Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

Berlin, Yu. A.; Burin, Alexander L.; Friedrich, J.; Köhler, Jürgen

doi:10.1016/j.plrev.2006.09.001

Cited by 37 publications

(70 citation statements)

References 103 publications

(139 reference statements)

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“…Spectral hole burning has been widely used to probe energy landscapes and low-temperature dynamics in various glasses, polymers and proteins [1][2][3] . Information on energy landscapes can be obtained from observing the burning process (HGK, hole growth kinetics), the recovery of the spectral hole and its broadening at fixed temperature as well as recovery and broadening upon thermocycling 2,[4][5][6][7] .…”

Section: Introductionmentioning

confidence: 99%

Probing Energy Landscapes of Cytochrome b₆f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent

et al. 2017

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In non-photochemical spectral hole burning (NPHB) and spectral hole recovery experiments, cytochrome bf protein exhibits behavior that is almost independent of the deuteration of the buffer/glycerol glassy matrix containing the protein, apart from some differences in heat dissipation. On the other hand, strong dependence of the hole burning properties on sample preparation procedures was observed and attributed to a large increase of the electron-phonon coupling and shortening of the excited-state lifetime occurring when n-dodecyl β-d-maltoside (DM) is used as a detergent instead of n-octyl β-d-glucopyranoside (OGP). The data was analyzed assuming that the tunneling parameter distribution or barrier distribution probed by NPHB and encoded into the spectral holes contains contributions from two nonidentical components with accidentally degenerate excited state λ-distributions. Both components likely reflect protein dynamics, although with some small probability one of them (with larger md) may still represent the dynamics involving specifically the -OH groups of the water/glycerol solvent. Single proton tunneling in the water/glycerol solvent environment or in the protein can be safely excluded as the origin of observed NPHB and hole recovery dynamics. The intensity dependence of the hole growth kinetics in deuterated samples likely reflects differences in heat dissipation between protonated and deuterated samples. These differences are most probably due to the higher interface thermal resistivity between (still protonated) protein and deuterated water/glycerol outside environment.

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Section: Introductionmentioning

confidence: 99%

Probing Energy Landscapes of Cytochrome b₆f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent

et al. 2017

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“…3 Transitions between the wells of the lower tier of the energy landscape (fine structures are the bottoms of the deep wells) contribute mostly to the width of the spectral hole or spectral line. 5 Before being resonantly excited with a photon with energy ΔE 1 , the pigment−protein system is assumed to be in state 1. As the barriers in the excited electronic state (red) are lower than in the ground state (blue), the system is more likely to experience a conformational change while the pigment is in the excited state and end up in state 2, characterized by different transition energy ΔE 2 .…”

Section: Introductionmentioning

confidence: 99%

Conformational Changes in Pigment–Protein Complexes at Low Temperatures—Spectral Memory and a Possibility of Cooperative Effects

et al. 2015

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We employed nonphotochemical hole burning (NPHB) and fluorescence line narrowing (FLN) spectroscopies to explore protein energy landscapes and energy transfer processes in dimeric Cytochrome b6f, containing one chlorophyll molecule per protein monomer. The parameters of the energy landscape barrier distributions quantitatively agree with those reported for other pigment-protein complexes involved in photosynthesis. Qualitatively, the distributions of barriers between protein substates involved in the light-induced conformational changes (i.e., -NPHB) are close to glass-like ∼1/√V (V is the barrier height) and not to Gaussian. There is a high degree of correlation between the heights of the barriers in the ground and excited states in individual pigment-protein systems, as well as nearly perfect spectral memory. Both NPHB and hole recovery are due to phonon-assisted tunneling associated with the increase of the energy of a scattered phonon. As the latter is unlikely for simultaneously both the hole burning and the hole recovery, proteins must exhibit a NPHB mechanism involving diffusion of the free volume toward the pigment. Entities involved in the light-induced conformational changes are characterized by md(2) value of about 1.0 × 10(-46) kg·m(2). Thus, these entities are protons or, alternatively, small groups of atoms experiencing sub-Å shifts. However, explaining all spectral hole burning and recovery data simultaneously, employing just one barrier distribution, requires a drastic decrease in the attempt frequency to about 100 MHz. This decrease may occur due to cooperative effects. Evidence is presented for excitation energy transfer between the chlorophyll molecules of the adjacent monomers. The magnitude of the dipole-dipole coupling deduced from the Δ-FLN spectra is in good agreement with the structural data, indicating that the explored protein was intact.

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“…Since the energies of the electronic energy levels of a chromophore are very sensitive to its interactions with the local surroundings, conformational fluctuations of the protein lead to changes in the chromophore-protein interactions that show up as spectral fluctuations (spectral diffusion) of the probe molecule. Therefore, optical spectroscopy provides a versatile tool with which to monitor the microscopic structure and relaxation dynamics of a protein via the spectral diffusion of the probe molecule 8,[10][11][12][13] . However, as a consequence of the conformational heterogeneity, protein ensembles exist in a broad variety of structures, which manifests itself as a dramatic increase in dynamic heterogeneity reflecting the distribution of the associated barriers that separate the various structures.…”

Section: Introductionmentioning

confidence: 99%

Conformational Memory of a Protein Revealed by Single-Molecule Spectroscopy

et al. 2015

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Proteins are supramolecular machines that carry out a wide range of different functions, many of which require flexibility. Up until now spontaneous conformational fluctuations of proteins have always been assumed to reflect a stochastic random process. However, if changing between different conformational states was random, then it would be difficult to understand how conformational control of protein function could have evolved. Here we demonstrate that a single protein can show conformational memory. This is exactly the process that can facilitate the evolution of control of switching between two conformational states that can then be used to regulate protein function.

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Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

Cited by 37 publications

References 103 publications

Probing Energy Landscapes of Cytochrome b₆f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent

Probing Energy Landscapes of Cytochrome b₆f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent

Conformational Changes in Pigment–Protein Complexes at Low Temperatures—Spectral Memory and a Possibility of Cooperative Effects

Conformational Memory of a Protein Revealed by Single-Molecule Spectroscopy

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Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles

Cited by 37 publications

References 103 publications

Probing Energy Landscapes of Cytochrome b6f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent

Probing Energy Landscapes of Cytochrome b6f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent

Conformational Changes in Pigment–Protein Complexes at Low Temperatures—Spectral Memory and a Possibility of Cooperative Effects

Conformational Memory of a Protein Revealed by Single-Molecule Spectroscopy

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Probing Energy Landscapes of Cytochrome b₆f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent

Probing Energy Landscapes of Cytochrome b₆f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent