1
|
Rastogi H, Chowdhury PK. Correlating the Local and Global Dynamics of an Enzyme in the Crowded Milieu. J Phys Chem B 2022; 126:3208-3223. [PMID: 35442681 DOI: 10.1021/acs.jpcb.1c09759] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Enzymes are dynamic biological macromolecules, with their catalytic function(s) being largely influenced by the changes in local fluctuations of amino acid side chains as well as global structural modulations that the enzyme undergoes. Such local and global motions can be highly affected inside the crowded physiological interior of the cell. Here, we have addressed the role of dynamic structural flexibility in affecting the activation energy barrier of a flexible multidomain enzyme adenylate kinase (AK3L1, UniProtKB: Q9UIJ7). Activation energy profiles of both local (at three different sites along the polypeptide backbone) and global dynamics of the enzyme have been monitored using solvation studies on the subnanosecond time scale and tryptophan quenching studies over the temperature range of 278-323 K, respectively, under crowded conditions (Ficoll 70, Dextran 40, Dextran 70, and PEG 8). This study not only provides the site-specific mapping of dynamics but reveals that the activation energies associated with these local motions undergo a significant decrease in the presence of macromolecular crowders, providing new insights into how crowding affects internal protein dynamics. The crowded scenario also aids in enhancing the coupling between the local and global motions of the enzyme. Moreover, select portions/regions of the enzyme when taken together can well mirror the overall dynamics of the biomolecule, showing possible energy hotspots along the polypeptide backbone.
Collapse
Affiliation(s)
- Harshita Rastogi
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India 110016
| | - Pramit K Chowdhury
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi, India 110016
| |
Collapse
|
2
|
Katava M, Stirnemann G, Pachetti M, Capaccioli S, Paciaroni A, Sterpone F. Specific Interactions and Environment Flexibility Tune Protein Stability under Extreme Crowding. J Phys Chem B 2021; 125:6103-6111. [PMID: 34100611 DOI: 10.1021/acs.jpcb.1c01511] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Macromolecular crowding influences protein mobility and stability in vivo. A precise description of the crowding effect on protein thermal stability requires the estimate of the combined effects of excluded volume, specific protein-environment interactions, as well as the thermal response of the crowders. Here, we explore an ideal model system, the lysozyme protein in powder state, to dissect the factors controlling the melting of the protein under extreme crowding. By deploying state-of-the art molecular simulations, supported by calorimetric experiments, we assess the role of the environment flexibility and of intermolecular electrostatic interactions. In particular, we show that the temperature-dependent flexibility of the macromolecular crowders, along with specific interactions, significantly alleviates the stabilizing contributions of the static volume effect.
Collapse
Affiliation(s)
- Marina Katava
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Guillaume Stirnemann
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Maria Pachetti
- Elettra-Sincrotrone Trieste, S.S. 14 km 163.5, Area Science Park, 34149 Trieste, Italy.,Department of Physics, University of Trieste, Via Valerio 2, 34127 Trieste, Italy
| | - Simone Capaccioli
- Dipartimento di Fisica, Universitá di Pisa, largo Pontecorvo 3, 56127 Pisa, Italy.,CISUP, Centro per l'Integrazione della Strumentazione dell'Università di Pisa, Lungarno Pacinotti 43, I-56127 Pisa, Italy
| | - Alessandro Paciaroni
- Dipartimento di Fisica e Geologia, Universitá di Perugia, via A. Pascoli, 06123 Perugia, Italy
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, Université Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France
| |
Collapse
|
3
|
