1
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Mazal H, Wieser FF, Sandoghdar V. Insights into protein structure using cryogenic light microscopy. Biochem Soc Trans 2023; 51:2041-2059. [PMID: 38015555 PMCID: PMC10754291 DOI: 10.1042/bst20221246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 11/13/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023]
Abstract
Fluorescence microscopy has witnessed many clever innovations in the last two decades, leading to new methods such as structured illumination and super-resolution microscopies. The attainable resolution in biological samples is, however, ultimately limited by residual motion within the sample or in the microscope setup. Thus, such experiments are typically performed on chemically fixed samples. Cryogenic light microscopy (Cryo-LM) has been investigated as an alternative, drawing on various preservation techniques developed for cryogenic electron microscopy (Cryo-EM). Moreover, this approach offers a powerful platform for correlative microscopy. Another key advantage of Cryo-LM is the strong reduction in photobleaching at low temperatures, facilitating the collection of orders of magnitude more photons from a single fluorophore. This results in much higher localization precision, leading to Angstrom resolution. In this review, we discuss the general development and progress of Cryo-LM with an emphasis on its application in harnessing structural information on proteins and protein complexes.
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Affiliation(s)
- Hisham Mazal
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
| | - Franz-Ferdinand Wieser
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
| | - Vahid Sandoghdar
- Max Planck Institute for the Science of Light, 91058 Erlangen, Germany
- Max-Planck-Zentrum für Physik und Medizin, 91058 Erlangen, Germany
- Friedrich-Alexander University of Erlangen-Nürnberg, 91058 Erlangen, Germany
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2
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Shafiei G, Levenberg A, Lujan MA, Picorel R, Zazubovich V. Evidence of Simultaneous Spectral Hole Burning Involving Two Tiers of the Protein Energy Landscape in Cytochrome b6f. J Phys Chem B 2019; 123:10930-10938. [PMID: 31763829 DOI: 10.1021/acs.jpcb.9b09515] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cytochrome b6f, with one chlorophyll molecule per protein monomer, is a simple model system whose studies can help achieve a better understanding of nonphotochemical spectral hole burning (NPHB) and single-complex spectroscopy results obtained in more complicated photosynthetic chlorophyll-protein complexes. We are reporting new data and proposing an alternative explanation for spectral dynamics that was recently observed in cytochrome b6f using NPHB. The relevant distribution of the tunneling parameter λ is a superposition of two components that are nearly degenerate in terms of the resultant NPHB yield and represent two tiers of the energy landscape responsible for NPHB. These two components likely burn competitively; we present the first demonstration of modeling a competitive NPHB process. Similar values of the NPHB yield result from distinctly different combinations of barrier heights, shifts along the generalized coordinate d, and/or masses of the entities involved in conformational changes m, with md2 parameter different by a factor of 2.7. Consequently, in cytochrome b6f, the first (at least) 10 h of fixed-temperature recovery preferentially probe different components of the barrier- and λ-distributions encoded into the spectral holes than thermocycling experiments. Both components most likely represent dynamics of the protein and not of the surrounding buffer/glycerol glass.
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Affiliation(s)
- Golia Shafiei
- Department of Physics , Concordia University , 7141 Sherbrooke Str. West , Montreal , Quebec H4B 1R6 , Canada
| | - Alexander Levenberg
- Department of Physics , Concordia University , 7141 Sherbrooke Str. West , Montreal , Quebec H4B 1R6 , Canada
| | - Maria A Lujan
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005 , 50059 Zaragoza , Spain
| | - Rafael Picorel
- Estacion Experimental de Aula Dei (CSIC) , Avda. Montañana 1005 , 50059 Zaragoza , Spain
| | - Valter Zazubovich
- Department of Physics , Concordia University , 7141 Sherbrooke Str. West , Montreal , Quebec H4B 1R6 , Canada
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3
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Adolphs J, Berrer M, Renger T. Hole-Burning Spectroscopy on Excitonically Coupled Pigments in Proteins: Theory Meets Experiment. J Am Chem Soc 2016; 138:2993-3001. [PMID: 26811003 PMCID: PMC4786881 DOI: 10.1021/jacs.5b08246] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
A theory for the calculation of resonant
and nonresonant hole-burning
(HB) spectra of pigment–protein complexes is presented and
applied to the water-soluble chlorophyll-binding protein (WSCP) from
cauliflower. The theory is based on a non-Markovian line shape theory
(Renger and Marcus2002, 116, 9997) and includes exciton delocalization, vibrational
sidebands, and lifetime broadening. An earlier approach by Reppert
(2011, 2, 2716) is found to describe nonresonant HB spectra only. Here we present
a theory that can be used for a quantitative description of HB data
for both nonresonant and resonant burning conditions. We find that
it is important to take into account the excess energy of the excitation
in the HB process. Whereas excitation of the zero-phonon transition
of the lowest exciton state, that is, resonant burning allows the
protein to access only its conformational substates in the neighborhood
of the preburn state, any higher excitation gives the protein full
access to all conformations present in the original inhomogeneous
ensemble. Application of the theory to recombinant WSCP from cauliflower,
reconstituted with chlorophyll a or chlorophyll b, gives excellent agreement with experimental data by Pieper
et al. (2011, 115, 405321417356) and allows us to obtain an upper bound of the lifetime of the upper
exciton state directly from the HB experiments in agreement with lifetimes
measured recently in time domain 2D experiments by Alster et al. (2014, 118, 352424627983).
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Affiliation(s)
- Julian Adolphs
- Institut für Theoretische Physik, Johannes Kepler Universität Linz , Altenberger Str. 69, 4040 Linz, Austria
| | - Manuel Berrer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz , Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz , Altenberger Str. 69, 4040 Linz, Austria
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4
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Schörner M, Beyer SR, Southall J, Cogdell RJ, Köhler J. Conformational Memory of a Protein Revealed by Single-Molecule Spectroscopy. J Phys Chem B 2015; 119:13964-70. [PMID: 26420643 DOI: 10.1021/acs.jpcb.5b07494] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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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Affiliation(s)
- Mario Schörner
- Experimental Physics IV and Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth , 95447 Bayreuth, Germany
| | - Sebastian Reinhardt Beyer
- Experimental Physics IV and Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth , 95447 Bayreuth, Germany
| | - June Southall
- Institute of Molecular, Cell & Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow , Glasgow G12 8QQ, United Kingdom
| | - Richard J Cogdell
- Institute of Molecular, Cell & Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow , Glasgow G12 8QQ, United Kingdom
| | - Jürgen Köhler
- Experimental Physics IV and Bayreuth Institute for Macromolecular Research (BIMF), University of Bayreuth , 95447 Bayreuth, Germany
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5
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Najafi M, Zazubovich V. Monte Carlo Modeling of Spectral Diffusion Employing Multiwell Protein Energy Landscapes: Application to Pigment-Protein Complexes Involved in Photosynthesis. J Phys Chem B 2015; 119:7911-21. [PMID: 26020801 DOI: 10.1021/acs.jpcb.5b02764] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We are reporting development and initial applications of the light-induced and thermally induced spectral diffusion modeling software, covering nonphotochemical spectral hole burning (NPHB), hole recovery, and single-molecule spectroscopy and involving random generation of the multiwell protein energy landscapes. The model includes tunneling and activated barrier-hopping in both ground and excited states of a protein-chromophore system. Evolution of such a system is predicted by solving the system of rate equations. Using the barrier parameters from the range typical for the energy landscapes of the pigment-protein complexes involved in photosynthesis, we (a) show that realistic cooling of the sample must result in proteins quite far from thermodynamic equilibrium, (b) demonstrate hole evolution in the cases of burning, fixed-temperature recovery and thermocycling that mostly agrees with the experiment and modeling based on the NPHB master equation, and (c) explore the effects of different protein energy landscapes on the antihole shape. Introducing the multiwell energy landscapes and starting the hole burning experiments in realistic nonequilibrium conditions are not sufficient to explain all experimental observations even qualitatively. Therefore, for instance, one is required to invoke the modified NPHB mechanism where a complex interplay of several small conformational changes is poising the energy landscape of the pigment-protein system for downhill tunneling.
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Affiliation(s)
- Mehdi Najafi
- Department of Physics, Concordia University, Montreal H4B 1R6, Quebec, Canada
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal H4B 1R6, Quebec, Canada
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6
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Frauenfelder H, Young RD, Fenimore PW. Dynamics and the Free-Energy Landscape of Proteins, Explored with the Mössbauer Effect and Quasi-Elastic Neutron Scattering. J Phys Chem B 2013; 117:13301-7. [DOI: 10.1021/jp403832n] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hans Frauenfelder
- T6, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Robert D. Young
- Center
for Theoretical Biological Physics, Arizona State University, P.O. Box 871504, Tempe, Arizona 85287-1504, United States
| | - Paul W. Fenimore
- T6, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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7
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Tian Y, Navarro P, Kozankiewicz B, Orrit M. Spectral Diffusion of Single Dibenzoterrylene Molecules in 2,3-Dimethylanthracene. Chemphyschem 2012; 13:3510-5. [DOI: 10.1002/cphc.201200463] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2012] [Indexed: 11/07/2022]
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8
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Coupling of protein and environment fluctuations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:916-21. [PMID: 21621015 DOI: 10.1016/j.bbapap.2011.05.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2010] [Revised: 05/02/2011] [Accepted: 05/06/2011] [Indexed: 11/21/2022]
Abstract
We review the concepts of protein dynamics developed over the last 35years and extend applications of the unified model of protein dynamics to heat flow and spatial fluctuations in hydrated myoglobin (Mb) powders. Differential scanning calorimetry (DSC) and incoherent neutron scattering (INS) data on hydration Mb powders are explained by the temperature-dependence of the hydration-shell β(h) process measured by dielectric relaxation spectroscopy (DRS). The unified model explains the temperature dependence of DSC and INS data as a kinetic effect due to a fixed experimental time window and a broad distribution of hydration-shell β(h) fluctuation rates. We review the slaving of large scale protein motions to the bulk solvent α process, and the metastability of Mb molecules in glass forming bulk solvent at low temperatures. This article is part of a Special Issue entitled: "Protein Dynamics: Experimental and Computational Approaches".
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9
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Herascu N, Najafi M, Amunts A, Pieper J, Irrgang KD, Picorel R, Seibert M, Zazubovich V. Parameters of the protein energy landscapes of several light-harvesting complexes probed via spectral hole growth kinetics measurements. J Phys Chem B 2011; 115:2737-47. [PMID: 21391534 DOI: 10.1021/jp108775y] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The parameters of barrier distributions on the protein energy landscape in the excited electronic state of the pigment/protein system have been determined by means of spectral hole burning for the lowest-energy pigments of CP43 core antenna complex and CP29 minor antenna complex of spinach Photosystem II (PS II) as well as of trimeric and monomeric LHCII complexes transiently associated with the pea Photosystem I (PS I) pool. All of these complexes exhibit sixty to several hundred times lower spectral hole burning yields as compared with molecular glassy solids previously probed by means of the hole growth kinetics measurements. Therefore, the entities (groups of atoms), which participate in conformational changes in protein, appear to be significantly larger and heavier than those in molecular glasses. No evidence of a small (∼1 cm(-1)) spectral shift tier of the spectral diffusion dynamics has been observed. Therefore, our data most likely reflect the true barrier distributions of the intact protein and not those related to the interface or surrounding host. Possible applications of the barrier distributions as well as the assignments of low-energy states of CP29 and LHCII are discussed in light of the above results.
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Affiliation(s)
- Nicoleta Herascu
- Department of Physics, Concordia University, Montreal, Quebec, Canada
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10
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Krause S, Kowerko D, Börner R, Hübner CG, von Borczyskowski C. Spectral Diffusion of Single Molecules in a Hierarchical Energy Landscape. Chemphyschem 2011; 12:303-12. [DOI: 10.1002/cphc.201000678] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Revised: 11/08/2010] [Indexed: 11/10/2022]
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11
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Tan YW, Yang H. Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments. Phys Chem Chem Phys 2010; 13:1709-21. [PMID: 21183988 DOI: 10.1039/c0cp02412k] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Enzymes are remarkable molecular machines that make many difficult biochemical reactions possible under mild biological conditions with incredible precision and efficiency. Our understanding of the working principles of enzymes, however, has not reached the level where one can readily deduce the mechanism and the catalytic rates from an enzyme's structure. Resolving the dynamics that relate the three-dimensional structure of an enzyme to its function has been identified as a key issue. While still challenging to implement, single-molecule techniques have emerged as one of the most useful methods for studying enzymes. We review enzymes studied using single-molecule fluorescent methods but placing them in the context of results from other complementary experimental work done on bulk samples. This review primarily covers three enzyme systems--flavoenzymes, dehydrofolate reductase, and adenylate kinase--with additional enzymes mentioned where appropriate. When the single-molecule experiments are discussed together with other methods aiming at the same scientific question, the weakness, strength, and unique contributions become clear.
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Affiliation(s)
- Yan-Wen Tan
- Department of Physics, Fudan University, No. 220, Handan Rd., Shanghai 200433, China.
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12
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Eremchev IY, Vainer YG, Naumov AV, Kador L. Low-temperature dynamics in amorphous polymers and low-molecular-weight glasses--what is the difference? Phys Chem Chem Phys 2010; 13:1843-8. [PMID: 21183979 DOI: 10.1039/c0cp01690j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Numerous experiments have shown that the low-temperature dynamics of a wide variety of disordered solids is qualitatively universal. However, most of these results were obtained with ensemble-averaging techniques which hide the local parameters of the dynamic processes. We used single-molecule (SM) spectroscopy for direct observation of the dynamic processes in disordered solids with different internal structure and chemical composition. The surprising result is that the dynamics of low-molecular-weight glasses and short-chain polymers does not follow, on a microscopic level, the current concept of low-temperature glass dynamics. An extra contribution to the dynamics was detected causing irreproducible jumps and drifts of the SM spectra on timescales between milliseconds and minutes. In most matrices consisting of small molecules and oligomers, the spectral dynamics was so fast that SM spectra could hardly or not at all be recorded and only irregular fluorescence flares were observed. These results provide new mechanistic insight into the behavior of glasses in general: At low temperatures, the local dynamics of disordered solids is not universal but depends on the structure and chemical composition of the material.
