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Wagie HE, Geissinger P. Hole-burning spectroscopy as a probe of nano-environments and processes in biomolecules: a review. APPLIED SPECTROSCOPY 2012; 66:609-627. [PMID: 22732531 DOI: 10.1366/12-06655] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Hole-burning spectroscopy, a high-resolution spectroscopic technique, allows details of heterogeneous nano-environments in biological systems to be obtained from broad absorption bands. Recently, this technique has been applied to proteins, nucleic acids, cells, and substructures of water to probe the electrostatic conditions created by macromolecules and the surrounding solvent. Starting with the factors that obscure the homogeneous linewidth of a chromophore within an inhomogeneously broadened absorption or emission band, we describe properties and processes in biological systems that are reflected in the measured hole spectra. The technique also lends itself to the resolution of perturbation experiments, such as temperature cycling to elucidate energy landscape barriers, applied external electric fields (Stark effect) to measure net internal electric fields, and applied hydrostatic pressure to find the volume compressibility of proteins.
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Ormos P. Dynamic fluctuation of proteins watched in real time. HFSP JOURNAL 2008; 2:297-301. [PMID: 19436491 DOI: 10.2976/1.2978985] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Indexed: 11/19/2022]
Abstract
The dynamic nature of protein function is a fundamental concept in the physics of proteins. Although the basic general ideas are well accepted most experimental evidence has an indirect nature. The detailed characterization of the dynamics is necessary for the understanding in detail. The dynamic fluctuations thought crucial for the function span an extremely broad time, starting from the picosecond regime. Recently, a few new experimental techniques emerged that permit the observation of dynamical phenomena directly. Notably, pulsed infrared (IR) spectroscopy has been applied with great success to observe structural changes with picosecond time resolution. Using two-dimensional-IR vibrational echo chemical exchange spectroscopy Ishikawa and co-workers [Ishikawa et al. (2008), Proc. Natl. Acad. Sci. U.S.A. 101, 14402-14407] managed to observe the transition between well defined conformational substrates of carbonmonoxy myoglobin directly. This is an important step in improving our insight into the details of protein function.
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Affiliation(s)
- Pál Ormos
- Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt 62. H-6726 Szeged, Hungary
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Abstract
Fluorescence line-narrowing (FLN) spectroscopy at 10 K was used to study the effect of high pressure through the prosthetic group in horseradish peroxidase (HRP), which was Mg-mesoporphyrin (MgMP) replacing the heme of the enzyme. The same measurement was performed on MgMP in a solid-state amorphous organic matrix, dimethyl sulfoxide (DMSO). Series of FLN spectra were registered to determine the (0, 0) band shape through the inhomogeneous distribution function (IDF). In the range of 0-2 GPa a red-shift of the IDF was determined, and yielded the isothermal compressibility of MgMP-HRP as 0.066 GPa(-1), which is significantly smaller than that found earlier as 0.106 GPa(-1) by fine-tuning the pressure in the range up to 1.1 MPa. The vibrational frequencies also shifted with pressure increase, as expected. The compressibility in the DMSO matrix was smaller, 0.042 GPa(-1), both when the pressure was applied at room temperature before cooling to 10 K, or at 10 K. At 200 K or above, the bimodal (0, 0) band shape in DMSO showed a population conversion under pressure that was not observed at or below 150 K. A significant atomic rearrangement was estimated from the volume change, 3.3 +/- 0.7 cm(3)/mol upon conversion. The compressibility in proteins and in amorphous solids seems not to significantly depend on the temperature and in the protein it decreases toward higher pressures.
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Affiliation(s)
- László Smeller
- Institute of Biophysics and Radiation Biology, Semmelweis University, Budapest H-1444, Hungary.
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Tautomerism involving other than five-and six-membered rings. ADVANCES IN HETEROCYCLIC CHEMISTRY 2000. [DOI: 10.1016/s0065-2725(00)77003-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
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Köhler M, Friedrich J, Fidy J. Proteins in electric fields and pressure fields: basic aspects. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1386:255-88. [PMID: 9733978 DOI: 10.1016/s0167-4838(98)00098-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
This paper emphasizes the basic aspects of the interactions of chromoproteins at low temperatures with external pressure fields and electric fields. We discuss how the respective spectral properties can be modified and what we can learn from the spectral changes about the thermodynamic, electrostatic, functional and structural properties of proteins. A few examples are discussed in more detail.
