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Kim CW, Park JW, Rhee YM. Effect of Chromophore Potential Model on the Description of Exciton-Phonon Interactions. J Phys Chem Lett 2015; 6:2875-2880. [PMID: 26267173 DOI: 10.1021/acs.jpclett.5b01141] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
System-bath interactions in nonadiabatic simulations are often depicted by first performing molecular dynamics calculations and then by evaluating excitation energies at the trajectory snapshots. Usually, molecular mechanics models and quantum chemical calculations are used in a mixed manner toward a trade-off between efficiency and accuracy. Here we investigate how this mixing scheme affects that depiction by using various potential energy surfaces (PESs) of coumarin-153 chromophore, with the help of interpolated PESs that can closely match the accuracies of quantum chemical calculations. We find that although spectral densities are computed only with second stage data the PES characteristics during the first sampling stage can still prevail in the densities, with limited influences on related reorganization energies. Our results suggest that using the mixed scheme can be acceptable when dynamics is mainly governed by the integrated effect of all phonon modes, but care must be taken for understanding detailed effects from individual modes.
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Affiliation(s)
- Chang Woo Kim
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
| | - Jae Woo Park
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
| | - Young Min Rhee
- Center for Self-Assembly and Complexity, Institute for Basic Science (IBS), Pohang 790-784, Korea
- Department of Chemistry, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
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2
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Rad AM, Moosavi-Movahedi AA, Ghourchian H, Safari N, Hong J, Moosavi-Movahedi Z, Nazari K, Saboury AA, Jamaat PR. Effects of substituted metal-free porphyrins in apo-horseradish peroxidase. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424607000965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The peroxidase-like catalytic activities of some synthetic porphyrins following substitution in apo-horseradish peroxidase (apo-HRP) were studied by UV-vis and fluorescence spectrophotometries in buffer potassium phosphate solution at pH 7. The insertion of these synthetic porphyrins in apo-HRP is very difficult, due to steric hindrances between coordinated metals in porphyrins and the side-chains of amino acids in native protein. However, because of planar coordination following insertion in an active site of apo-HRP tetrapyridylporphyrin(TPyP), a metal-free porphyrin, adsorbs free metal ions from the environment and shows higher peroxidase-like catalytic activity than other new synthetic porphyrins. The results indicate that the metal-free porphyrins with optimum Reinheitzahl (RZ) show higher catalytic activity relative to others. The fluorescence emission of TPyP only, and of apo-HRP-TPyP, displayed significantly different wavelengths for the maximum aromatic fluorescence intensity. The λmaxfor apo-HRP-TPyP was around 447 nm, while for TPyP, alone, it increased to 463 nm, which showed that the aromatic groups' surroundings changed upon substitution of porphyrins in a low polar environment.
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Affiliation(s)
- A. Molaei Rad
- Institute of Biochemistry and Biophysics, University of Tehran, Enghelab Ave., Tehran, Iran
| | | | | | - Nasser Safari
- Department of Chemistry, Shahid Beheshti University, Evin, Tehran, Iran
| | - Jun Hong
- Institute of Biochemistry and Biophysics, University of Tehran, Enghelab Ave., Tehran, Iran
| | - Zinab Moosavi-Movahedi
- Institute of Biochemistry and Biophysics, University of Tehran, Enghelab Ave., Tehran, Iran
| | | | - A. Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Enghelab Ave., Tehran, Iran
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3
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Jankowiak R, Reppert M, Zazubovich V, Pieper J, Reinot T. Site Selective and Single Complex Laser-Based Spectroscopies: A Window on Excited State Electronic Structure, Excitation Energy Transfer, and Electron–Phonon Coupling of Selected Photosynthetic Complexes. Chem Rev 2011; 111:4546-98. [DOI: 10.1021/cr100234j] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Mike Reppert
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal H4B1R6 Quebec, Canada
| | - Jörg Pieper
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University of Berlin, Germany
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
| | - Tonu Reinot
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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4
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Reppert M, Naibo V, Jankowiak R. Accurate modeling of fluorescence line narrowing difference spectra: Direct measurement of the single-site fluorescence spectrum. J Chem Phys 2010; 133:014506. [DOI: 10.1063/1.3455890] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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5
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Müh F, Renger T, Zouni A. Crystal structure of cyanobacterial photosystem II at 3.0 A resolution: a closer look at the antenna system and the small membrane-intrinsic subunits. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2008; 46:238-64. [PMID: 18313317 DOI: 10.1016/j.plaphy.2008.01.003] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2007] [Indexed: 05/04/2023]
Abstract
Photosystem II (PSII) is a homodimeric protein-cofactor complex embedded in the thylakoid membrane that catalyses light-driven charge separation accompanied by the water splitting reaction during oxygenic photosynthesis. In the first part of this review, we describe the current state of the crystal structure at 3.0 A resolution of cyanobacterial PSII from Thermosynechococcus elongatus [B. Loll et al., Towards complete cofactor arrangement in the 3.0 A resolution structure of photosystem II, Nature 438 (2005) 1040-1044] with emphasis on the core antenna subunits CP43 and CP47 and the small membrane-intrinsic subunits. The second part describes first the general theory of optical spectra and excitation energy transfer and how the parameters of the theory can be obtained from the structural data. Next, structure-function relationships are discussed that were identified from stationary and time-resolved experiments and simulations of optical spectra and energy transfer processes.