Golub M, Moldenhauer M, Schmitt FJ, Lohstroh W, Maksimov EG, Friedrich T, Pieper J. Solution Structure and Conformational Flexibility in the Active State of the Orange Carotenoid Protein. Part II: Quasielastic Neutron Scattering. J Phys Chem B 2019; 123:9536-9545. [PMID: 31550157 DOI: 10.1021/acs.jpcb.9b05073] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Orange carotenoid proteins (OCPs), which are protecting cyanobacterial light-harvesting antennae from photodamage, undergo a pronounced structural change upon light absorption. In addition, the active state is anticipated to boost a significantly higher molecular flexibility similar to a "molten globule" state. Here, we used quasielastic neutron scattering to directly characterize the vibrational and conformational molecular dynamics of OCP in its ground and active states, respectively, on the picosecond time scale. At a temperature of 100 K, we observe mainly (vibronic) inelastic features with peak energies at 5 and 6 meV (40 and 48 cm-1, respectively). At physiological temperatures, however, two (Lorentzian) quasielastic components represent localized protein motions, that is, stochastic structural fluctuations of protein side chains between various conformational substates of the protein. Global diffusion of OCP is not observed on the given time scale. The slower Lorentzian component is affected by illumination and can be well-characterized by a jump-diffusion model. While the jump diffusion constant D is (2.82 ± 0.01) × 10-5 cm2/s at 300 K in the ground state, it is increased by ∼20% to (3.48 ± 0.01) × 10-5 cm2/s in the active state, revealing a strong enhancement of molecular mobility. The increased mobility is also reflected in the average atomic mean square displacement ⟨u2⟩; we determine a ⟨u2⟩ of 1.47 ± 0.05 Å in the ground state, but 1.86 ± 0.05 Å in the active state (at 300 K). This effect is assigned to two factors: (i) the elongated structure of the active state with two widely separated protein domains is characterized by a larger number of surface residues with a concomitantly higher degree of motional freedom and (ii) a larger number of hydration water molecules bound at the surface of the protein. We thus conclude that the active state of the orange carotenoid protein displays an enhanced conformational dynamics. The higher degree of flexibility may provide additional channels for nonradiative decay so that harmful excess energy can be more efficiently converted to heat.
Collapse
Affiliation(s)
- Maksym Golub
- Institute of Physics , University of Tartu , 50411 Tartu , Estonia
| | - Marcus Moldenhauer
- Technische Universität Berlin , Institute of Chemistry, Physical Chemistry , 10623 Berlin , Germany
| | - Franz-Josef Schmitt
- Technische Universität Berlin , Institute of Chemistry, Physical Chemistry , 10623 Berlin , Germany
| | - Wiebke Lohstroh
- Heinz Maier-Leibnitz Zentrum , Technische Universität München , Garching , Germany
| | - Eugene G Maksimov
- Department of Biophysics , M. V. Lomonosov Moscow State University , Moscow , Russia
| | - Thomas Friedrich
- Technische Universität Berlin , Institute of Chemistry, Physical Chemistry , 10623 Berlin , Germany
| | - Jörg Pieper
- Institute of Physics , University of Tartu , 50411 Tartu , Estonia
| |
Collapse
|
4
|
Golub M, Rusevich L, Irrgang KD, Pieper J. Rigid versus Flexible Protein Matrix: Light-Harvesting Complex II Exhibits a Temperature-Dependent Phonon Spectral Density. J Phys Chem B 2018; 122:7111-7121. [DOI: 10.1021/acs.jpcb.8b02948] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Maksym Golub
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| | - Leonid Rusevich
- Institute of Physical Energetics, Krivu 11, LV-1006 Riga, Latvia
- Institute of Solid State Physics, University of Latvia, Kengaraga 8, LV-1063 Riga, Latvia
| | - Klaus-Dieter Irrgang
- Department of Life Science & Technology, Laboratory of Biochemistry, University for Applied Sciences, 10318 Berlin, Germany
| | - Jörg Pieper
- Institute of Physics, University of Tartu, W. Ostwaldi 1, 50411 Tartu, Estonia
| |
Collapse
|
5
|
Biswas R, Bagchi B. Anomalous water dynamics at surfaces and interfaces: synergistic effects of confinement and surface interactions. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2018; 30:013001. [PMID: 29205175 DOI: 10.1088/1361-648x/aa9b1d] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
