Dataset Information

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles.

ABSTRACT: 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 ?-helix and ?-sheet regions of the protein are similar to crystal grains so that the string-like collective atomic motion is concentrated in regions between the ?-helix and ?-sheet domains.

SUBMITTER: Haddadian EJ

PROVIDER: S-EPMC5296861 | biostudies-literature | 2017 Feb

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles.

Haddadian Esmael J EJ Zhang Hao H Freed Karl F KF Douglas Jack F JF

Scientific reports 20170208

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 part ...[more]

PMID: 28176808

Similar Datasets

Project description:Most condensed materials exhibit a significant fraction of atoms, molecules or particles that are strongly interacting with each other, while being configured geometrically at any instant of time in an 'amorphous' state having a relatively uniform density. Recently, both simulations and experiments have revealed that the dynamics of diverse condensed amorphous materials is generally characterized by significant heterogeneity in the local mobility and by progressively increasing collective motion upon cooling that takes the form of string-like collective particle rearrangements. The direct experimental observation of this type of collective motion, which has been directly linked to the growing relaxation times of glass-forming materials, and its quantification under different thermodynamic conditions, has so far been restricted to colloidal and driven granular fluids. The present work addresses the fundamental problem of how to determine the scale of this type of collective motion in materials composed of molecules or atoms. The basic premise of our work is that large scale dynamic particle clustering in amorphous materials must give rise to large fluctuations in particle mobility so that transport properties, especially those related to particle mobility, should naturally exhibit noise related to the cooperative motion scale. In our initial exploratory study seeking a relationship of this kind, we find 1/fα or 'colored noise', in both potential energy and particle displacements fluctuations of the atoms within the glassy interfacial layer of Ni nanoparticles (NPs). A direct relation between the particle displacement (mobility) noise exponent α and the average polymerization index of the string-like collective motion L is observed for a range of NP sizes, temperatures and for surface doping of the NPs with other metal atoms (Ag, Au, Pt) to change of fragility of the glassy interfacial layer at the surface of the Ni NPs. We also introduce a successful analytic model to understand this relationship between α and L.

Dataset Information

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles.

Publications

Comparative Study of the Collective Dynamics of Proteins and Inorganic Nanoparticles.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets