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A Long Journey into the Investigation of the Structure–Dynamics–Function Paradigm in Proteins through the Activities of the Palermo Biophysics Group. BIOPHYSICA 2022. [DOI: 10.3390/biophysica2040040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
An overview of the biophysics activity at the Department of Physics and Chemistry Emilio Segrè of the University of Palermo is given. For forty years, the focus of the research has been on the protein structure–dynamics–function paradigm, with the aim of understanding the molecular basis of the relevant mechanisms and the key role of solvent. At least three research lines are identified; the main results obtained in collaboration with other groups in Italy and abroad are presented. This review is dedicated to the memory of Professors Massimo Ugo Palma, Maria Beatrice Palma Vittorelli, and Lorenzo Cordone, which were the founders of the Palermo School of Biophysics. We all have been, directly or indirectly, their pupils; we miss their enthusiasm for scientific research, their deep physical insights, their suggestions, their strict but always constructive criticisms, and, most of all, their friendship. This paper is dedicated also to the memory of Prof. Hans Frauenfelder, whose pioneering works on nonexponential rebinding kinetics, protein substates, and energy landscape have inspired a large part of our work in the field of protein dynamics.
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Ferrara V, Marchetti M, Alfieri D, Targetti L, Scopelliti M, Pignataro B, Pavone F, Vetri V, Sancataldo G. Blue Light Activated Photodegradation of Biomacromolecules by N-doped Titanium Dioxide in a Chitosan Hydrogel Matrix. J Photochem Photobiol A Chem 2022. [DOI: 10.1016/j.jphotochem.2022.114451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Tominaga T, Nakagawa H, Sahara M, Oda T, Inoue R, Sugiyama M. Data Collection for Dilute Protein Solutions via a Neutron Backscattering Spectrometer. Life (Basel) 2022; 12:life12050675. [PMID: 35629343 PMCID: PMC9145923 DOI: 10.3390/life12050675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Revised: 04/12/2022] [Accepted: 04/29/2022] [Indexed: 11/16/2022] Open
Abstract
Understanding protein functions requires not only static but also dynamic structural information. Incoherent quasi-elastic neutron scattering (QENS), which utilizes the highly incoherent scattering ability of hydrogen, is a powerful technique for revealing the dynamics of proteins in deuterium oxide (D2O) buffer solutions. The background scattering of sample cells suitable for aqueous protein solution samples, conducted with a neutron backscattering spectrometer, was evaluated. It was found that the scattering intensity of an aluminum sample cell coated with boehmite using D2O was lower than that of a sample cell coated with regular water (H2O). The D2O-Boehmite coated cell was used for the QENS measurement of a 0.8 wt.% aqueous solution of an intrinsically disordered protein in an intrinsically disordered region of a helicase-associated endonuclease for a fork-structured type of DNA. The cell was inert against aqueous samples at 283–363 K. In addition, meticulous attention to cells with small individual weight differences and the positional reproducibility of the sample cell relative to the spectrometer neutron beam position enabled the accurate subtraction of the scattering profiles of the D2O buffer and the sample container. Consequently, high-quality information on protein dynamics could be extracted from dilute protein solutions.
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Affiliation(s)
- Taiki Tominaga
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Ibaraki 319-1106, Japan;
- Correspondence:
| | - Hiroshi Nakagawa
- Materials Sciences Research Center, Japan Atomic Energy Agency, Ibaraki 319-1195, Japan;
- J-PARC Center, Japan Atomic Energy Agency, Ibaraki 319-1195, Japan
| | - Masae Sahara
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society (CROSS), 162-1 Shirakata, Ibaraki 319-1106, Japan;
| | - Takashi Oda
- Department of Life Science, Rikkyo University, Nishi-Ikebukuro, Toshima-ku, Tokyo 171-8501, Japan;
| | - Rintaro Inoue
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan; (R.I.); (M.S.)
| | - Masaaki Sugiyama
- Institute for Integrated Radiation and Nuclear Science, Kyoto University, Kumatori, Sennan-gun, Osaka 590-0494, Japan; (R.I.); (M.S.)
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Tavagnacco L, Chiessi E, Zanatta M, Orecchini A, Zaccarelli E. Water-Polymer Coupling Induces a Dynamical Transition in Microgels. J Phys Chem Lett 2019; 10:870-876. [PMID: 30735054 PMCID: PMC6416711 DOI: 10.1021/acs.jpclett.9b00190] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.
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Affiliation(s)
- Letizia Tavagnacco
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| | - Ester Chiessi
- Department
of Chemical Sciences and Technologies, University
of Rome Tor Vergata, Via della Ricerca Scientica I, 00133 Rome, Italy
| | - Marco Zanatta
- Department
of Computer Science, University of Verona, Strada Le Grazie 15, 37138 Verona, Italy
| | - Andrea Orecchini
- Department
of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM
c/o Department of Physics and Geology, University
of Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
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5
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Zhang M, Wei D, Tang M, Shi C, Cui HL, Du C. Molecular dynamics simulations of conformation and chain length dependent terahertz spectra of alanine polypeptides. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1059429] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Schmidt M, Saldin DK. Enzyme transient state kinetics in crystal and solution from the perspective of a time-resolved crystallographer. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2014; 1:024701. [PMID: 26798774 PMCID: PMC4711602 DOI: 10.1063/1.4869472] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/13/2014] [Indexed: 05/29/2023]
Abstract
With recent technological advances at synchrotrons [Graber et al., J. Synchrotron Radiat. 18, 658-670 (2011)], it is feasible to rapidly collect time-resolved crystallographic data at multiple temperature settings [Schmidt et al., Acta Crystallogr. D 69, 2534-2542 (2013)], from which barriers of activation can be extracted. With the advent of fourth generation X-ray sources, new opportunities emerge to investigate structure and dynamics of biological macromolecules in real time [M. Schmidt, Adv. Condens. Matter Phys. 2013, 1-10] in crystals and potentially from single molecules in random orientation in solution [Poon et al., Adv. Condens. Matter Phys. 2013, 750371]. Kinetic data from time-resolved experiments on short time-scales must be interpreted in terms of chemical kinetics [Steinfeld et al., Chemical Kinetics and Dynamics, 2nd ed. (Prentience Hall, 1985)] and tied to existing time-resolved experiments on longer time-scales [Schmidt et al., Acta Crystallogr. D 69, 2534-2542 (2013); Jung et al., Nat. Chem. 5, 212-220 (2013)]. With this article, we will review and outline steps that are required to routinely determine the energetics of reactions in biomolecules in crystal and solution with newest X-ray sources. In eight sections, we aim to describe concepts and experimental details that may help to inspire new approaches to collect and interpret these data.
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Affiliation(s)
- Marius Schmidt
- Physics Department, University of Wisconsin , Milwaukee, Wisconsin 53211, USA
| | - Dilano K Saldin
- Physics Department, University of Wisconsin , Milwaukee, Wisconsin 53211, USA
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7
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Miao Y, Yi Z, Glass DC, Hong L, Tyagi M, Baudry J, Jain N, Smith JC. Temperature-Dependent Dynamical Transitions of Different Classes of Amino Acid Residue in a Globular Protein. J Am Chem Soc 2012; 134:19576-9. [DOI: 10.1021/ja3097898] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yinglong Miao
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Zheng Yi
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Dennis C. Glass
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Graduate School of Genome Science
and Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Liang Hong
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg,
Maryland 20899, United States
- Department of Materials Science, University of Maryland, College Park, Maryland 20742,
United States
| | - Jerome Baudry
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Nitin Jain
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Jeremy C. Smith
- University of Tennessee/Oak
Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee
37831, United States
- Department
of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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Yi Z, Miao Y, Baudry J, Jain N, Smith JC. Derivation of mean-square displacements for protein dynamics from elastic incoherent neutron scattering. J Phys Chem B 2012; 116:5028-36. [PMID: 22471396 DOI: 10.1021/jp2102868] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The derivation of mean-square displacements from elastic incoherent neutron scattering (EINS) of proteins is examined, with the aid of experiments on camphor-bound cytochrome P450cam and complementary molecular dynamics simulations. It is shown that a q(4) correction to the elastic incoherent structure factor (where q is the scattering vector) can be simply used to reliably estimate from the experiment both the average mean-square atomic displacement, <Δr(2)> of the nonexchanged hydrogen atoms in the protein and its variance, σ(2). The molecular dynamics simulation results are in broad agreement with the experimentally derived <Δr(2)> and σ(2) derived from EINS on instruments at two different energy resolutions, corresponding to dynamics on the ∼100 ps and ∼1 ns time scales. Significant dynamical heterogeneity is found to arise from methyl-group rotations. The easy-to-apply q(4) correction extends the information extracted from elastic incoherent neutron scattering experiments and should be of wide applicability.
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Affiliation(s)
- Zheng Yi
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics , P.O. Box 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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GLOBUS T, WOOLARD D, BYKHOVSKAIA M, GELMONT B, WERBOS L, SAMUELS A. THZ-FREQUENCY SPECTROSCOPIC SENSING OF DNA AND RELATED BIOLOGICAL MATERIALS. ACTA ACUST UNITED AC 2011. [DOI: 10.1142/s0129156403002083] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The terahertz frequency absorption spectra of DNA molecules reflect low-frequency internal helical vibrations involving rigidly bound subgroups that are connected by the weakest bonds, including the hydrogen bonds of the DNA base pairs, and/or non-bonded interactions. Although numerous difficulties make the direct identification of terahertz phonon modes in biological materials very challenging, recent studies have shown that such measurements are both possible and useful. Spectra of different DNA samples reveal a large number of modes and a reasonable level of sequence-specific uniqueness. This chapter utilizes computational methods for normal mode analysis and theoretical spectroscopy to predict the low-frequency vibrational absorption spectra of short artificial DNA and RNA. Here the experimental technique is described in detail, including the procedure for sample preparation. Careful attention was paid to the possibility of interference or etalon effects in the samples, and phenomena were clearly differentiated from the actual phonon modes. The results from Fourier-transform infrared spectroscopy of DNA macromolecules and related biological materials in the terahertz frequency range are presented. In addition, a strong anisotropy of terahertz characteristics is demonstrated. Detailed tests of the ability of normal mode analysis to reproduce RNA vibrational spectra are also conducted. A direct comparison demonstrates a correlation between calculated and experimentally observed spectra of the RNA polymers, thus confirming that the fundamental physical nature of the observed resonance structure is caused by the internal vibration modes in the macromolecules. Application of artificial neural network analysis for recognition and discrimination between different DNA molecules is discussed.
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Affiliation(s)
- T. GLOBUS
- Dept. of Electrical and Computer Engineering, UVA, Charlottesville, VA, USA
| | - D. WOOLARD
- U.S. Army Research Laboratory, ARO, Research Triangle Park, NC, USA
| | - M. BYKHOVSKAIA
- Dept. of Biological Sciences, Lehigh University, Bethlehem, PA, USA
| | - B. GELMONT
- Dept. of Electrical and Computer Engineering, UVA, Charlottesville, VA, USA
| | | | - A. SAMUELS
- Edgewood Chemical and Biological Center, Aberdeen Proving Ground, MD, USA
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10
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Vural D, Glyde HR. Vibrational dynamics of hydrogen in proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:031922. [PMID: 21517538 DOI: 10.1103/physreve.83.031922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2010] [Revised: 11/01/2010] [Indexed: 05/30/2023]
Abstract
Biological macromolecules expand with increasing temperature and this dynamic expansion is associated with the onset of function. The expansion is typically characterized by the mean square vibrational displacement (MSD), <u²> of specific constituents such as hydrogen within the macromolecules. The <u²> increases with increasing temperature and the slope of <u²> versus temperature can increase significantly at a temperature T{D} identified as a dynamical transition. We illustrate that the observed expansion and change in slope of <u²> with temperature at T{D} can be reproduced within a simple model of the vibration, an atom in an anharmonic potential, V(u). Given V(u), only the temperature is varied in the model. A simple Gaussian potential or a potential containing a hard wall is particularly effective is reproducing the observed change in the slope of <u²> with temperature around T{D}.
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Affiliation(s)
- Derya Vural
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716-2570, USA
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11
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Leu BM, Zhang Y, Bu L, Straub JE, Zhao J, Sturhahn W, Alp EE, Sage JT. Resilience of the iron environment in heme proteins. Biophys J 2008; 95:5874-89. [PMID: 18835904 PMCID: PMC2599821 DOI: 10.1529/biophysj.108.138198] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2008] [Accepted: 07/22/2008] [Indexed: 11/18/2022] Open
Abstract
Conformational flexibility is essential to the functional behavior of proteins. We use an effective force constant introduced by Zaccai, the resilience, to quantify this flexibility. Site-selective experimental and computational methods allow us to determine the resilience of heme protein active sites. The vibrational density of states of the heme Fe determined using nuclear resonance vibrational spectroscopy provides a direct experimental measure of the resilience of the Fe environment, which we compare quantitatively with values derived from the temperature dependence of atomic mean-squared displacements in molecular dynamics simulations. Vibrational normal modes in the THz frequency range dominate the resilience. Both experimental and computational methods find a higher resilience for cytochrome c than for myoglobin, which we attribute to the increased number of covalent links to the peptide in the former protein. For myoglobin, the resilience of the iron environment is larger than the average resilience previously determined for hydrogen sites using neutron scattering. Experimental results suggest a slightly reduced resilience for cytochrome c upon oxidation, although the change is smaller than reported in previous Mössbauer investigations on a bacterial cytochrome c, and is not reproduced by the simulations. Oxidation state also has no significant influence on the compressibility calculated for cyt c, although a slightly larger compressibility is predicted for myoglobin.
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Affiliation(s)
- Bogdan M Leu
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts, USA
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12
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Kamerzell TJ, Russell Middaugh C. The Complex Inter-Relationships Between Protein Flexibility and Stability. J Pharm Sci 2008; 97:3494-517. [DOI: 10.1002/jps.21269] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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13
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A physical picture of protein dynamics and conformational changes. J Biol Phys 2008; 33:371-87. [PMID: 19669525 DOI: 10.1007/s10867-008-9102-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Accepted: 06/25/2008] [Indexed: 10/21/2022] Open
Abstract
A physical model is reviewed which explains different aspects of protein dynamics consistently. At low temperatures, the molecules are frozen in conformational substates. Their average energy is 3/2RT. Solid-state vibrations occur on a time scale of femtoseconds to nanoseconds. Above a characteristic temperature, often called the dynamical transition temperature, slow modes of motions can be observed occurring on a time scale between about 140 and 1 ns. These motions are overdamped, quasidiffusive, and involve collective motions of segments of the size of an alpha-helix. Molecules performing these types of motion are in the "flexible state". This state is reached by thermal activation. It is shown that these motions are essential for conformational relaxation. Based on this picture, a new approach is proposed to understand conformational changes. It connects structural fluctuations and conformational transitions.
