Cytochrome c in a Dry Trehalose Matrix: Structural and Dynamical Effects Probed by X-Ray Absorption Spectroscopy

Giachini, Lisa; Francia, Francesco; Cordone, Lorenzo; Boscherini, Federico; Venturoli, Giovanni

doi:10.1529/biophysj.106.092338

Cited by 18 publications

(39 citation statements)

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“…Furthermore, along each simulated trajectory, the sugar molecules are found mainly bonding the carboxylate oxygen atoms of glutamate and aspartate residues as well as the peptide oxygen atoms, in agreement with IR data on trehalose-protein systems [8]. XAFS studies of cytochrome c in trehalose glasses at different content of residual water [52] pointed out a reduction of the mean square displacements of the central iron atom with respect to the first coordination shell and a distortion of the porphirin group. The authors suggested that the matrix induces conformational changes in the protein, which in turn result in structural distortions of heme group at the local atomic scale.…”

Section: Molecular Dynamicssupporting

confidence: 81%

Proteins in amorphous saccharide matrices: Structural and dynamical insights on bioprotection

et al. 2013

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Abstract. Bioprotection by sugars, and in particular trehalose peculiarity, is a relevant topic due to the implications in several fields. The underlying mechanisms are not yet clearly elucidated, and remain the focus of current investigations. Here we revisit data obtained at our lab on binary sugar/water and ternary protein/sugar/water systems, in wide ranges of water content and temperature, in the light of the current literature. The data here discussed come from complementary techniques (Infrared Spectroscopy, Molecular Dynamics simulations, Small Angle X-ray Scattering and Calorimetry), which provided a consistent description of the bioprotection by sugars from the atomistic to the macroscopic level. We present a picture, which suggests that protein bioprotection can be explained in terms of a strong coupling of the biomolecule surface to the matrix via extended hydrogen-bond networks, whose properties are defined by all components of the systems, and are strongly dependent on water content. Furthermore, the data show how carbohydrates having similar hydrogen-bonding capabilities exhibit different efficiency in preserving biostructures.

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Section: Molecular Dynamicssupporting

confidence: 81%

Proteins in amorphous saccharide matrices: Structural and dynamical insights on bioprotection

et al. 2013

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“…From this similarity, it has been inferred that, in dehydrated trehalose matrices, the thermal fluctuations between conformational substates, as well as relaxation from the dark-adapted to the lightadapted state are strongly reduced even at RT over the time scale of charge recombination. This interpretation is supported by a large body of spectroscopic studies [19,22,53,54], as well as molecular dynamics simulations [55], mainly performed on myoglobin (Mb), indicating a strong hindrance of the internal dynamics when the protein is incorporated into a dehydrated trehalose glass. Besides affecting reversibly the kinetics of P Áþ 865 Q ÁÀ A recombination, progressive drying of the RC/trehalose sample also leads to the arrest of Q ÁÀ A -to-Q B electron transfer in a progressively increasing fraction of the RC population [56], again mimicking at RT an effect observed in RCs frozen in the dark in water-glycerol mixtures [48].…”

Section: Conformational Substates and Dynamicsmentioning

confidence: 85%

The Magic of Disaccharide Glass Matrices for Protein Function as Decoded by High-Field EPR and FTIR Spectroscopy

et al. 2015

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The structural and dynamical interaction of proteins with their microenvironment in disordered matrices plays a decisive role for their function; EPR spectroscopy is a powerful tool for shading light onto the molecular mechanisms of this protein-matrix interplay. To clarify the molecular mechanisms of disaccharide bioprotection, we studied the structure and dynamics of spin-labeled systems and photosynthetic reaction centers (RCs) in sucrose and trehalose matrices at different hydration levels by means of cw and pulse high-field 95 GHz (W-band) EPR as well as by FTIR. In this minireview, we summarize and discuss EPR and FTIR experiments showing that the anhydrobiotic state of the RC-trehalose system (1) is not the result of matrix-induced changes of the local structure of the charge-separated radical-pair cofactors, P Áþ 865 and Q ÁÀ A , and (2) is not the result of changes of local dynamics and local hydrogen bonding of Q A in its binding pocket. Rather, the extreme impairment of RC dynamics caused by incorporation into the dehydrated trehalose matrix, which also protects it against thermal denaturation, originates in the high rigidity, already at room temperature, of the dry trehalose glass matrix coating the RC protein surface. This surface hydrogen-bonding scaffold shifts the correlation time of thermal conformational fluctuations into the non-biological time domain. Another intriguing aspect of disaccharide bioprotection is the superior The authors dedicate this work to Giovanni Giacometti on the occasion of his 85th birthday. AppliedMagnetic Resonance efficiency of trehalose versus sucrose matrices in stabilizing the anhydrobiotic state of proteins. To clarify the molecular basis of this specificity, glassy trehalose-water and sucrose-water binary systems, incorporating a nitroxide radical as spin probe, have been studied by high-field W-band EPR spectroscopy at different water contents. Analysis of the EPR spectra revealed a different structural and dynamical organization in the sucrose and trehalose matrix, only the trehalose being homogeneous in terms of residual water and nitroxide distribution.

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“…The distortion of the C heme atoms located in the fourth shell from iron, as probed by XAFS measurements, could be then attributed to protein-matrix interactions extending from the surface down to the protein interior, to a significant length scale [167].…”

Section: T F O R D I S T R I B U T I O Nmentioning

confidence: 99%

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

Cordone¹,

Cupane²,

Emanuele

et al. 2015

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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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Cytochrome c in a Dry Trehalose Matrix: Structural and Dynamical Effects Probed by X-Ray Absorption Spectroscopy

Cited by 18 publications

References 50 publications

Proteins in amorphous saccharide matrices: Structural and dynamical insights on bioprotection

Proteins in amorphous saccharide matrices: Structural and dynamical insights on bioprotection

The Magic of Disaccharide Glass Matrices for Protein Function as Decoded by High-Field EPR and FTIR Spectroscopy

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

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