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Affiliation(s)
- Ivan Yu Eremchev
- Molecular Spectroscopy Department, Institute for Spectroscopy, Russian Academy of Sciences, Troitsk, Moscow reg., 142190, Russia
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14
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Purchase R, Völker S. Spectral hole burning: examples from photosynthesis. PHOTOSYNTHESIS RESEARCH 2009; 101:245-66. [PMID: 19714478 PMCID: PMC2744831 DOI: 10.1007/s11120-009-9484-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Accepted: 07/31/2009] [Indexed: 05/14/2023]
Abstract
The optical spectra of photosynthetic pigment-protein complexes usually show broad absorption bands, often consisting of a number of overlapping, "hidden" bands belonging to different species. Spectral hole burning is an ideal technique to unravel the optical and dynamic properties of such hidden species. Here, the principles of spectral hole burning (HB) and the experimental set-up used in its continuous wave (CW) and time-resolved versions are described. Examples from photosynthesis studied with hole burning, obtained in our laboratory, are then presented. These examples have been classified into three groups according to the parameters that were measured: (1) hole widths as a function of temperature, (2) hole widths as a function of delay time and (3) hole depths as a function of wavelength. Two examples from light-harvesting (LH) 2 complexes of purple bacteria are given within the first group: (a) the determination of energy-transfer times from the chromophores in the B800 ring to the B850 ring, and (b) optical dephasing in the B850 absorption band. One example from photosystem II (PSII) sub-core complexes of higher plants is given within the second group: it shows that the size of the complex determines the amount of spectral diffusion measured. Within the third group, two examples from (green) plants and purple bacteria have been chosen for: (a) the identification of "traps" for energy transfer in PSII sub-core complexes of green plants, and (b) the uncovering of the lowest k = 0 exciton-state distribution within the B850 band of LH2 complexes of purple bacteria. The results prove the potential of spectral hole burning measurements for getting quantitative insight into dynamic processes in photosynthetic systems at low temperature, in particular, when individual bands are hidden within broad absorption bands. Because of its high-resolution wavelength selectivity, HB is a technique that is complementary to ultrafast pump-probe methods. In this review, we have provided an extensive bibliography for the benefit of scientists who plan to make use of this valuable technique in their future research.
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Affiliation(s)
- Robin Purchase
- Huygens and Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
| | - Silvia Völker
- Huygens and Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
- Department of Biophysics, Faculty of Exact Sciences, Vrije Universiteit Amsterdam, 1081 HV Amsterdam, The Netherlands
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15
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Abstract
Protein functions require conformational motions. We show here that the dominant conformational motions are slaved by the hydration shell and the bulk solvent. The protein contributes the structure necessary for function. We formulate a model that is based on experiments, insights from the physics of glass-forming liquids, and the concepts of a hierarchically organized energy landscape. To explore the effect of external fluctuations on protein dynamics, we measure the fluctuations in the bulk solvent and the hydration shell with broadband dielectric spectroscopy and compare them with internal fluctuations measured with the Mössbauer effect and neutron scattering. The result is clear. Large-scale protein motions are slaved to the fluctuations in the bulk solvent. They are controlled by the solvent viscosity, and are absent in a solid environment. Internal protein motions are slaved to the beta fluctuations of the hydration shell, are controlled by hydration, and are absent in a dehydrated protein. The model quantitatively predicts the rapid increase of the mean-square displacement above approximately 200 K, shows that the external beta fluctuations determine the temperature- and time-dependence of the passage of carbon monoxide through myoglobin, and explains the nonexponential time dependence of the protein relaxation after photodissociation.
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16
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Finkelstein IJ, Zheng J, Ishikawa H, Kim S, Kwak K, Fayer MD. Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy. Phys Chem Chem Phys 2007; 9:1533-49. [PMID: 17429547 DOI: 10.1039/b618158a] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ultrafast 2D IR vibrational echo spectroscopy is described and a number of experimental examples are given. Details of the experimental method including the pulse sequence, heterodyne detection, and determination of the absorptive component of the 2D spectrum are outlined. As an initial example, the 2D spectrum of the stretching mode of CO bound to the protein myoglobin (MbCO) is presented. The time dependence of the 2D spectrum of MbCO, which is caused by protein structural evolution, is presented and its relationship to the frequency-frequency correlation function is described and used to make protein structural assignments based on comparisons to molecular dynamics simulations. The 2D vibrational echo experiments on the protein horseradish peroxidase are presented. The time dependence of the 2D spectra of the enzyme in the free form and with a substrate bound at the active site are compared and used to examine the influence of substrate binding on the protein's structural dynamics. The application of 2D vibrational echo spectroscopy to the study of chemical exchange under thermal equilibrium conditions is described. 2D vibrational echo chemical exchange spectroscopy is applied to the study of formation and dissociation of organic solute-solvent complexes and to the isomerization around a carbon-carbon single bond of an ethane derivative.
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17
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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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18
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Baldini G, Cannone F, Chirico G, Collini M, Campanini B, Bettati S, Mozzarelli A. Evidence of discrete substates and unfolding pathways in green fluorescent protein. Biophys J 2006; 92:1724-31. [PMID: 17142282 PMCID: PMC1796838 DOI: 10.1529/biophysj.106.093567] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We present evidence of conformational substates of a green fluorescent protein mutant, GFPmut2, and of their relationship with the protein behavior during chemical unfolding. The fluorescence of single molecules, excited by two infrared photons from a pulsed laser, was detected in two separate channels that simultaneously collected the blue or the green emission from the protein chromophore chemical states (anionic or neutral, respectively). Time recording of the fluorescence signals from molecules in the native state shows that the chromophore, an intrinsic probe sensitive to conformational changes, switches between the two states with average rates that are found to assume distinct values, thereby suggesting a multiplicity of protein substates. Furthermore, under denaturing conditions, the chromophore switching rate displays different and reproducible time evolutions that are characterized by discrete unfolding times. The correlation that is found between native molecules' switching rate values and unfolding times appears as direct evidence that GFPmut2 can unfold only along distinct paths that are determined by the initial folded substate of the protein.