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Affiliation(s)
- M Köhler
- Lehrstuhl für Physik Weihenstephan, Technische Universität München, Freising, Germany
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Fidy J, Balog E, Köhler M. Proteins in electric fields and pressure fields: experimental results. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1386:289-303. [PMID: 9733987 DOI: 10.1016/s0167-4838(98)00099-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Experimental results obtained by Stark effect and pressure tuning optical spectroscopy are discussed with the emphasis on studies aimed at unraveling the coupling of prosthetic groups to proteins. A comparative, detailed analysis is given concerning the coupling of the heme group to the apoprotein in various heme proteins based on spectral hole burning data. Electrochromism and electric dichroism experiments related to the coupling problem are also discussed in the context of other protein systems.
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Affiliation(s)
- J Fidy
- Institute of Biophysics, Semmelweis University of Medicine, Budapest, Hungary.
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Herenyi L, Suisalu A, Mauring K, Kis-Petik K, Fidy J, Kikas J. Variety in the Coupling of Mesoporphyrin IX to Apohorseradish Peroxidase C Studied by Energy Selected Fluorescence Excitation and Vibronic Hole Burning Spectroscopy. J Phys Chem B 1998. [DOI: 10.1021/jp981176e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Levente Herenyi
- Institute of Biophysics, Semmelweis Medical University, P.O. Box 263, H1444 Budapest, Hungary, Institute of Physics, Riia 142, EE2400 Tartu, Estonia, and Department of Physics, University of Tartu, Tahe 4, EE2400 Tartu, Estonia
| | - Artur Suisalu
- Institute of Biophysics, Semmelweis Medical University, P.O. Box 263, H1444 Budapest, Hungary, Institute of Physics, Riia 142, EE2400 Tartu, Estonia, and Department of Physics, University of Tartu, Tahe 4, EE2400 Tartu, Estonia
| | - Koit Mauring
- Institute of Biophysics, Semmelweis Medical University, P.O. Box 263, H1444 Budapest, Hungary, Institute of Physics, Riia 142, EE2400 Tartu, Estonia, and Department of Physics, University of Tartu, Tahe 4, EE2400 Tartu, Estonia
| | - Katalin Kis-Petik
- Institute of Biophysics, Semmelweis Medical University, P.O. Box 263, H1444 Budapest, Hungary, Institute of Physics, Riia 142, EE2400 Tartu, Estonia, and Department of Physics, University of Tartu, Tahe 4, EE2400 Tartu, Estonia
| | - Judit Fidy
- Institute of Biophysics, Semmelweis Medical University, P.O. Box 263, H1444 Budapest, Hungary, Institute of Physics, Riia 142, EE2400 Tartu, Estonia, and Department of Physics, University of Tartu, Tahe 4, EE2400 Tartu, Estonia
| | - Jaak Kikas
- Institute of Biophysics, Semmelweis Medical University, P.O. Box 263, H1444 Budapest, Hungary, Institute of Physics, Riia 142, EE2400 Tartu, Estonia, and Department of Physics, University of Tartu, Tahe 4, EE2400 Tartu, Estonia
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Vanderkooi JM, Angiolillo PJ, Laberge M. Fluorescence line narrowing spectroscopy: a tool for studying proteins. Methods Enzymol 1997; 278:71-94. [PMID: 9170310 DOI: 10.1016/s0076-6879(97)78007-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Perhaps the most important contribution of FLN is that it provides an experimental approach to relate physical changes in the protein to predicted dynamical behavior. It is clear that the sample is inhomogeneously broadened in a continuous manner, consistent with the damped motion of proteins. At the same time configurational substates can be selected, suggesting that there is indeed a hierarchy of protein motion and structure. As yet, identification of the structure, and relating it to the spectra, has not been achieved. It is clear that the electric field exerted by neighboring atoms shifts the electronic transition, and the inhomogeneity is greater when the surrounding disorder is greater. The inhomogeneity for the chromophore in the protein is dependent on the protein conformation and is intermediate between that of a crystal and a glass. The phonon coupling also depends on the chromophore and the protein. Fluorescence line narrowing provides in addition ground- and excited-state vibrational frequencies, thereby allowing for structural differences between the excited-state and the ground-state molecule to be detected.
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Affiliation(s)
- J M Vanderkooi
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia 19104, USA
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Köhler M, Gafert J, Friedrich J, Falk H, Meyer J. Hole-Burning Spectroscopy of Proteins in External Fields: Human Serum Albumin Complexed with the Hypericinate Ion. ACTA ACUST UNITED AC 1996. [DOI: 10.1021/jp9531016] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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