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Affiliation(s)
- Frank Müh
- Institut für Chemie und Biochemie/Kristallographie, Freie Universität Berlin, Takustrasse 6, D-14195 Berlin, Germany
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6
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Fluorescence line-narrowing spectroscopy for probing purposes in bioanalytical and environmental chemistry. Trends Analyt Chem 2008. [DOI: 10.1016/j.trac.2008.01.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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7
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Berlin Y, Burin A, Friedrich J, Köhler J. Spectroscopy of proteins at low temperature. Part I: Experiments with molecular ensembles. Phys Life Rev 2006. [DOI: 10.1016/j.plrev.2006.09.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Kaposi AD, Vanderkooi JM, Stavrov SS. Infrared absorption study of the heme pocket dynamics of carbonmonoxyheme proteins. Biophys J 2006; 91:4191-200. [PMID: 16980362 PMCID: PMC1635657 DOI: 10.1529/biophysj.105.068254] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The temperature dependencies of the infrared absorption CO bands of carboxy complexes of horseradish peroxidase (HRP(CO)) in glycerol/water mixture at pH 6.0 and 9.3 are interpreted using the theory of optical absorption bandshape. The bands' anharmonic behavior is explained assuming that there is a higher-energy set of conformational substates (CSS(h)), which are populated upon heating and correspond to the protein substates with disordered water molecules in the heme pocket. Analysis of the second moments of the CO bands of the carboxy complexes of myoglobin (Mb(CO)) and hemoglobin (Hb(CO)), and of HRP(CO) with benzohydroxamic acid (HRP(CO)+BHA), shows that the low energy CSS(h) exists also in the open conformation of Mb(CO), where the heme pocket is spacious enough to accommodate a water molecule. In the HRP(CO)+BHA and closed conformations of Mb(CO) and Hb(CO), the heme pocket is packed with BHA and different amino acids, the CSS(h) has much higher energy and is hardly populated even at the highest temperatures. Therefore only motions of these amino acids contribute to the band broadening. These motions are linked to the protein surface and frozen in the glassy matrix, whereas in the liquid solvent they are harmonic. Thus the second moment of the CO band is temperature-independent in glass and is proportional to the temperature in liquid. The temperature dependence of the second moment of the CO peak of HRP(CO) in the trehalose glass exhibits linear coupling to an oscillator. This oscillator can be a moving water molecule locked in the heme pocket in the whole interval of temperatures or a trehalose molecule located in the heme pocket.