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19
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Somoza MM, Ponkratov VV, Friedrich J. Investigation of spectral diffusion in ribonuclease by photolabeling of intrinsic aromatic amino acids. J Chem Phys 2006; 125:194713. [PMID: 17129156 DOI: 10.1063/1.2395938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Spectral diffusion dynamics in ribonuclease A was observed via the broadening of photochemical holes burned into the absorption spectrum of intrinsic tyrosine residues. Unlike previous results based on hole burning of chromophores in the pockets of heme proteins, where spectral diffusion develops according to a power law in time, the dynamics in ribonuclease follow a logarithmic law. The results suggest that the experiment preferentially labels the tyrosines located on the surface of the protein where the two-level system dynamics of the glass host matrix exert a strong influence.
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Affiliation(s)
- Mark M Somoza
- E14 and Lehrstuhl für Physik Weihenstephan, Physics Department, Technische Universität München, 85350 Freising, Germany.
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20
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Somoza MM, Friedrich J. Thermal-cycling-induced spectral diffusion and thermal barriers in anisole-doped cyclohexane, an unusual multiphase host-guest system. J Phys Chem B 2006; 110:18828-33. [PMID: 16986873 DOI: 10.1021/jp055194p] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The host-guest system of anisole incorporated into a cyclohexane matrix was investigated in a series of hole-burning experiments. This system is unusual in that cyclohexane can freeze into coexisting solid phases. The hole-burning experiments support the existence of two crystalline phases and one disordered phase. A second surprising characteristic of this system is that the quasi-line absorption features of the spectra appear inverted at low temperature because of unexpected dominance of fluorescence and phosphorescence.
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Affiliation(s)
- Mark M Somoza
- Physik Department E14, Lehrstuhl für Physik Weihenstephan, Technische Universität München, An der Saatzucht 5, D-85350 Freising, Germany.
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21
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Lesch H, Hecht C, Friedrich J. Protein phase diagrams: the physics behind their elliptic shape. J Chem Phys 2006; 121:12671-5. [PMID: 15606293 DOI: 10.1063/1.1824900] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We relate the condition for the elliptic shape of the phase diagram of proteins to the degree of correlation in the fluctuations of the changes of enthalpy and volume at the denaturing-refolding transition. Since this degree cannot be larger than 1, hyperbolically shaped diagrams are not likely to exist. Experiments show that the correlation factor is actually quite low for proteins implying that one-order parameter is not enough to describe the folding-denaturing transition. These findings seem to be the thermodynamic manifestation of the glasslike properties of proteins despite the fact that the transition itself is of first order.
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Affiliation(s)
- Harald Lesch
- Physik Department E14, Lehrstuhl für Physik Weihenstephan, Technische Universität München, An der Saatzucht 5, D-85350 Freising, Germany
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22
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McIntire MJ, Yamaguchi M, Kol'chenko MA, Vainer YG, Chronister EL. High-Pressure Studies of Optical Dephasing in Polymer Glasses. J Phys Chem B 2006; 110:227-33. [PMID: 16471526 DOI: 10.1021/jp0582686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The effect of high pressure on the optical dephasing of chromophores in organic polymers at low temperature is evaluated within the stochastic sudden jump two-level-system (TLS) model. The approximations within the "standard" TLS model cannot account for the observed pressure dependence of the pure dephasing rate without ad hoc assumptions about changes in the TLS density of states. However, the photon echo model of Geva and Skinner for disordered systems can be used to model pressure-dependent optical dephasing results for a variety of doped polymer systems without assuming changes in the TLS density of states. The relative importance of pressure-induced changes in TLS density, chromophore-TLS coupling, and TLS-phonon coupling is evaluated by fitting experimental high-pressure photon echo results to the TLS model.
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Affiliation(s)
- Michael J McIntire
- Department of Chemistry, Natural and Applied Sciences, University of Wisconsin-Green Bay, Green Bay, Wisconsin 54311, USA
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Fenimore PW, Frauenfelder H, McMahon BH, Young RD. Bulk-solvent and hydration-shell fluctuations, similar to alpha- and beta-fluctuations in glasses, control protein motions and functions. Proc Natl Acad Sci U S A 2004; 101:14408-13. [PMID: 15448207 PMCID: PMC521939 DOI: 10.1073/pnas.0405573101] [Citation(s) in RCA: 405] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The concept that proteins exist in numerous different conformations or conformational substates, described by an energy landscape, is now accepted, but the dynamics is incompletely explored. We have previously shown that large-scale protein motions, such as the exit of a ligand from the protein interior, follow the dielectric fluctuations in the bulk solvent. Here, we demonstrate, by using mean-square displacements (msd) from Mossbauer and neutron-scattering experiments, that fluctuations in the hydration shell control fast fluctuations in the protein. We call the first type solvent-slaved or alpha-fluctuations and the second type hydration-shell-coupled or beta-fluctuations. Solvent-slaved motions are similar to the alpha-fluctuations in glasses. Their temperature dependence can be approximated by a Vogel-Tammann-Fulcher relation and they are absent in a solid environment. Hydration-shell-coupled fluctuations are similar to the beta-relaxation in glasses. They can be approximated by a Ferry or an Arrhenius relation, are much reduced or absent in dehydrated proteins, and occur in hydrated proteins even if embedded in a solid. They can be responsible for internal processes such as the migration of ligands within myoglobin. The existence of two functionally important fluctuations in proteins, one slaved to bulk motions and the other coupled to hydration-shell fluctuations, implies that the environment can control protein functions through different avenues and that no real protein transition occurs at approximately 200 K. The large number of conformational substates is essential; proteins cannot function without this reservoir of entropy, which resides mainly in the hydration shell.
