Labeling Proteins via Hole Burning of Their Aromatic Amino Acids: Pressure Tuning Spectroscopy of BPTI

Stübner, Markus; Hecht, C.; Friedrich, J.

doi:10.1016/s0006-3495(02)75355-1

Cited by 12 publications

(10 citation statements)

References 37 publications

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“…However, in densely packed systems like proteins or organic solids, the respective temperature dependence seems to be only marginal. As far as proteins are concerned, this seems to be true at least in a water/glycerol solvent, as is reflected in many experiments where data can be compared (14,(18)(19)(20). The question is whether this apparent insensitivity of the compressibility against temperature variations has its origin in some systematic errors of the experimental procedures or in specific structural features of proteins.…”

Section: Approximations Involvedmentioning

confidence: 99%

“…These findings render a great deal of confidence to the respective numbers as determined from optical experiments and open new perspectives. For instance, instead of chromophores as local probes, aromatic amino acids, e.g., tyrosine, can be used (20). If the protein contains several tyrosines, it is possible to measure local compressibilities in various regions of the protein.…”

Section: Summarizing Conclusionmentioning

confidence: 99%

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Local Compressibilities of Proteins: Comparison of Optical Experiments and Simulations for Horse Heart Cytochrome-c

Scharnagl

Reif

Friedrich

2005

Biophysical Journal

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Spectroscopy with probe molecules yields local information on the environment of the probe. In this article we compare local compressibilities of cytochrome-c as obtained from molecular dynamics simulations with experimental results as obtained from spectroscopic measurements. The simulations show that the protein-core around the heme is much less compressible in a glycerol/water solvent than in pure water. The pocket is also much less compressible than the protein as a whole, although the compressibility of the water inside the rather incompressible protein-core is almost liquidlike. We show that the local compressibility values capture the collective correlations of local volume fluctuations with volume fluctuations in the surrounding protein-solvent system. The decoupling of the volume fluctuations of the core from the solvent shell explains the reduction of the heme-core-compressibility in glycerol/water solvent. This decoupling could be traced back to the suppression of the exchange between pocket-water and hydration-shell-water upon addition of glycerol as co-solvent.

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Section: Approximations Involvedmentioning

confidence: 99%

Section: Summarizing Conclusionmentioning

confidence: 99%

Local Compressibilities of Proteins: Comparison of Optical Experiments and Simulations for Horse Heart Cytochrome-c

Scharnagl

Reif

Friedrich

2005

Biophysical Journal

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“…[18][19][20] If hole burning experiments are carried out at many frequencies within the inhomogeneous band, the frequency shift of the hole per pressure p / ⌬p depends in a linear fashion on the burn frequency , as has been predicted theoretically 21 and experimentally verified in numerous papers, 1,2 The "chromophore" can be a dye molecule, for instance, Zn-mesoporphyrin as in the present case, but it could as well be an intrinsic aromatic amino acid, e.g., tyrosine, which was shown to be an efficient hole burning probe.…”

Section: General Aspectsmentioning

confidence: 99%

Experiments with proteins at low temperature: What do we learn on properties in their functional state?

Ponkratov

Wiedersich

Friedrich

et al. 2007

The Journal of Chemical Physics

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The authors compared the spectral response of Zn-substituted horseradish peroxidase in a glycerol/water solvent to hydrostatic pressure at 2 K and ambient temperature. The low temperature experiments clearly demonstrate the presence of at least three different conformations with drastically different elastic properties. However, the main conformation, which determines the fluorescence spectrum at ambient temperature, did not show any significant difference between low and high temperature and pressure. The authors conclude that the local compressibility of the heme pocket of the protein depends only very weakly on temperature.

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“…Based on the pressure-shift data, pure thermal shifts could be uncovered, and their frequency dependence compared with the predictions of the model. The available pressure shifts of narrow holes in the protein spectra (15)(16)(17) are reconsidered from the point of view of realistic interaction potentials that include repulsive, dispersive, and electrostatic forces. A comparison of the properties of the holes and the broadband spectra is carried out in the last section.…”

Section: Introductionmentioning

confidence: 99%

Pigment Spectra and Intermolecular Interaction Potentials in Glasses and Proteins

Renge

Grondelle

Dekker

2007

Biophysical Journal

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A model is proposed for chromophore optical spectra in solids over a wide range of temperatures and pressures. Inhomogeneous band shapes and their pressure dependence, as well as baric shift coefficients of spectral lines, selected by the frequency, were derived using Lennard-Jones potentials of the ground and excited states. Quadratic electron-phonon coupling constants, describing the thermal shift and broadening of zero-phonon lines, were also calculated. Experimentally, thermal shift and broadening of spectral holes were studied between 5 and 40 K for a synthetic pigment, chlorin, embedded in polymer hosts. The baric effects on holes were determined by applying hydrostatic He gas pressure up to 200 bar, at 6 K. Absorption spectra of pheophytin a, chlorophyll a, and beta-carotene in polymers and plant photosystem II CP47 complex were measured between 5 (or 77) and 300 K, and subject to Voigtian deconvolution. A narrowing of inhomogeneous bandwidth with increasing temperature, predicted on the basis of hole behavior, was observed as the shrinking of Gaussian spectral component. The Lorentzian broadening was ascribed to optical dephasing up to 300 K in transitions with weak to moderate linear electron-phonon coupling strength. The thermal broadening is purely Gaussian in multiphonon transitions (S(2) band of beta-carotene, Soret bands of tetrapyrrolic pigments), and the Lorentz process appears to be suppressed, indicating a lack of exponential dephasing. Density, polarity, polarizability, compressibility, and other local parameters of the pigment binding sites in biologically relevant systems can be deduced from spectroscopic data, provided that sufficient background information is available.

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Labeling Proteins via Hole Burning of Their Aromatic Amino Acids: Pressure Tuning Spectroscopy of BPTI

Cited by 12 publications

References 37 publications

Local Compressibilities of Proteins: Comparison of Optical Experiments and Simulations for Horse Heart Cytochrome-c

Local Compressibilities of Proteins: Comparison of Optical Experiments and Simulations for Horse Heart Cytochrome-c

Experiments with proteins at low temperature: What do we learn on properties in their functional state?

Pigment Spectra and Intermolecular Interaction Potentials in Glasses and Proteins

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