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Affiliation(s)
- Andras D Kaposi
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary
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9
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Vanderkooi JM, Dashnau JL, Zelent B. Temperature excursion infrared (TEIR) spectroscopy used to study hydrogen bonding between water and biomolecules. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2005; 1749:214-33. [PMID: 15927875 DOI: 10.1016/j.bbapap.2005.03.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 02/15/2005] [Accepted: 03/09/2005] [Indexed: 11/22/2022]
Abstract
Water is a highly polar molecule that is capable of making four H-bonding linkages. Stability and specificity of folding of water-soluble protein macromolecules are determined by the interplay between water and functional groups of the protein. Yet, under some conditions, water can be replaced with sugar or other polar protic molecules with retention of protein structure. Infrared (IR) spectroscopy allows one to probe groups on the protein that interact with solvent, whether the solvent is water, sugar or glycerol. The basis of the measurement is that IR spectral lines of functional groups involved in H-bonding show characteristic spectral shifts with temperature excursion, reflecting the dipolar nature of the group and its ability to H-bond. For groups involved in H-bonding to water, the stretching mode absorption bands shift to lower frequency, whereas bending mode absorption bands shift to higher frequency as temperature decreases. The results indicate increasing H-bonding and decreasing entropy occurring as a function of temperature, even at cryogenic temperatures. The frequencies of the amide group modes are temperature dependent, showing that as temperature decreases, the amide group H-bonds to water strengthen. These results are relevant to protein stability as a function of temperature. The influence of solvent relaxation is demonstrated for tryptophan fluorescence over the same temperature range where the solvent was examined by infrared spectroscopy.
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Affiliation(s)
- Jane M Vanderkooi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, 19104-6059, USA.
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10
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Zelent B, Kaposi AD, Nucci NV, Sharp KA, Dalosto SD, Wright WW, Vanderkooi JM. Water Channel of Horseradish Peroxidase Studied by the Charge-Transfer Absorption Band of Ferric Heme. J Phys Chem B 2004. [DOI: 10.1021/jp037664q] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- B. Zelent
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - A. D. Kaposi
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - N. V. Nucci
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - K. A. Sharp
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - S. D. Dalosto
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - W. W. Wright
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
| | - J. M. Vanderkooi
- Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, and Department of Biophysics and Radiation Biology, Semmelweis University of Medicine, H-1444 P.O.B. 263, Budapest, Hungary
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11
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Gun'ko VM, Klyueva AV, Levchuk YN, Leboda R. Photon correlation spectroscopy investigations of proteins. Adv Colloid Interface Sci 2003; 105:201-328. [PMID: 12969646 DOI: 10.1016/s0001-8686(03)00091-5] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Physical principles of photon correlation spectroscopy (PCS), mathematical treatment of the PCS data (converting autocorrelation functions to distribution functions or average characteristics), and PCS applications to study proteins and other biomacromolecules in aqueous media are described and analysed. The PCS investigations of conformational changes in protein molecules, their aggregation itself or in consequence of interaction with other molecules or organic (polymers) and inorganic (e.g. fumed silica) fine particles as well as the influence of low molecular compounds (surfactants, drugs, salts, metal ions, etc.) reveal unique capability of the PCS techniques for elucidation of important native functions of proteins and other biomacromolecules (DNA, RNA, etc.) or microorganisms (Escherichia coli, Pseudomonas putida, Dunaliella viridis, etc.). Special attention is paid to the interaction of proteins with fumed oxides and the impact of polymers and fine oxide particles on the motion of living flagellar microorganisms analysed by means of PCS.
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Affiliation(s)
- Vladimir M Gun'ko
- Institute of Surface Chemistry, 17 General Naumov Street, Kiev 03164, Ukraine.
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12
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Abstract
The pressure-temperature phase diagram of various biomolecules is reviewed. Special attention is focused on the elliptic phase diagram of proteins. The phenomenological thermodynamic theory describing this diagram explains the heat, cold and pressure denaturations in a unified picture. The limitations and possible developments of this theory are discussed as well. It is pointed out that a more complex diagram can be obtained when the intermolecular interactions are also taken into account. In this case metastable states appear on the pressure-temperature (p-T) diagram due to intermolecular interactions. Pressure-temperature phase diagrams of other biopolymers are also discussed. While the p-T diagrams of helix-coil transition of nucleic acids and of gel-liquid crystal transition of lipid bilayers are non-elliptical, those of gelatinization of starch and of phase separation of some synthetic polymers show an elliptic profile, similar to that of proteins. Finally, the p-T diagram of bacterial inactivation is shown to be elliptic. From the point of view of basic science, this fact shows that the key factor of inactivation should be the protein type, and from the viewpoint of practical applications, it serves as the theoretical basis of pressure treatment of biosystems.
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Affiliation(s)
- László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, Budapest, Hungary.
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13
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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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14
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Abstract
In 1970, three laboratories independently made a discovery that, for aromatic fluorophores embedded into different rigid and highly viscous media, the spectroscopic properties do not conform to classical rules. The fluorescence spectra can depend on excitation wavelength, and the excited-state energy transfer, if present, fails at the "red" excitation edge. These red-edge effects were related to the existence of excited-state distribution of fluorophores on their interaction energy with the environment and the slow rate of dielectric relaxation of this environment. In these conditions the site-selection can be provided by variation of the energy of illuminating light quanta, and the behaviour of selected species can be followed as a function of time and other variables. These observations found extensive application in different areas of research: colloid and polymer science, molecular biophysics, photochemistry and photobiology. In particular, they led to the development of very productive methods of studying the dynamics of dielectric relaxations in protein and membranes, using the tryptophan emission and the emission of a variety of probes. These studies were extended to the time domain with the observation of new site-selective effects in emission intensity and anisotropy decays. They stimulated the emergence and development of cryogenic energy-selective and single-molecular techniques that became valuable tools in their own right in chemistry and biophysics research. Site-selection effects were discovered for electron-transfer and proton-transfer reactions if they depended on the dynamics of the environment. This review is focused on the progress in the field of red-edge effects, their applications and prospects.
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Affiliation(s)
- Alexander P Demchenko
- The Palladin Institute of Biochemistry, Academy of Sciences of Ukraine, Kiev 252030, Ukraine.
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15
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Szocs K, Csík G, Kaposi AD, Fidy J. In situ detection of ALA-stimulated porphyrin metabolic products in Escherichia coli B by fluorescence line narrowing spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1541:170-8. [PMID: 11755211 DOI: 10.1016/s0167-4889(01)00140-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
In a recent work [Photochem. Photobiol. B: Biol. 50 (1999) 8] the successful photodynamic inactivation of Escherichia coli bacteria by visible light was reported based on delta-aminolevulinic acid (ALA)-induced endogenous porphyrin accumulation. In this work, the identification of these porphyrin derivatives in intact bacteria was performed by low-temperature conventional fluorescence and fluorescence line narrowing (FLN) techniques. Conventional fluorescence emission spectroscopy at cryogenic temperatures revealed the presence of the free-base porphyrins, identified earlier by high-performance liquid chromatography analysis of disintegrated bacterial cells after ALA induction; however, emission maxima characteristic for metal porphyrins were also observed. We demonstrated that the primary reason for this signal is that metal porphyrins are formed from free-base porphyrins by Mg2+ ions present in the culturing medium. Incorporation of Zn ions originating from the glassware could also be supposed. In the FLN experiment, the energy selection effect could be clearly demonstrated for (0,0) emissions of both the free-base and the metal porphyrins. The comparison of the conventional emission spectra and the bands revealed by the FLN experiment show that the dominant monomeric structural population is that of metal porphyrins. The intensity and the shape of the FLN lines indicate an aggregated population of the free-base porphyrins, beside a small monomeric population.
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Affiliation(s)
- K Szocs
- Laser Application Department, Research Institute for Solid State Physics and Optics, Budapest, Hungary.
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16
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Suisalu A, Mauring K, Kikas J, Herenyi L, Fidy J. Energy selection is not correlated in the Qx and Qy bands of a Mg-porphyrin embedded in a protein. Biophys J 2001; 80:498-504. [PMID: 11159420 PMCID: PMC1301251 DOI: 10.1016/s0006-3495(01)76032-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The Qx-Qy splitting observed in the fluorescence excitation spectra of Mg-mesoporphyrin-IX substituted horseradish peroxidase (MgMP-HRP) and of its complex with naphthohydroxamic acid (NHA) was studied by spectral hole burning techniques. The width of a hole directly burnt in the Qy band and that of a satellite hole indirectly produced in Qy as a result of hole burning in Qx was compared. We also studied the dependence of the satellite hole in the Qy band on the burning frequency used in the Qx band. Both the directly and indirectly burnt holes were very broad in the (higher energy) Qy band. The width of the satellite hole in the Qy band was equal to the entire width of the inhomogeneously broadened band, independently from the position of hole burning in Qx. This is indicative of a clear lack of correlation between the electronic transition energies of the Qx and Qy bands. A photoproduct was produced by laser irradiation of the MgMP-HRP/NHA complex and was identified as a species with lowered Q-splitting. Conversion of the photoproduct could be achieved by thermal activation measured in temperature-cycling experiments, with a characteristic temperature of 25 K. We attribute the phototransformation to a conformational change of MgMP.
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Affiliation(s)
- A Suisalu
- Institute of Physics, University of Tartu, EE2400 Tartu, Estonia
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17
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Kaposi AD, Fidy J, Manas ES, Vanderkooi JM, Wright WW. Horseradish peroxidase monitored by infrared spectroscopy: effect of temperature, substrate and calcium. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1435:41-50. [PMID: 10561536 DOI: 10.1016/s0167-4838(99)00206-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Horseradish peroxidase was examined as a function of Ca and substrate binding using infrared spectroscopy in the temperature range of 10-300 K. The Ca complex could be identified by the carboxylate stretches. The amide peak positions indicate that the protein remains stable from room temperature to 10 K. Shifts in these peaks are consistent with increased hydrogen bonding as temperature decreases, but the protein conformation is maintained at cryogenic temperatures. The substrate, benzohydroxamic acid, produced no detectable change in the infrared spectrum, consistent with X-ray crystallography results. With removal of Ca, the protein maintained its overall helicity.
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Affiliation(s)
- A D Kaposi
- Institute of Biophysics and Radiation Biology, Semmelweis University of Medicine, Puskin u. 9, Budapest, Hungary.
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18
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Kornblatt JA, Kornblatt MJ, Lange R, Mombelli E, Guillemette JG. The individual tyrosines of proteins: their spectra may or may not differ from those in water or other solvents. BIOCHIMICA ET BIOPHYSICA ACTA 1999; 1431:238-48. [PMID: 10209296 DOI: 10.1016/s0167-4838(99)00044-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The overall derivative spectrum of a protein is the sum of the individual derivative spectra just as the overall ultraviolet spectrum of a protein is the sum of its component parts. The RNase and DNA binding protein Sso7d has two tyrosines and one tryptophan. We used two mutant forms of the protein to show that the individual aromatics contribute derivative spectra that can be explained on the basis of their environments. We used mutant forms of iso-1-cytochrome c to estimate the contributions of the single tryptophan and three of the five tyrosines to the overall derivative spectrum. The tryptophan spectrum is not exceptional. The comparable tyrosine spectra are more complex. The derivative spectrum of individual tyrosines does not correspond to that expected on the basis of concentration. This is a reflection of two factors: (1) the extent to which mutations are sensed distally through the introduction and compression of packing defects; and (2) the extent to which electronic transitions of tyrosine are influenced by nearby atoms. This influence could take the form of tyrosine residing in an area where the dielectric coefficient is not uniform; it could also result from tyrosine bumping into neighboring atoms with lower frequency than it does in solution.
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Affiliation(s)
- J A Kornblatt
- Departments of Biology, Chemistry and Biochemistry, Concordia University, 1455 de Maisonneuve, Montreal, Que. H3G 1M8, Canada.
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19
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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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20
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Laberge M. Intrinsic protein electric fields: basic non-covalent interactions and relationship to protein-induced Stark effects. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1386:305-30. [PMID: 9733989 DOI: 10.1016/s0167-4838(98)00100-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Knowledge of the interactions involving charged, polar and polarizable groups in proteins is fundamental, not only because they are important determinants for gaining insight into biophysical molecular recognition and assembly processes, but also for understanding how the matrix of a protein can be viewed as an electric field capable of inducing Stark perturbations on the spectral properties of biological optical centers. This review describes the essential features of noncovalent interactions in protein systems and discusses the concept of the dielectric constant of a protein in the context of different microscopic and macroscopic modeling approaches. It also provides an account of a specific type of high resolution vibrational and optical Stark spectroscopy attempting to correlate the observed spectral properties of biological optical centers to the intrinsic protein fields induced by the matrix in which they reside.
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Affiliation(s)
- M Laberge
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia 19104, USA.
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Abstract
Three ways are generally used to visualize proteins: (1) a static model in which the atomic positions are defined, (2) a dynamic model taking into account fluctuations, and (3) a reactive model that reflects the internal and external electric fields of the molecule. The properties of chromophoric prosthetic groups can be probed by optical spectroscopy, and when high resolution techniques are used, the results reveal information about the local electric fields in proteins, as influenced and determined by atomic positions and dynamics.
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Affiliation(s)
- J M Vanderkooi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, School of Medicine, University of Pennsylvania, Philadelphia 19104, USA.
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