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Affiliation(s)
- P W Fenimore
- Theory Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Jankowiak R, Rogan EG, Cavalieri EL. Role of Fluorescence Line-Narrowing Spectroscopy and Related Luminescence-Based Techniques in the Elucidation of Mechanisms of Tumor Initiation by Polycyclic Aromatic Hydrocarbons and Estrogens†. J Phys Chem B 2004. [DOI: 10.1021/jp0402838] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Hofmann C, Aartsma TJ, Michel H, Köhler J. Direct observation of tiers in the energy landscape of a chromoprotein: a single-molecule study. Proc Natl Acad Sci U S A 2003; 100:15534-8. [PMID: 14671325 PMCID: PMC307602 DOI: 10.1073/pnas.2533896100] [Citation(s) in RCA: 112] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Single-molecule spectroscopic techniques were applied to individual pigments embedded in a chromoprotein. A sensitive tool to monitor structural fluctuations of the protein backbone in the local environment of the chromophore is provided by recording the changes of the spectral positions of the pigment absorptions as a function of time. The data provide information about the organization of the energy landscape of the protein in tiers that can be characterized by an average barrier height. Additionally, a correlation between the average barrier height within a distinct tier and the time scale of the structural fluctuations is observed.
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Affiliation(s)
- Clemens Hofmann
- Experimental Physics IV and Bayreuther Institut für Makromolekülforschung, University of Bayreuth, 95440 Bayreuth, Germany
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Borovykh I, Kulik L, Gast P, Dzuba S. Conformation transition in the protein of a photosynthetic reaction center observed at the nanometer range of distances at cryogenic temperatures. Chem Phys 2003. [DOI: 10.1016/s0301-0104(03)00323-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Frauenfelder H, McMahon BH, Fenimore PW. Myoglobin: the hydrogen atom of biology and a paradigm of complexity. Proc Natl Acad Sci U S A 2003; 100:8615-7. [PMID: 12861080 PMCID: PMC166357 DOI: 10.1073/pnas.1633688100] [Citation(s) in RCA: 172] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- H Frauenfelder
- Center for Nonlinear Studies, MS B258, and Theoretical Biology and Biophysics Group (T-10), MS K710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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Fenimore PW, Frauenfelder H, McMahon BH, Parak FG. Slaving: solvent fluctuations dominate protein dynamics and functions. Proc Natl Acad Sci U S A 2002; 99:16047-51. [PMID: 12444262 PMCID: PMC138562 DOI: 10.1073/pnas.212637899] [Citation(s) in RCA: 489] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein motions are essential for function. Comparing protein processes with the dielectric fluctuations of the surrounding solvent shows that they fall into two classes: nonslaved and slaved. Nonslaved processes are independent of the solvent motions; their rates are determined by the protein conformation and vibrational dynamics. Slaved processes are tightly coupled to the solvent; their rates have approximately the same temperature dependence as the rate of the solvent fluctuations, but they are smaller. Because the temperature dependence is determined by the activation enthalpy, we propose that the solvent is responsible for the activation enthalpy, whereas the protein and the hydration shell control the activation entropy through the energy landscape. Bond formation is the prototype of nonslaved processes; opening and closing of channels are quintessential slaved motions. The prevalence of slaved motions highlights the importance of the environment in cells and membranes for the function of proteins.
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Affiliation(s)
- P W Fenimore
- Center for Nonlinear Studies, MS B258, and Theoretical Biophysics Group, MS K-710, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Ponkratov VV, Friedrich J, Vanderkooi JM. Solvent effects on conformational dynamics of proteins: Cytochrome c in a dried trehalose film. J Chem Phys 2002. [DOI: 10.1063/1.1498459] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Mizutani Y, Kitagawa T. Ultrafast dynamics of myoglobin probed by time-resolved resonance Raman spectroscopy. CHEM REC 2002; 1:258-75. [PMID: 11895123 DOI: 10.1002/tcr.1012] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent experimental work carried out in this laboratory on the ultrafast dynamics of myoglobin (Mb) is summarized with a stress on structural and vibrational energy relaxation. Studies on the structural relaxation of Mb following CO photolysis revealed that the structural change of heme itself, caused by CO photodissociation, is completed within the instrumental response time of the time-resolved resonance Raman apparatus used (approximately 2 ps). In contrast, changes in the intensity and frequency of the iron-histidine (Fe-His) stretching mode upon dissociation of the trans ligand were found to occur in the picosecond regime. The Fe-His band is absent for the CO-bound form, and its appearance upon photodissociation was not instantaneous, in contrast with that observed in the vibrational modes of heme, suggesting appreciable time evolution of the Fe displacement from the heme plane. The band position of the Fe-His stretching mode changed with a time constant of about 100 ps, indicating that tertiary structural changes of the protein occurred in a 100-ps range. Temporal changes of the anti-Stokes Raman intensity of the v4 and v7 bands demonstrated immediate generation of vibrationally excited heme upon the photodissociation and decay of the excited populations, whose time constants were 1.1 +/- 0.6 and 1.9 +/- 0.6 ps, respectively. In addition, the development of the time-resolved resonance Raman apparatus and prospects in this research field are described.