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14
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Ngai KL, Capaccioli S, Shinyashiki N. The Protein “Glass” Transition and the Role of the Solvent. J Phys Chem B 2008; 112:3826-32. [DOI: 10.1021/jp710462e] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. L. Ngai
- Naval Research Laboratory, Washington, DC, 20375-5320, Dipartimento di Fisica, Università di Pisa, Largo B. Pontecorvo 3, I-56127, Pisa, Italy, and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127, Pisa, Italy, and Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
| | - S. Capaccioli
- Naval Research Laboratory, Washington, DC, 20375-5320, Dipartimento di Fisica, Università di Pisa, Largo B. Pontecorvo 3, I-56127, Pisa, Italy, and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127, Pisa, Italy, and Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
| | - N. Shinyashiki
- Naval Research Laboratory, Washington, DC, 20375-5320, Dipartimento di Fisica, Università di Pisa, Largo B. Pontecorvo 3, I-56127, Pisa, Italy, and polyLab, CNR-INFM, Largo B. Pontecorvo 3, I-56127, Pisa, Italy, and Department of Physics, Tokai University, Hiratsuka, Kanagawa 259-1292, Japan
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Rai BK, Prohofsky EW, Durbin SM. Single-atom test of all-atom empirical potentials: Fe in myoglobin. J Phys Chem B 2007; 109:18983-7. [PMID: 16853444 DOI: 10.1021/jp052950i] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The measured Fe vibrational density of states in deoxy-myoglobin, obtained from nuclear resonance vibrational spectroscopy, is compared to results from a normal-mode analysis using an all-atom empirical potential. Substantial disagreement reveals that for this one atom, the empirical potential does not accurately describe the actual forces. A Green function technique is developed to calculate the iron vibrational spectrum of deoxy-myoglobin by coupling the independently calculated heme and globin normal modes; nonbonded interactions between the heme molecule and the protein are essential for a good fit to the measurements. A projection of the eigenvectors from this potential onto the displacements induced by binding of CO demonstrates that normal modes over a broad range centered around 50-150 cm(-1) may drive the ligand-induced structural changes.
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Affiliation(s)
- Brajesh K Rai
- Department of Physics, Purdue University, West Lafayette, Indiana 47907, USA
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16
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Vetri V, Librizzi F, Militello V, Leone M. Effects of succinylation on thermal induced amyloid formation in Concanavalin A. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:733-41. [PMID: 17554534 DOI: 10.1007/s00249-007-0181-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 04/24/2007] [Accepted: 05/07/2007] [Indexed: 10/23/2022]
Abstract
We have recently shown that upon slight thermal destabilization the legume lectin Concanavalin A may undergo two different aggregation processes, leading, respectively, to amyloid fibrils at high pH and amorphous aggregates at low pH. Here we present an experimental study on the amyloid aggregation of Succinyl Concanavalin A, which is a dimeric active variant of Concanavalin. The results show that, as for the native protein, the fibrillation process appears to be favoured by alkaline pH, far from the isoelectric point of the protein. Moreover, it strongly depends on temperature and requires large conformational changes both at secondary and tertiary structure level. With respect to the native protein, the succinyl derivative forms amyloid fibrils in considerably longer times and with a minor exposure of hydrophobic regions. At physiological conditions, Concanavalin A still displays a sizeable tendency to form amyloid fibril, while the succinyl variant does not. A close correlation was observed between the progress of amyloid formation and a narrowing of the tryptophans fluorescence emission band, indicating a reduction of protein conformational heterogeneity in amyloid fibrils.
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Affiliation(s)
- Valeria Vetri
- Dipartimento di Scienze Fisiche e Astronomiche, Università di Palermo, Via Archirafi 36, Palermo, Italy.
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17
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Adams KL, Tsoi S, Yan J, Durbin SM, Ramdas AK, Cramer WA, Sturhahn W, Alp EE, Schulz C. Fe vibrational spectroscopy of myoglobin and cytochrome f. J Phys Chem B 2006; 110:530-6. [PMID: 16471565 DOI: 10.1021/jp053440r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Fe vibrational density of states (VDOS) has been determined for the heme proteins deoxymyoglobin, metmyoglobin, and cytochrome f in the oxidized and reduced states, using nuclear resonance vibrational spectroscopy (NRVS). For cytochrome f in particular, the NRVS spectrum is compared with multiwavelength resonance Raman spectra to identify those Raman modes with significant Fe displacement. Modes not seen by Raman due to optical selection rules appear in the NRVS spectrum. The mean Fe force constant extracted from the VDOS illustrates how Fe dynamics varies among these four monoheme proteins, and is correlated with oxidation and spin state trends seen in model heme compounds. The protein's contribution to Fe motion is dominant at low frequencies, where coupling to the backbone tightly constrains Fe displacements in cytochrome f, in contrast to enhanced heme flexibility in myoglobin.
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Affiliation(s)
- Kristl L Adams
- Department of Physics, Purdue University, West Lafayette, Indiana 47907, USA
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18
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Starovoitova V, Budarz TE, Wyllie GRA, Scheidt WR, Sturhahn W, Alp EE, Prohofsky EW, Durbin SM. Vibrational spectroscopy and normal-mode analysis of Fe(II) octaethylporphyrin. J Phys Chem B 2006; 110:13277-82. [PMID: 16805642 PMCID: PMC1525052 DOI: 10.1021/jp060345p] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The normal-mode spectrum for the four-coordinated heme compound Fe(II) octaethylporphyrin, Fe(OEP), has been determined by refining force constants to the experimental Fe vibrational density of states measured with nuclear resonance vibrational spectroscopy (NRVS). Convergence of the calculated spectrum to the data was achieved by first imposing D4 symmetry on the model structure as well as the force constants, progressively including different internal coordinates of motion, then allowing the true Ci (or S2) point group symmetry of the C(i)1 Fe(OEP) crystal structure. The NRVS-refined normal modes are in good agreement with Raman and IR spectra at high frequencies. Prior density functional theory predictions for a model porphyrin are similar to the core modes computed with the best-fit force field, but significant differences between D4 and Ci modes underline the sensitivity of porphyrin Fe normal modes to structural details. Some differences between the Ci best fit and the NRVS data can be attributed to intermolecular contacts not included in the normal-mode analysis.
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19
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Caronna C, Natali F, Cupane A. Incoherent elastic and quasi-elastic neutron scattering investigation of hemoglobin dynamics. Biophys Chem 2005; 116:219-25. [PMID: 15908102 DOI: 10.1016/j.bpc.2005.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2005] [Accepted: 02/17/2005] [Indexed: 11/24/2022]
Abstract
In this work we investigate the dynamic properties of hemoglobin in glycerolD(8)/D(2)O solution using incoherent elastic (ENS) and quasi-elastic (QENS) neutron scattering. Taking advantage of complementary energy resolutions of backscattering spectrometers at ILL (Grenoble), we explore motions in a large space-time window, up to 1 ns and 14 A; moreover, in order to cover the harmonic and anharmonic protein dynamics regimes, the elastic experiments have been performed over the wide temperature interval of 20-300 K. To study the dependence of the measured dynamics upon the protein quaternary structure, both deoxyhemoglobin (in T quaternary conformation) and carbonmonoxyhemoglobin (in R quaternary conformation) have been investigated. From the ENS data the mean square displacements of the non-exchangeable hydrogen atoms of the protein and their temperature dependence are obtained. In agreement with previous results on hydrated powders, a dynamical transition at about 220 K is detected. The results show interesting differences between the two hemoglobin quaternary conformations, the T-state protein appearing more rigid and performing faster motions than the R-state one; however, these differences involve motions occurring in the nanosecond time scale and are not detected when only faster atomic motions in the time scale up to 100 ps are investigated. The QENS results put in evidence a relevant Lorentzian quasi-elastic contribution. Analysis of the dependence of the Elastic Incoherent Structure Factor (EISF) and of the Lorentzian halfwidth upon the momentum transfer suggests that the above quasi-elastic contribution arises from the diffusion inside a confined space, values of confinement radius and local diffusion coefficient being compatible with motions of hydrogen atoms of the amino acid side chains. When averaged over the whole range of momentum transfer the QENS data put in evidence differences between deoxy and carbonmonoxy hemoglobin and confirm the quaternary structure dependence of the protein dynamics in the nanosecond time scale.
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Affiliation(s)
- Chiara Caronna
- INFM OGG & CRS-SOFT, 6 rue Jules Horowitz, BP 156-38042 Grenoble Cedex 9, France
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20
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Cupane A, Cammarata M, Cordone L, Leone M, Vitrano E, Engler N, Parak F. Spectral broadening of the Soret band in myoglobin: an interpretation by the full spectrum of low-frequency modes from a normal modes analysis. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2005; 34:881-9. [PMID: 16215751 DOI: 10.1007/s00249-004-0458-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2004] [Revised: 12/09/2004] [Accepted: 12/17/2004] [Indexed: 11/28/2022]
Abstract
In this work the temperature dependence of the Soret band line shape in carbon-monoxy myoglobin is re-analyzed by using both the full correlator approach in the time domain and the frequency domain approach. The new analyses exploit the full density of vibrational states of carbon-monoxy myoglobin available from normal modes analysis, and avoid the artificial division of the entire set of vibrational modes coupled to the Soret transition into "high-frequency" and "low-frequency" subsets; the frequency domain analysis, however, makes use of the so-called short-times approximation, while the time domain one avoids it. Time domain and frequency domain analyses give very similar results, thus supporting the applicability of the short-times approximation to the analysis of hemeprotein spectra; in particular, they clearly indicate the presence of spectral heterogeneity in the Soret band of carbon-monoxy myoglobin. The analyses also show that a temperature dependence of the Gaussian width parameter steeper than the hyperbolic cotangent law predicted by the Einstein harmonic oscillator and/or a temperature dependence of inhomogeneous broadening are not sufficient to obtain quantitative information on the magnitude of an-harmonic contributions to the iron-heme plane motion. However, the dependence of the previous two quantities may be used to obtain semiquantitative information on the overall coupling of the Soret transition to the low-frequency modes and therefore on the dynamic properties of the heme pocket in different states of the protein.
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Affiliation(s)
- Antonio Cupane
- Istituto Nazionale per la Fisica della Materia (INFM), Dipartimento di Scienze Fisiche e Astronomiche dell'Università, Via Archirafi 36, 90123 Palermo, Italy.
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21
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Curtis JE, Tarek M, Tobias DJ. Methyl group dynamics as a probe of the protein dynamical transition. J Am Chem Soc 2005; 126:15928-9. [PMID: 15584703 DOI: 10.1021/ja0480623] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrated proteins undergo a dynamical transition around 200 K from glasslike to liquidlike motion. Molecular dynamics simulations have been used to study the temperature dependence of the dynamics of ribonuclease A in the hydrated crystal, a model dehydrated powder, and aqueous solution. Changes in the dynamics accompanying the transition throughout the protein have been quantified in terms of the mean-squared fluctuations (MSFs) of methyl hydrogen atoms on the 100 ps time scale. In solution at 300 K the MSFs span a broad distribution, consistent with NMR relaxation measurements. The MSF distribution in the hydrated crystal at 300 K is qualitatively similar to the solution result, except for a slight shift to lower values, and dehydration results in a dramatic shift of the MSFs to lower values. As the temperature is lowered, the whole distribution of methyl group fluctuations in the hydrated crystal shifts to lower values. Most of the methyl groups in the hydrated protein display a nonlinear temperature dependence with a dynamical transition at approximately 200 K, but most methyl groups do not undergo a transition in the dehydrated protein. We conclude that the dynamical transition occurs throughout most of the protein and that solvent is required for the transition.
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Affiliation(s)
- Joseph E Curtis
- NIST Center for Neutron Research, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, USA
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22
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23
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Cao ZW, Xue Y, Han LY, Xie B, Zhou H, Zheng CJ, Lin HH, Chen YZ. MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids. Nucleic Acids Res 2004; 32:W679-85. [PMID: 15215475 PMCID: PMC441522 DOI: 10.1093/nar/gkh384] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Analysis of vibrational motions and thermal fluctuational dynamics is a widely used approach for studying structural, dynamic and functional properties of proteins and nucleic acids. Development of a freely accessible web server for computation of vibrational and thermal fluctuational dynamics of biomolecules is thus useful for facilitating the relevant studies. We have developed a computer program for computing vibrational normal modes and thermal fluctuational properties of proteins and nucleic acids and applied it in several studies. In our program, vibrational normal modes are computed by using modified AMBER molecular mechanics force fields, and thermal fluctuational properties are computed by means of a self-consistent harmonic approximation method. A web version of our program, MoViES (Molecular Vibrations Evaluation Server), was set up to facilitate the use of our program to study vibrational dynamics of proteins and nucleic acids. This software was tested on selected proteins, which show that the computed normal modes and thermal fluctuational bond disruption probabilities are consistent with experimental findings and other normal mode computations. MoViES can be accessed at http://ang.cz3.nus.edu.sg/cgi-bin/prog/norm.pl.
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Affiliation(s)
- Z W Cao
- Department of Computational Science, National University of Singapore, Blk SOC1, Level 7, 3 Science Drive 2, Singapore 117543, Singapore
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24
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Zhang C, Tarhan E, Ramdas AK, Weiner AM, Durbin SM. Broadened Far-Infrared Absorption Spectra for Hydrated and Dehydrated Myoglobin. J Phys Chem B 2004. [DOI: 10.1021/jp049933y] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Chenfeng Zhang
- Department of Physics and School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907
| | - Enver Tarhan
- Department of Physics and School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907
| | - A. K. Ramdas
- Department of Physics and School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907
| | - A. M. Weiner
- Department of Physics and School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907
| | - Stephen M. Durbin
- Department of Physics and School of Electrical and Computer Engineering, Purdue University, West Lafayette, Indiana 47907
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25
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Santangelo MG, Levantino M, Vitrano E, Cupane A. Ferricytochrome c encapsulated in silica hydrogels: correlation between active site dynamics and solvent structure. Biophys Chem 2003; 103:99-107. [PMID: 12568933 DOI: 10.1016/s0301-4622(02)00246-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ferricytochrome c encapsulated in silica hydrogels has been prepared by the sol-gel technique following, with some modifications, the procedure originally developed by Zink et al. A suitable preparation of hydrogels enables to have both 'wet' and 'dry' samples. Wet samples have a high water content: as the temperature is lowered below approximately 260 K water freezes and the samples crack. On the contrary, dry samples have a low water content (hydration h approximately 0.35): in these conditions water does not freeze even at cryogenic temperatures and the samples remain transparent and non-cracking. The dynamics of ferricytochrome c and its dependence on the surrounding medium have been studied by optical absorption spectroscopy in the temperature range 10-300 K. At each temperature, spectra were collected both in the Soret region and in the near infrared at approximately 1.45 microm (the water overtone band); this enables to probe the local dynamics of the protein active site as well as the 'structure' of water molecules present in the sample. The data show that sol-gel encapsulation 'per se' does not alter the protein active site dynamics, but rather introduces an increased local heterogeneity. At difference, we find a correlation between active site dynamics and water structure: in the wet hydrogel, freezing of water quenches the ensemble of soft modes linearly coupled to the Soret transition; while, in the dry hydrogel, water does not freeze, and an active site dynamic behavior-similar to the non-freezing water/glycerol solution-is observed.
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Affiliation(s)
- Maria Grazia Santangelo
- National Institute for the Physics of Matter (INFM) and Department of Physical and Astronomical Sciences (DSFA), University of Palermo, via Archirafi 36, I-90123 Palermo, Italy
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26
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Santangelo MG, Levantino M, Vitrano E, Cupane A. Ferricytochrome c encapsulated in silica hydrogels: correlation between active site dynamics and solvent structure. Biophys Chem 2003; 103:67-75. [PMID: 12504255 DOI: 10.1016/s0301-4622(02)00235-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Ferricytochrome c encapsulated in silica hydrogels has been prepared by the sol-gel technique following, with some modifications, the procedure originally developed by Ellerby et al. (Science 255 1113 (1992)). A suitable preparation of hydrogels enables having both 'wet' and 'dry' samples. Wet samples have a high water content: as the temperature is lowered below approximately 260 K, water freezes and the samples crack. On the contrary, dry samples have a low water content (hydration h approximately equal 0.35): in these conditions water does not freeze even at cryogenic temperatures and the samples remain transparent and non-cracking. The dynamics of ferricytochrome c and its dependence on the surrounding medium have been studied by optical absorption spectroscopy in the temperature range 10-300 K. At each temperature, spectra were collected both in the Soret region and in the near infrared at approximately 1.45 microm (the water overtone band); this enables probing the local dynamics of the protein active site as well as the 'structure' of water molecules present in the sample. The data show that sol-gel encapsulation 'per se' does not alter the protein active site dynamics, but rather introduces an increased local heterogeneity. We find a correlation between active site dynamics and water structure: in the wet hydrogel, freezing of water quenches the ensemble of soft modes linearly coupled to the Soret transition; while, in the dry hydrogel, water does not freeze and an active site dynamic behavior--similar to the non-freezing water/glycerol solution--is observed.
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Affiliation(s)
- Maria Grazia Santangelo
- National Institute for the Physics of Matter and Department of Physical and Astronomical Sciences, University of Palermo, via Archirafi 36, I-90123, Palermo, Italy
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27
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Cao ZW, Chen X, Chen YZ. Correlation between normal modes in the 20-200 cm-1 frequency range and localized torsion motions related to certain collective motions in proteins. J Mol Graph Model 2003; 21:309-19. [PMID: 12479929 DOI: 10.1016/s1093-3263(02)00185-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
In certain biologically relevant collective motions, such as protein domain motions and sub-domain motions, large amplitude movements are localized in one or a few flexible regions consisting of a small number of residues. This paper explores the possible use of normal mode analysis in probing localized vibrational torsion motions in these flexible regions that may be related to certain collective motions. The normal modes of 10 structures of five proteins in different conformation (TRP repressor, calmodulin, calbindin D(9k), HIV-1 protease and troponin C), known to have shear or hinge domain or sub-domain motion, respectively, are analyzed. Our study identifies, for each structure, unique normal modes in the 20-200 cm-1 frequency range, whose corresponding motions are primarily concentrated in the region where large amplitude torsion movements of a known domain or sub-domain motion occur. This suggests possible correlation between normal modes at 20-200 cm-1 frequency range and initial fluctuational motions leading to localized collective motions in proteins, and thus the potential application of normal mode analysis in facilitating the study of biologically important localized motions in biomolecules.
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Affiliation(s)
- Z W Cao
- Department of Computational Science, National University of Singapore, 3 Science Drive 2, Singapore 117543, Singapore
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28
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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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29
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Militello V, Leone M, Cupane A, Santucci R, Desideri A. Local dynamic properties of the heme pocket in native and solvent-induced molten-globule-like states of cytochrome c. Biophys Chem 2002; 97:121-8. [PMID: 12050004 DOI: 10.1016/s0301-4622(02)00044-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We report the Soret absorption band, down to cryogenic temperature, of native and molten-globule-like state of horse heart cytochrome c. The band profile is analyzed in terms of vibronic coupling of the heme normal modes to the electronic transition in the framework of the Franck-Condon approximation. From the temperature dependence of the Gaussian broadening and of the peak position, we obtain information on the 'bath' of low frequency harmonic motions of the heme group within the heme pocket. The reported data indicate that, compared to the native state, the less rigid tertiary structure of the molten globule is reflected in a higher flexibility of the heme pocket and in greater conformational disorder, allowing the transduction of large-amplitude motion of the protein to the dynamics of the heme pocket.
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Affiliation(s)
- V Militello
- Istituto Nazionale per la Fisica della Materia and Dipartimento di Medicina Sperimentale, University of Palermo, Corso Tukory 129, Palermo, Italy.
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30
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Achterhold K, Keppler C, Ostermann A, van Bürck U, Sturhahn W, Alp EE, Parak FG. Vibrational dynamics of myoglobin determined by the phonon-assisted Mössbauer effect. PHYSICAL REVIEW E 2002; 65:051916. [PMID: 12059602 DOI: 10.1103/physreve.65.051916] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2001] [Indexed: 11/07/2022]
Abstract
The phonon-assisted Mössbauer effect is used to determine the partial phonon density of states of the iron within the active center of deoxymyoglobin, carboxymyoglobin, and dry and wet metmyoglobin between 40 and 300 K. Between 0 and 1 meV the iron density of states increases quadratically with the energy, as in a Debye solid. Mean sound velocities are extracted from this slope. Between 1 and 3 meV a nearly quadratic "Debye-like" increase follows due to the similar strength of intermolecular and intramolecular forces. Above 3 meV, optical vibrations are characteristic for the iron-ligand conformation. The overall mean square displacements of the heme iron atom obtained from the density of states agree well with the values of Mössbauer absorption experiments below 180 K. In the physiological temperature regime the data confirm the existence of harmonic vibrations in addition to the protein specific dynamics measured by Mössbauer absorption. In the Debye energy regime the mean square displacement of the iron is in agreement with that of the hydrogens measured by incoherent neutron scattering demonstrating the global character of these modes. At higher energies the vibration of the heavy iron atom at 33 meV in metmyoglobin is as large as that of the lightweight hydrogens at that energy. A freeze dried, rehydrated (h=0.38 g H2O/g protein) metmyoglobin sample shows an excess of states above the Debye law between 1 and 3 meV, similar to neutron scattering experiments. The room temperature density of states below 3 meV exhibit an increase of the density compared to the low temperature data, which can be interpreted as mode softening.
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Affiliation(s)
- K Achterhold
- Physik-Department E17, Technische Universität München, 85747 Garching, Germany
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31
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Franzen S. Carbonmonoxy Rebinding Kinetics in H93G Myoglobin: Separation of Proximal and Distal Side Effects. J Phys Chem B 2002. [DOI: 10.1021/jp015567w] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695
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32
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Jung C. Cytochrome P-450-CO and substrates: lessons from ligand binding under high pressure. BIOCHIMICA ET BIOPHYSICA ACTA 2002; 1595:309-28. [PMID: 11983405 DOI: 10.1016/s0167-4838(01)00353-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An overview of the application of high-pressure studies on the carbon monoxide complex of cytochrome P-450 is given. Different approaches to characterize ligand binding steps, the conformational states and substates and the compressibility of the ligand-bound complex are reviewed. A particular focus is the effect of substrates on these properties. It is shown that substrate mobility, compressibility and water accessibility are interrelated and may have functional meaning.
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Affiliation(s)
- Christiane Jung
- Max-Delbrück-Center for Molecular Medicine, Protein Dynamics Laboratory, Berlin, Germany.
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33
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Kaposi AD, Vanderkooi JM, Wright WW, Fidy J, Stavrov SS. Influence of static and dynamic disorder on the visible and infrared absorption spectra of carbonmonoxy horseradish peroxidase. Biophys J 2001; 81:3472-82. [PMID: 11721008 PMCID: PMC1301802 DOI: 10.1016/s0006-3495(01)75978-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Spectroscopy of horseradish peroxidase with and without the substrate analog, benzohydroxamic acid, was monitored in a glycerol/water solvent as a function of temperature. It was determined from the water infrared (IR) absorption that the solvent has a glass transition at 170-180 K. In the absence of substrate, both the heme optical Q(0,0) absorption band and the IR absorption band of CO bound to heme broaden markedly upon heating from 10-300 K. The Q(0,0) band broadens smoothly in the whole temperature interval, whereas the IR bandwidth is constant in the glassy matrix and increases from 7 to 16 cm(-1) upon heating above the glass transition. Binding of substrate strongly diminishes temperature broadening of both the bands. The results are consistent with the view that the substrate strongly reduces the amplitude of motions of amino acids forming the heme pocket. The main contribution to the Q(0,0) bandwidth arises from the heme vibrations that are not affected by the phase transition. The CO band thermal broadening stems from the anharmonic coupling with motions of the heme environment, which, in the glassy state, are frozen in. Unusually strong temperature broadening of the CO band is interpreted to be caused by thermal population of a very flexible excited conformational substrate. Analysis of literature data on the thermal broadening of the A(0) band of Mb(CO) (Ansari et al., 1987. Biophys. Chem. 26:337-355) shows that such a state presents itself also in myoglobin.
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Affiliation(s)
- A D Kaposi
- Institute of Biophysics and Radiation Biology, Semmelweis University of Medicine, Budapest H-1088, Hungary
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34
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Palmer AG. Nmr probes of molecular dynamics: overview and comparison with other techniques. ANNUAL REVIEW OF BIOPHYSICS AND BIOMOLECULAR STRUCTURE 2001; 30:129-55. [PMID: 11340055 DOI: 10.1146/annurev.biophys.30.1.129] [Citation(s) in RCA: 250] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
NMR spin relaxation spectroscopy is a powerful approach for characterizing intramolecular and overall rotational motions in proteins. This review describes experimental methods for measuring laboratory frame spin relaxation rate constants by high-resolution solution-state NMR spectroscopy, together with theoretical approaches for interpreting spin relaxation data in order to quantify protein conformational dynamics on picosecond-nanosecond time scales. Recent applications of these techniques to proteins are surveyed, and investigations of the contribution of conformational chain entropy to protein function are highlighted. Insights into the dynamical properties of proteins obtained from NMR spin relaxation spectroscopy are compared with results derived from other experimental and theoretical techniques.
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Affiliation(s)
- A G Palmer
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10027, USA.
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35
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Sage JT, Durbin SM, Sturhahn W, Wharton DC, Champion PM, Hession P, Sutter J, Alp EE. Long-range reactive dynamics in myoglobin. PHYSICAL REVIEW LETTERS 2001; 86:4966-4969. [PMID: 11384393 DOI: 10.1103/physrevlett.86.4966] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/1999] [Indexed: 05/23/2023]
Abstract
We report the complete vibrational spectrum of the probe nucleus 57Fe at the oxygen-binding site of the protein myoglobin. The Fe-pyrrole nitrogen stretching modes of the heme group, identified here, probe asymmetric interactions with the protein environment. Collective oscillations of the polypeptide, rather than localized heme vibrations, dominate the low frequency region. We conclude that the heme "doming" mode is significantly delocalized, so that distant sites respond to oxygen binding on vibrational time scales. This has ramifications for understanding long-range interactions in biomolecules, such as those that mediate cooperativity in allosteric proteins.
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Affiliation(s)
- J T Sage
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
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36
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Cottone G, Cordone L, Ciccotti G. Molecular dynamics simulation of carboxy-myoglobin embedded in a trehalose-water matrix. Biophys J 2001; 80:931-8. [PMID: 11159460 PMCID: PMC1301291 DOI: 10.1016/s0006-3495(01)76072-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
We report on a molecular dynamics (MD) simulation of carboxy-myoglobin (MbCO) embedded in a water-trehalose system. The mean square fluctuations of protein atoms, calculated at different temperatures in the 100-300 K range, are compared with those from a previous MD simulation on an H2O-solvated MbCO and with experimental data from Mössbauer spectroscopy and incoherent elastic neutron scattering on trehalose-coated MbCO. The results show that, for almost all the atomic classes, the amplitude of the nonharmonic motions stemming from the interconversion among the protein's conformational substates is reduced with respect to the H2O-solvated system, and their onset is shifted toward higher temperature. Moreover, our simulation shows that, at 300 K, the heme performs confined diffusive motions as a whole, leaving the underlying harmonic vibrations unaltered.
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Affiliation(s)
- G Cottone
- INFM and Physics Department, University of Rome La Sapienza, 00185 Rome, Italy
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37
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38
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Réat V, Dunn R, Ferrand M, Finney JL, Daniel RM, Smith JC. Solvent dependence of dynamic transitions in protein solutions. Proc Natl Acad Sci U S A 2000; 97:9961-6. [PMID: 10963663 PMCID: PMC27638 DOI: 10.1073/pnas.97.18.9961] [Citation(s) in RCA: 104] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2000] [Indexed: 11/18/2022] Open
Abstract
A transition as a function of increasing temperature from harmonic to anharmonic dynamics has been observed in globular proteins by using spectroscopic, scattering, and computer simulation techniques. We present here results of a dynamic neutron scattering analysis of the solvent dependence of the picosecond-time scale dynamic transition behavior of solutions of a simple single-subunit enzyme, xylanase. The protein is examined in powder form, in D(2)O, and in four two-component perdeuterated single-phase cryosolvents in which it is active and stable. The scattering profiles of the mixed solvent systems in the absence of protein are also determined. The general features of the dynamic transition behavior of the protein solutions follow those of the solvents. The dynamic transition in all of the mixed cryosolvent-protein systems is much more gradual than in pure D(2)O, consistent with a distribution of energy barriers. The differences between the dynamic behaviors of the various cryosolvent protein solutions themselves are remarkably small. The results are consistent with a picture in which the picosecond-time scale atomic dynamics respond strongly to melting of pure water solvent but are relatively invariant in cryosolvents of differing compositions and melting points.
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Affiliation(s)
- V Réat
- Department of Physics and Astronomy, University College London, Gower Street, London WCIE, 6BT, England
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39
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Schweitzer-Stenner R, Cupane A, Leone M, Lemke C, Schott J, Dreybrodt W. Anharmonic Protein Motions and Heme Deformations in Myoglobin Cyanide Probed by Absorption and Resonance Raman Spectroscopy. J Phys Chem B 2000. [DOI: 10.1021/jp991599w] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Reinhard Schweitzer-Stenner
- FB1−Institut für Experimentelle Physik, Universität Bremen, 28359 Bremen, Germany, Department of Chemistry, University of Puerto Rico, P.O. Box 23346, San Juan, PR00931, USA, and Istituto Nazionale di Fisica della Materia and Dipartimento di Scienze Fisiche e Astronomiche, Universita di' Palermo, 90123 Palermo, Italy
| | - Antonio Cupane
- FB1−Institut für Experimentelle Physik, Universität Bremen, 28359 Bremen, Germany, Department of Chemistry, University of Puerto Rico, P.O. Box 23346, San Juan, PR00931, USA, and Istituto Nazionale di Fisica della Materia and Dipartimento di Scienze Fisiche e Astronomiche, Universita di' Palermo, 90123 Palermo, Italy
| | - Maurizio Leone
- FB1−Institut für Experimentelle Physik, Universität Bremen, 28359 Bremen, Germany, Department of Chemistry, University of Puerto Rico, P.O. Box 23346, San Juan, PR00931, USA, and Istituto Nazionale di Fisica della Materia and Dipartimento di Scienze Fisiche e Astronomiche, Universita di' Palermo, 90123 Palermo, Italy
| | - Christina Lemke
- FB1−Institut für Experimentelle Physik, Universität Bremen, 28359 Bremen, Germany, Department of Chemistry, University of Puerto Rico, P.O. Box 23346, San Juan, PR00931, USA, and Istituto Nazionale di Fisica della Materia and Dipartimento di Scienze Fisiche e Astronomiche, Universita di' Palermo, 90123 Palermo, Italy
| | - Joachim Schott
- FB1−Institut für Experimentelle Physik, Universität Bremen, 28359 Bremen, Germany, Department of Chemistry, University of Puerto Rico, P.O. Box 23346, San Juan, PR00931, USA, and Istituto Nazionale di Fisica della Materia and Dipartimento di Scienze Fisiche e Astronomiche, Universita di' Palermo, 90123 Palermo, Italy
| | - Wolfgang Dreybrodt
- FB1−Institut für Experimentelle Physik, Universität Bremen, 28359 Bremen, Germany, Department of Chemistry, University of Puerto Rico, P.O. Box 23346, San Juan, PR00931, USA, and Istituto Nazionale di Fisica della Materia and Dipartimento di Scienze Fisiche e Astronomiche, Universita di' Palermo, 90123 Palermo, Italy
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40
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Engler N, Ostermann A, Gassmann A, Lamb DC, Prusakov VE, Schott J, Schweitzer-Stenner R, Parak FG. Protein dynamics in an intermediate state of myoglobin: optical absorption, resonance Raman spectroscopy, and x-ray structure analysis. Biophys J 2000; 78:2081-92. [PMID: 10733986 PMCID: PMC1300800 DOI: 10.1016/s0006-3495(00)76755-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
A metastable state of myoglobin is produced by reduction of metmyoglobin at low temperatures. This is done either by irradiation with x-rays at 80 K or by electron transfer from photoexcited tris(2, 2'-bipyridine)-ruthenium(II) at 20 K. At temperatures above 150 K, the conformational transition toward the equilibrium deoxymyoglobin is observed. X-ray crystallography, Raman spectroscopy, and temperature-dependent optical absorption spectroscopy show that the metastable state has a six-ligated iron low-spin center. The x-ray structure at 115K proves the similarity of the metastable state with metmyoglobin. The Raman spectra yield the high-frequency vibronic modes and give additional information about the distortion of the heme. Analysis of the temperature dependence of the line shape of the Soret band reveals that a relaxation within the metastable state starts at approximately 120 K. Parameters representative of static properties of the intermediate state are close to those of CO-ligated myoglobin, while parameters representative of dynamics are close to deoxymyoglobin. Thus within the metastable state the relaxation to the equilibrium is initiated by changes in the dynamic properties of the active site.
