago, Chicago, IL 60637, USA.
Karl F
KF
Freed
Materials Science and Engineering Division, Materials Measurement Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA.
Jack F
JF
Douglas
D000465:Algorithms; D005990:Glycerol / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D053758:Nanoparticles / Q000737:chemistry*; D000072756:Protein Conformation, alpha-Helical; D011506:Proteins / Q000737:chemistry*; D012996:Solutions; D025801:Ubiquitin / Q000737:chemistry
D011506:Proteins; D012996:Solutions; D025801:Ubiquitin; D005990:Glycerol