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Affiliation(s)
- Y Mizutani
- Institute for Molecular Science, Okazaki National Research Institutes, Myodaiji, Japan
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32
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Schlichter J, Friedrich J, Herenyi L, Fidy J. Deuteration Effects on the Conformational Dynamics of Proteins in a Trehalose Glass. J Phys Chem B 2002. [DOI: 10.1021/jp012316e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Groot ML, Vos MH, Schlichting I, van Mourik F, Joffre M, Lambry JC, Martin JL. Coherent infrared emission from myoglobin crystals: an electric field measurement. Proc Natl Acad Sci U S A 2002; 99:1323-8. [PMID: 11818575 PMCID: PMC122189 DOI: 10.1073/pnas.251662698] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2001] [Accepted: 12/12/2001] [Indexed: 11/18/2022] Open
Abstract
We introduce coherent infrared emission interferometry as a chi(2) vibrational spectroscopy technique and apply it to studying the initial dynamics upon photoactivation of myoglobin (Mb). By impulsive excitation (using 11-fs pulses) of a Mb crystal, vibrations that couple to the optical excitation are set in motion coherently. Because of the order in the crystal lattice the coherent oscillations of the different proteins in the crystal that are associated with charge motions give rise to a macroscopic burst of directional multi-teraHertz radiation. This radiation can be detected in a phase-sensitive way by heterodyning with a broad-band reference field. In this way both amplitude and phase of the different vibrations can be obtained. We detected radiation in the 1,000-1,500 cm(-1) frequency region, which contains modes sensitive to the structure of the heme macrocycle, as well as peripheral protein modes. Both in carbonmonoxy-Mb and aquomet-Mb we observed emission from six modes, which were assigned to heme vibrations. The phase factors of the modes contributing to the protein electric field show a remarkable consistency, taking on values that indicate that the dipoles are created "emitting" at t = 0, as one would expect for impulsively activated modes. The few deviations from this behavior in Mb-CO we propose are the result of these modes being sensitive to the photodissociation process and severely disrupted by it.
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Affiliation(s)
- Marie-Louise Groot
- Laboratory for Optical Biosciences, INSERM U451, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7645, Ecole Polytechnique-Ecole Nationale Supárievre de Techniques Avancáes ENSTA, 91128 Palaiseau Cedex, France
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Machida S, Sugihara K, Takahashi I, Horie K, Jiang DL, Aida T. Persistent spectral hole-burning study on dendrimer porphyrins. ACTA ACUST UNITED AC 2002. [DOI: 10.1002/polb.10084] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Avetisov VA, Bikulov AH, Kozyrev SV, Osipov VA. p-adic models of ultrametric diffusion constrained by hierarchical energy landscapes. ACTA ACUST UNITED AC 2002. [DOI: 10.1088/0305-4470/35/2/301] [Citation(s) in RCA: 150] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Abstract
One major goal of biological physics is the discovery and understanding of the concepts and laws that govern biomolecules, in particular proteins. Since there exist at least 10(5) different proteins, the choice of a suitable prototype is necessary. Myoglobin (Mb) has for many years played the role of such a prototype. It appears to be simple enough so that many of its properties can be understood, yet it is complex enough to display many of the fascinating characteristics of biomolecules. One major achievement in the study of any protein would be the establishment of convincing connections among structure, kinetics, energy landscape, dynamics, and function. We believe that this goal has not yet been reached in any protein, but the present knowledge of Mb gives some hope that the end is near in this case. Here, we sketch some of the results that have been obtained in the past 50 or more years in the research on Mb, obtained by an army of investigators.
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Affiliation(s)
- H Frauenfelder
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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38
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Abstract
IR vibrational echo experiments are used to study dynamics in myoglobin (Mb) by investigating the dephasing of the CO-stretching mode of CO bound at the active site of the protein (Mb-CO). The temperature dependence and the viscosity dependence of Mb-CO pure dephasing have been measured in several solvents. In low-temperature, glassy solvents, the pure dephasing has a power law temperature dependence, T(1.3), that reflects glasslike protein dynamics. In liquids, the temperature dependence is much steeper and arises from a combination of pure temperature dependence and the influence of decreasing solvent viscosity with increasing temperature. As the solvent viscosity decreases, the ability of the protein's surface to undergo topological fluctuations increases, which in turn increases the internal protein-structural fluctuations. The protein-structural motions are coupled to the CO bound at the active site by electric field fluctuations that accompany movements of polar residues. The dynamic electric field-coupling mechanism is tested by observing differences in the temperature dependence of the pure dephasing of Mb-CO mutations.
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Affiliation(s)
- M D Fayer
- Department of Chemistry, Stanford University, Stanford, California 94305, USA.