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Affiliation(s)
- N Engler
- Physik-Department E17, Technische Universität München, 85747 Garching, Germany
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41
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Bitler A, Stavrov SS. Iron-histidine resonance Raman band of deoxyheme proteins: effects of anharmonic coupling and glass-liquid phase transition. Biophys J 1999; 77:2764-76. [PMID: 10545375 PMCID: PMC1300549 DOI: 10.1016/s0006-3495(99)77109-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Weak anharmonic coupling of two soft molecular vibrations is shown to cause pronounced temperature dependence of the corresponding resonance Raman bands. The developed theory is used to interpret the temperature dependence of the iron-histidine band of deoxyheme proteins and model compounds. It is shown that anharmonic coupling of the iron-histidine and heme doming vibrations must cause pronounced broadening of the band, its asymmetry, and shift of its maximum to the red upon heating. It also can lead to a structured shape of this band at room temperature. Proper consideration of the anharmonic coupling allows simulation of the temperature dependence of the iron-histidine band shape of horse heart myoglobin in the temperature interval of 10-300 K, using the minimum number of necessary parameters. Analysis of this temperature dependence clearly shows that the iron-histidine band of deoxyheme proteins is sensitive to the glass-liquid phase transition in the protein hydration shell, which takes place at 160-190 K.
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Affiliation(s)
- A Bitler
- Department of Physiology and Pharmacology, Tel Aviv University, Ramat Aviv, Tel Aviv 69978, Israel
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42
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Daniel RM, Finney JL, Réat V, Dunn R, Ferrand M, Smith JC. Enzyme dynamics and activity: time-scale dependence of dynamical transitions in glutamate dehydrogenase solution. Biophys J 1999; 77:2184-90. [PMID: 10512837 PMCID: PMC1300498 DOI: 10.1016/s0006-3495(99)77058-x] [Citation(s) in RCA: 79] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
We have examined the temperature dependence of motions in a cryosolution of the enzyme glutamate dehydrogenase (GDH) and compared these with activity. Dynamic neutron scattering was performed with two instruments of different energy resolution, permitting the separate determination of the average dynamical mean square displacements on the sub-approximately 100 ps and sub-approximately 5 ns time scales. The results demonstrate a marked dependence on the time scale of the temperature profile of the mean square displacement. The lowest temperature at which anharmonic motion is observed is heavily dependent on the time window of the instrument used to observe the dynamics. Several dynamical transitions (inflexions of the mean squared displacement) are observed in the slower dynamics. Comparison with the temperature profile of the activity of the enzyme in the same solvent reveals dynamical transitions that have no effect on GDH function.
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Affiliation(s)
- R M Daniel
- Department of Biological Sciences, The University of Waikato, Hamilton, New Zealand.
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43
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Librizzi F, Vitrano E, Cordone L. Dehydration and crystallization of trehalose and sucrose glasses containing carbonmonoxy-myoglobin. Biophys J 1999; 76:2727-34. [PMID: 10233087 PMCID: PMC1300242 DOI: 10.1016/s0006-3495(99)77425-4] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We report a study wherein we contemporarily measured 1) the dehydration process of trehalose or sucrose glasses embedding carbonmonoxy-myoglobin (MbCO) and 2) the evolution of the A substates in saccharide-coated MbCO. Our results indicate that microcrystallization processes, sizeably different in the two saccharides, take place during dehydration; moreover, the microcrystalline structure is maintained unless the dry samples are equilibrated with a humidity >/=75% (>/=60%) at 25 degrees C for the trehalose (sucrose) sample. The evolution of the parameters that characterize the A substates of MbCO indicates that 1) the effects of water withdrawal are analogous in samples dried in the presence or in the absence of sugars, although much larger effects are observed in the samples without sugar; 2) the distribution of A substates is determined by the overall matrix structure and not only by the sample water content; and 3) the population of A0 substate (i. e., the substate currently put in relation with MbCO molecules having the distal histidine out of the heme pocket) is largely enhanced during the dehydration process. However, after rehumidification its population is largely decreased with respect to the values obtained, at similar water content, during the first dehydration run.
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Affiliation(s)
- F Librizzi
- Dipartimento di Scienze Fisiche ed Astronomiche, Università di Palermo and Istituto Nazionale di Fisica della Materia, 90123 Palermo, Italy
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44
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Cordone L, Ferrand M, Vitrano E, Zaccai G. Harmonic behavior of trehalose-coated carbon-monoxy-myoglobin at high temperature. Biophys J 1999; 76:1043-7. [PMID: 9916036 PMCID: PMC1300054 DOI: 10.1016/s0006-3495(99)77269-3] [Citation(s) in RCA: 198] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Embedding biostructures in saccharide glasses protects them against extreme dehydration and/or exposure to very high temperature. Among the saccharides, trehalose appears to be the most effective bioprotectant. In this paper we report on the low-frequency dynamics of carbon monoxy myoglobin in an extremely dry trehalose glass measured by neutron spectroscopy. Under these conditions, the mean square displacements and the density of state function are those of a harmonic solid, up to room temperature, in contrast to D2O-hydrated myoglobin, in which a dynamical transition to a nonharmonic regime has been observed at approximately 180 K (Doster et al., 1989. Nature. 337:754-756). The protective effect of trehalose is correlated, therefore, with a trapping of the protein in a harmonic potential, even at relatively high temperature.
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Affiliation(s)
- L Cordone
- Dipartimento di Scienze Fisiche ed Astronomiche dell'Universita di Palermo and Istituto Nazionale di Fisica della Materia, 90123 Palermo, Italy.
