Dynamics of hydrated proteins and bio-protectants: Caged dynamics, β-relaxation, and α-relaxation

Ngai, K. L.; Capaccioli, S.; Paciaroni, Alessandro

doi:10.1016/j.bbagen.2016.04.027

Cited by 30 publications

(46 citation statements)

References 85 publications

(220 reference statements)

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“…In addition, the solution setup does not reproduce highly stretched dynamics observed in protein powders. 12,19,29 We find that the agreement between theory and experiment 30 is much improved when stretched exponential dynamics from dielectric spectroscopy 31 are used in our model.…”

mentioning

confidence: 72%

“…The experimental results are recovered by multiplying τ(T ) from simulations by a factor of 2.65. While this factor is obviously arbitrary, the need for a correction might be related to our insufficient sampling of the long-time dynamics, extrapolation of the high-temperature relaxation times to lower temperatures, and the assumption of exponential dynamics not supported by measurements with protein powders 12,19,29 (see below). Despite some difficulties with the long-time dynamics in the cyt-Ox state, the short-time dynamics produced by simulations are consistent with experiment.…”

Section: Calculations Of Displacements Of the Heme Iron Based On Eqsmentioning

confidence: 99%

“…Correspondingly, the fluctuations of the long-range forces are mostly frozen at low temperatures when δ F 2 r is low, yielding δ x 2 ≃ δ x 2 vib . Since the relaxation time of the long-range forces τ(T ) depends on temperature according to the Arrhenius law, it shortens with increasing temperature, ultimately reaching the point 12,23,25,26 τ r ≃ τ(T d ), at which the high-temperature crossover occurs. Fluctuations of the long-range forces become dynamically unfrozen at this temperature, leading to an increase of both δ F 2 r and δ x 2 r .…”

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confidence: 99%

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Ergodicity breaking of iron displacement in heme proteins

Seyedi

Matyushov

2017

Soft Matter

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We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.

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mentioning

confidence: 72%

Section: Calculations Of Displacements Of the Heme Iron Based On Eqsmentioning

confidence: 99%

mentioning

confidence: 99%

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Ergodicity breaking of iron displacement in heme proteins

Seyedi

Matyushov

2017

Soft Matter

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“…In several papers we reported our analyses of the published data to show in many different glass-formers that the intensity of the caged dynamics exhibits a two-step increase at T gβ and T g . The phenomenon is general and found in polyalcohols [44], pharmaceuticals [44], many amorphous polymers [45], several small molecular van der Waals glass-formers [46,47], metallic glass [48], carbohydrates [49], and proteins [50,51]. In some cases, T gβ was determined directly by calorimetry, positronium annihilation lifetime spectroscopy (PALS).…”

Section: Caged Dynamics Senses the Primary (α) And The Secondary (Jgxmentioning

confidence: 99%

Absolutely necessary to consider the caged dynamics and the JGX β-relaxation in solving the glass transition problem

Ngai¹,

Capaccioli²,

Wang³

2019

Condens. Matter Phys.

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The 2003 seminal paper entitled "Is the Fragility of a Liquid Embedded in the Properties of Its Glass?" by Tullio Scopigno, Giancarlo Ruocco, Francesco Sette, and Giulio Monaco, reported that the properties of the structural α-relaxation of glass-formers are already present in the faster caged dynamics. Their important discovery has far-reaching implication of the processes faster than the structural α-relaxation that cannot be ignored in solving the glass transition problem. Since then, experiments and simulations performed on many glass-formers with diverse chemical and physical structures have found strong connections of the α-relaxation with not only the caged dynamics but also with the secondary relaxation of the special kind, called the JGX β-relaxation. The general results indicate that these fast processes are inseparable from the α-relaxation, and any attempt to solve the glass transition problem should take account of this fact. Examples of the connections are given in this paper to elucidate the developments and advances made since the inspiring publication of Scopigno et al.

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“…On the contrary, above~180 K protein internal dynamics is characterized by strong non-harmonic contributions, which are believed to be functionally important, since they provide the flexibility necessary for any function [1][2][3]. Given their importance, these additional motions have been widely investigated over the last 3 decades by a number of experimental techniques, such as Neutron Scattering [4][5][6][7], Mössbauer Spectroscopy [8], X-Rays and Neutron Crystallography [9,10] and many other spectroscopic methods [11][12][13]. These intense efforts allowed to highlight the relationship between the dynamical properties of proteins and their thermodynamic complexity, which can be well described in terms of a multiminima energy landscape (for a deeper discussion see e.g.…”

Section: Introductionmentioning

confidence: 99%