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39
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Schlichter J, Friedrich J, Parbel M, Scheer H. Influence of isotopic substitution on the conformational dynamics of frozen proteins. J Chem Phys 2001. [DOI: 10.1063/1.1369137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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40
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Schlichter J, Friedrich J. Glasses and proteins: Similarities and differences in their spectral diffusion dynamics. J Chem Phys 2001. [DOI: 10.1063/1.1367382] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Schlichter J, Friedrich J, Herenyi L, Fidy J. Trehalose effect on low temperature protein dynamics: fluctuation and relaxation phenomena. Biophys J 2001; 80:2011-7. [PMID: 11259314 PMCID: PMC1301390 DOI: 10.1016/s0006-3495(01)76171-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We performed spectral diffusion experiments in trehalose-enriched glycerol/buffer-glass on horseradish peroxidase where the heme was replaced by metal-free mesoporphyrin IX, and compared them with the respective behavior in a pure glycerol/buffer-glass (Schlichter et al., J. Chem. Phys. 2000, 112:3045-3050). Trehalose has a significant influence: spectral diffusion broadening speeds up compared to the trehalose-free glass. This speeding up is attributed to a shortening of the correlation time of the frequency fluctuations most probably by preventing water molecules from leaving the protein interior. Superimposed to the frequency fluctuation dynamics is a relaxation dynamics that manifests itself as an aging process in the spectral diffusion broadening. Although the trehalose environment speeds up the fluctuations, it does not have any influence on the relaxation. Both relaxation and fluctuations are governed by power laws in time. The respective exponents do not seem to change with the protein environment. From the spectral dynamics, the mean square displacement in conformation space can be determined. It is governed by anomalous diffusion. The associated frequency correlation time is incredibly long, demonstrating that proteins at low temperatures are truly nonergodic systems.
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Affiliation(s)
- J Schlichter
- Lehrstuhl für Physik Weihenstephan, Technische Universität München, D-85350 Freising, Germany
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43
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Schulze BG, Grubmüller H, Evanseck JD. Functional Significance of Hierarchical Tiers in Carbonmonoxy Myoglobin: Conformational Substates and Transitions Studied by Conformational Flooding Simulations. J Am Chem Soc 2000. [DOI: 10.1021/ja993788y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brita G. Schulze
- Contribution from the Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, and Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
| | - Helmut Grubmüller
- Contribution from the Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, and Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
| | - Jeffrey D. Evanseck
- Contribution from the Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, Florida 33146-0431, and Max-Planck-Institut für Biophysikalische Chemie, Göttingen, Germany
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Berg MA, Rector KD, Fayer MD. Two-pulse echo experiments in the spectral diffusion regime. J Chem Phys 2000. [DOI: 10.1063/1.1287172] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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Yang M, Fleming GR. Third-order nonlinear optical response and energy transfer in static disordered systems. J Chem Phys 2000. [DOI: 10.1063/1.1305886] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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46
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Asplund MC, Zanni MT, Hochstrasser RM. Two-dimensional infrared spectroscopy of peptides by phase-controlled femtosecond vibrational photon echoes. Proc Natl Acad Sci U S A 2000; 97:8219-24. [PMID: 10890905 PMCID: PMC26927 DOI: 10.1073/pnas.140227997] [Citation(s) in RCA: 454] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two-dimensional infrared spectra of peptides are introduced that are the direct analogues of two- and three-pulse multiple quantum NMR. Phase matching and heterodyning are used to isolate the phase and amplitudes of the electric fields of vibrational photon echoes as a function of multiple pulse delays. Structural information is made available on the time scale of a few picoseconds. Line narrowed spectra of acyl-proline-NH(2) and cross peaks implying the coupling between its amide-I modes are obtained, as are the phases of the various contributions to the signals. Solvent-sensitive structural differences are seen for the dipeptide. The methods show great promise to measure structure changes in biology on a wide range of time scales.
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Affiliation(s)
- M C Asplund
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA
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47
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Müller J, Maier H, Hannig G, Khodykin OV, Haarer D, Kharlamov BM. Long-time scale spectral diffusion in polymer glass. J Chem Phys 2000. [DOI: 10.1063/1.481864] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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48
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Schlichter J, Friedrich J, Herenyi L, Fidy J. Protein dynamics at low temperatures. J Chem Phys 2000. [DOI: 10.1063/1.480879] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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49
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Affiliation(s)
- Martin Karplus
- Laboratoire de Chimie Biophysique, ISIS, Université Louis Pasteur, 67000 Strasbourg France, and Department of Chemistry & Chemical Biology, Harvard University, Cambridge, Massachusetts 02138
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Goodno GD, Astinov V, Miller RJD. Femtosecond Heterodyne-Detected Four-Wave-Mixing Studies of Deterministic Protein Motions. 2. Protein Response. J Phys Chem A 1999. [DOI: 10.1021/jp993559y] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gregory D. Goodno
- Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627
| | - Vladimir Astinov
- Departments of Chemistry and Physics, 80 St. George Street, University of Toronto, Toronto, Ontario M5S 3H6 Canada
| | - R. J. Dwayne Miller
- Departments of Chemistry and Physics, 80 St. George Street, University of Toronto, Toronto, Ontario M5S 3H6 Canada
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