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45
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46
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Lichtenegger H, Doster W, Kleinert T, Birk A, Sepiol B, Vogl G. Heme-solvent coupling: a Mössbauer study of myoglobin in sucrose. Biophys J 1999; 76:414-22. [PMID: 9876153 PMCID: PMC1302530 DOI: 10.1016/s0006-3495(99)77208-5] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
Abstract
The Mössbauer effect of 57Fe-enriched samples was used to investigate the coupling of 80% sucrose/water, a protein-stabilizing solvent, to vibrational and diffusive modes of the heme iron of CO-myoglobin. For comparison we also determined the Mössbauer spectra of K4 57Fe (CN)6 (potassium ferrocyanide, PFC), where the iron is fully exposed in the same solvent. The temperature dependence of the Mössbauer parameters derived for the two samples proved to be remarkably similar, indicative of a strong coupling of the main heme displacements to the viscoelastic relaxation of the solvent. We show that CO escape out of the heme pocket couples to the same type of fluctuations, whereas intramolecular bond formation involves solvent-decoupled heme deformation modes that are less prominent in the Mössbauer spectrum. With respect to other solvents, however, sucrose shows a reduced viscosity effect on heme displacements and the kinetics of ligand binding due to preferential hydration of the protein. This result confirms thermodynamic predictions of the stabilizing action of sucrose by a dynamic method.
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Affiliation(s)
- H Lichtenegger
- Institut für Materialphysik, Universität Wien, 1090 Wien, Austria
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47
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Falconi M, Desideri A, Cupane A, Leone M, Ciccotti G, Peterson ES, Friedman JM, Gambacurta A, Ascoli F. Structural and dynamic properties of the homodimeric hemoglobin from Scapharca inaequivalvis Thr-72-->Ile mutant: molecular dynamics simulation, low temperature visible absorption spectroscopy, and resonance Raman spectroscopy studies. Biophys J 1998; 75:2489-503. [PMID: 9788944 PMCID: PMC1299923 DOI: 10.1016/s0006-3495(98)77693-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Molecular dynamics simulations, low temperature visible absorption spectroscopy, and resonance Raman spectroscopy have been performed on a mutant of the Scapharca inaequivalvis homodimeric hemoglobin, where residue threonine 72, at the subunit interface, has been substituted by isoleucine. Molecular dynamics simulation indicates that in the Thr-72-->Ile mutant several residues that have been shown to play a role in ligand binding fluctuate around orientations and distances similar to those observed in the x-ray structure of the CO derivative of the native hemoglobin, although the overall structure remains in the T state. Visible absorption spectroscopy data indicate that in the deoxy form the Soret band is less asymmetric in the mutant than in the native protein, suggesting a more planar heme structure; moreover, these data suggest a similar heme-solvent interaction in both the liganded and unliganded states of the mutant protein, at variance with that observed in the native protein. The "conformation sensitive" band III of the deoxy mutant protein is shifted to lower energy by >100 cm-1 with respect to the native one, about one-half of that observed in the low temperature photoproducts of both proteins, indicating a less polar or more hydrophobic heme environment. Resonance Raman spectroscopy data show a slight shift of the iron-proximal histidine stretching mode of the deoxy mutant toward lower frequency with respect to the native protein, which can be interpreted in terms of either a change in packing of the phenyl ring of Phe-97, as also observed from the simulation, or a loss of water in the heme pocket. In line with this latter interpretation, the number of water molecules that dynamically enters the intersubunit interface, as calculated by the molecular dynamics simulation, is lower in the mutant than in the native protein. The 10-ns photoproduct for the carbonmonoxy mutant derivative has a higher iron-proximal histidine stretching frequency than does the native protein. This suggests a subnanosecond relaxation that is slowed in the mutant, consistent with a stabilization of the R structure. Taken together, the molecular dynamics and the spectroscopic data indicate that the higher oxygen affinity displayed by the Thr-72-->Ile mutant is mainly due to a local perturbation in the dimer interface that propagates to the heme region, perturbing the polarity of the heme environment and propionate interactions. These changes are consistent with a destabilization of the T state and a stabilization of the R state in the mutant relative to the native protein.
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Affiliation(s)
- M Falconi
- Department of Biology and INFM, University of Rome "Tor Vergata," 00133 Roma, Italy
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48
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Garbers A, Reifarth F, Kurreck J, Renger G, Parak F. Correlation between protein flexibility and electron transfer from QA-* to QB in PSII membrane fragments from spinach. Biochemistry 1998; 37:11399-404. [PMID: 9708974 DOI: 10.1021/bi980296+] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To analyze a possible correlation between the extent of QA-* reoxidation and protein dynamics, fluorometric and Mössbauer spectroscopic measurements were performed in photosystem II membrane fragments from spinach. Numerical evaluation of the flash-induced change of the normalized fluorescence quantum yield revealed that the extent of reoxidation starts to decrease below 275 K and is almost completely suppressed at 230 K. Detailed analyses of Mössbauer spectra measured at different temperatures in 57Fe-enriched material indicate that the onset of fluctuations between conformational substates of the protein matrix occurs also at around 230 K. Based on this correspondence, protein flexibility is inferred to play a key role for QA-* reoxidation in photosystem II. Taking into account the striking similarities with purple bacteria and the latest structural information on these reaction centers [Stowell, M. H. B., McPhillips, T. M., Rees, D. C., Soltis, S. M., Abresch, E., and Feher, G. (1997) Science 276, 812-816], it appears most plausible that also the headgroup of plastoquinone-9 bound to the QB-site in PSII requires a structural reorientation for its reduction to the semiquinone.
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Affiliation(s)
- A Garbers
- Physik Department, Technische Universität München, Garching, Germany
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49
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Cupane A, Leone M, Unger E, Lemke C, Beck M, Dreybrodt W, Schweitzer-Stenner R. Dynamics of Various Metal-Octaethylporphyrins in Solution Studied by Resonance Raman and Low-Temperature Optical Absorption Spectroscopies. Role of the Central Metal. J Phys Chem B 1998. [DOI: 10.1021/jp980362h] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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50
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Réat V, Patzelt H, Ferrand M, Pfister C, Oesterhelt D, Zaccai G. Dynamics of different functional parts of bacteriorhodopsin: H-2H labeling and neutron scattering. Proc Natl Acad Sci U S A 1998; 95:4970-5. [PMID: 9560212 PMCID: PMC20197 DOI: 10.1073/pnas.95.9.4970] [Citation(s) in RCA: 129] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
We show that dynamics of specific amino acids within a protein can be characterized by neutron spectroscopy and hydrogen-deuterium labeling, and we present data on the motions of a selected set of groups within bacteriorhodopsin (BR), the retinal-based proton pump in the purple membrane of halophilic Archaea. Elastic incoherent neutron scattering experiments allow the definition of motions in the nano- to picosecond time scale and have revealed a dynamical transition from a harmonic to a softer, anharmonic atomic fluctuation regime in the global behavior of proteins. Biological activity in proteins is correlated with this transition, suggesting that flexibility is required for function. Elastic incoherent neutron scattering is dominated by H atom scattering, and to study the dynamics of a selected part of BR, fully deuterated purple membrane with BR containing H-retinal, H-tryptophan, and H-methionine was prepared biosynthetically in Halobacterium salinarum. These amino acids cluster in the functional center of the protein. In contrast to the protein globally, the thermal motions of the labeled atoms were found to be shielded from solvent melting effects at 260 K. Above this temperature, the labeled groups appear as more rigid than the rest of the protein, with a significantly smaller mean square amplitude of motion. These experimental results quantify the dynamical heterogeneity of BR (which meets the functional requirements of global flexibility), on the one hand, to allow large conformational changes in the molecule and of a more rigid region in the protein, on the other, to control stereo-specific selection of retinal conformations.
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Affiliation(s)
- V Réat
- Institut de Biologie Structurale Commissariat à l'Energie Atomique-Centre National de la Recherche Scientifique, 41 Avenue des Martyrs, F-38027 Grenoble Cedex 1, France
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