The “Protein Dynamical Transition” Does Not Require the Protein Polypeptide Chain

Schirò, Giorgio; Caronna, Chiara; Natali, Francesca; Koza, Michael Marek; Cupane, Antonio

doi:10.1021/jz200797g

Cited by 45 publications

(44 citation statements)

References 36 publications

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“…The Mean Square Displacements (MSDs) of the hydrogen atoms and the density of states resulted those of a harmonic solid, while in D 2O-hydrated myoglobin (Mb) a dynamical transition to a non-harmonic behavior was present at ~180 K [103][104][105][106], dependent on the hydration level. Therefore, it was suggested that, in the whole temperature range investigated, the trehalose matrix entraps myoglobin in a harmonic well.…”

Section: Atomistic Levelmentioning

confidence: 99%

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

Cordone¹,

Cupane²,

Emanuele

et al. 2015

COC

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Immobilization of proteins and other biomolecules in saccharide matrices leads to a series of peculiar properties that are relevant from the point of view of both biochemistry and biophysics, and have important implications on related fields such as food industry, pharmaceutics, and medicine. In the last years, the properties of biomolecules embedded into glassy matrices and/or highly concentrated solutions of saccharides have been thoroughly investigated, at the molecular level, through in vivo, in vitro, and in silico studies. These systems show an outstanding ability to protect biostructures against stress conditions; various mechanisms appear to be at the basis of such bioprotection, that in the case of some sugars (in particular trehalose) is peculiarly effective.Here we review recent results obtained in our and other laboratories on ternary protein-sugar-water systems that have been typically studied in wide ranges of water content and temperature. Data from a large set of complementary experimental techniques provide a consistent description of structural, dynamical and functional properties of these systems, from atomistic to thermodynamic level.In the emerging picture, the stabilizing effect induced on the encapsulated systems might be attributed to a strong biomolecule-matrix coupling, mediated by extended hydrogen-bond networks, whose specific properties are determined by the saccharide composition and structure, and depend on water content.

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Section: Atomistic Levelmentioning

confidence: 99%

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

Cordone¹,

Cupane²,

Emanuele

et al. 2015

COC

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“…Experimental studies show that the protein hydration water plays a key role in many aspects of protein behavior, which include the mean square displacement of the protein constituent atoms [2][3][4], the subpicosecond collective vibrations [5][6][7][8], the intraprotein α and β fluctuations [9,10], and the protein enzymatic activity [11]. Thus the study of the protein hydration water is crucial for the understanding of protein dynamics.…”

Section: Introductionmentioning

confidence: 99%

Hydration-dependent dynamic crossover phenomenon in protein hydration water

Wang

Fratini

et al. 2014

Phys. Rev. E

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The characteristic relaxation time τ of protein hydration water exhibits a strong hydration level h dependence. The dynamic crossover is observed when h is higher than the monolayer hydration level h c = 0.2-0.25 and becomes more visible as h increases. When h is lower than h c , τ only exhibits Arrhenius behavior in the measured temperature range. The activation energy of the Arrhenius behavior is insensitive to h, indicating a local-like motion. Moreover, the h dependence of the crossover temperature shows that the protein dynamic transition is not directly or solely induced by the dynamic crossover in the hydration water.

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“…What is the physical mechanism responsible for the water driven effect giving rise to the PDT? A clue is obtained from the fact that the same PDT onset temperature of $220 K is observed for chemically and structurally different hydrated peptide systems like native and denaturated proteins, HP (even for poly-G that accounts for the ''pure backbone'' contribution), amyloid fibrils [24] and amino acid mixtures lacking the polypeptide chain [25]. This implies that the ÁG and ÁG Ã values, that set the PDT onset temperature in these systems, are determined by hydration water.…”

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confidence: 99%

Physical Origin of Anharmonic Dynamics in Proteins: New Insights From Resolution-Dependent Neutron Scattering on Homomeric Polypeptides

2012

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Neutron scattering reveals a complex dynamics in polypeptide chains, with two main onsets of anharmonicity whose physical origin and biological role are still debated. In this study the dynamics of strategically selected homomeric polypeptides is investigated with elastic neutron scattering using different energy resolutions and compared with that of a real protein. Our data spotlight the dependence of anharmonic transition temperatures and fluctuation amplitudes on energy resolution, which we quantitatively explain in terms of a two-site model for the protein-hydration water energy landscape. Experimental data strongly suggest that the protein dynamical transition is not a mere resolution effect but is due to a real physical effect. Activation barriers and free energy values obtained for the protein dynamical transition allow us to make a connection with the two-well interaction potential of supercooledconfined water proposed to explain a low-density ! high-density liquid-liquid transition. DOI: 10.1103/PhysRevLett.109.128102 PACS numbers: 87.14.ef, 83.85.Hf, 87.15.HÀ Neutron scattering is a powerful technique to study protein dynamics and energetics. The structure factor SðE ¼ 0; Q; TÞ of elastic incoherent neutron scattering (EINS) is related to the time-position self correlation function of protein-solvent nuclei that, in turn, is related to the energy landscape of the system whose different tiers can be explored by the temperature dependence of the EINS signal. In particular, EINS on D 2 O-hydrated protein powders, which probes the mean square displacements (MSDs) of protein nonexchangeable H atoms, reveals two deviations from harmonic dynamics, at $100-150 K and at $220 K [1,2]. Molecular origin, physical nature and biological relevance of these ''transitions'' are still matter of discussion. The first one is attributed mainly to thermally activated motions of CH 3 methyl groups [1,[3][4][5][6] (for this reason hereon called methyl groups activation, MGA). The second one, called ''protein dynamical transition'' (PDT), has been first interpreted as a glasslike transition [2] directly correlated to the onset of biological activity [7], but this view has been later challenged. Several interpretations of the PDT have been proposed: (i) a change in the protein structural flexibility in response to the glass transition of hydration water [8]; (ii) a result of the protein structural relaxation reaching the limit of the experimental frequency window [9][10][11]; (iii) the protein response to a fragile-to-strong dynamic crossover in the hydration water at 220 K where water structure makes a low density liquid ðLDLÞ ! high density liquid (HDL) transition [12]; (iv) a change in the thermodynamic resilience of the waterprotein system [13]. These models propose physical pictures partially alternative, demonstrating that the question has not been definitively settled yet: (i) and (ii) ascribe the PDT to a temperature dependent relaxation time crossing the instrumental time-scale; (iii) and (iv) interpret the PDT as ...

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The “Protein Dynamical Transition” Does Not Require the Protein Polypeptide Chain

Cited by 45 publications

References 36 publications

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

Proteins in Saccharides Matrices and the Trehalose Peculiarity: Biochemical and Biophysical Properties

Hydration-dependent dynamic crossover phenomenon in protein hydration water

Physical Origin of Anharmonic Dynamics in Proteins: New Insights From Resolution-Dependent Neutron Scattering on Homomeric Polypeptides

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