In nature, water is often found in contact with surfaces that are extended on the scale of molecule size but small on a macroscopic scale. Examples include lipid bilayers and reverse micelles as well as biomolecules like proteins, DNA and zeolites, to name a few. While the presence of surfaces and interfaces interrupts the continuous hydrogen bond network of liquid water, confinement on a mesoscopic scale introduces new features. Even when extended on a molecular scale, natural and biological surfaces often have features (like charge, hydrophobicity) that vary on the scale of the molecular diameter of water. As a result, many new and exotic features, which are not seen in the bulk, appear in the dynamics of water close to the surface. These different behaviors bear the signature of both water-surface interactions and of confinement. In other words, the altered properties are the result of the synergistic effects of surface-water interactions and confinement. Ultrafast spectroscopy, theoretical modeling and computer simulations together form powerful synergistic approaches towards an understanding of the properties of confined water in such systems as nanocavities, reverse micelles (RMs), water inside and outside biomolecules like proteins and DNA, and also between two hydrophobic walls. We shall review the experimental results and place them in the context of theory and simulations. For water confined within RMs, we discuss the possible interference effects propagating from opposite surfaces. Similar interference is found to give rise to an effective attractive force between two hydrophobic surfaces immersed and kept fixed at a separation of d, with the force showing an exponential dependence on this distance. For protein and DNA hydration, we shall examine a multitude of timescales that arise from frustration effects due to the inherent heterogeneity of these surfaces. We pay particular attention to the role of orientational correlations and modification of the same due to interaction with the surfaces.
Collapse
|
6
|
Mamontov E, O'Neill H. Microscopic relaxations in a protein sustained down to 160K in a non-glass forming organic solvent. Biochim Biophys Acta Gen Subj 2016; 1861:3513-3519. [PMID: 27154287 DOI: 10.1016/j.bbagen.2016.04.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 04/24/2016] [Accepted: 04/25/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND We have studied microscopic dynamics of a protein in carbon disulfide, a non-glass forming solvent, down to its freezing temperature of ca. 160K. METHODS We have utilized quasielastic neutron scattering. RESULTS A comparison of lysozyme hydrated with water and dissolved in carbon disulfide reveals a stark difference in the temperature dependence of the protein's microscopic relaxation dynamics induced by the solvent. In the case of hydration water, the common protein glass-forming solvent, the protein relaxation slows down in response to a large increase in the water viscosity on cooling down, exhibiting a well-known protein dynamical transition. The dynamical transition disappears in non-glass forming carbon disulfide, whose viscosity remains a weak function of temperature all the way down to freezing at just below 160K. The microscopic relaxation dynamics of lysozyme dissolved in carbon disulfide is sustained down to the freezing temperature of its solvent at a rate similar to that measured at ambient temperature. CONCLUSIONS Our results demonstrate that protein dynamical transition is not merely solvent-assisted, but rather solvent-induced, or, more precisely, is a reflection of the temperature dependence of the solvent's glass-forming dynamics. GENERAL SIGNIFICANCE We hypothesize that, if the long debated idea regarding the direct link between the microscopic relaxations and the biological activity in proteins is correct, then not only the microscopic relaxations, but also the activity, could be sustained in proteins all the way down to the freezing temperature of a non-glass forming solvent with a weak temperature dependence of its viscosity. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
Collapse
Affiliation(s)
- E Mamontov
- Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States.
| | - H O'Neill
- Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| |
Collapse
|
7
|
Malferrari M, Francia F, Venturoli G. Retardation of Protein Dynamics by Trehalose in Dehydrated Systems of Photosynthetic Reaction Centers. Insights from Electron Transfer and Thermal Denaturation Kinetics. J Phys Chem B 2015; 119:13600-18. [DOI: 10.1021/acs.jpcb.5b02986] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Malferrari
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Francesco Francia
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
| | - Giovanni Venturoli
- Laboratorio di Biochimica e Biofisica Molecolare, Dipartimento di
Farmacia e Biotecnologie, FaBiT, Università di Bologna, 40126 Bologna, Italy
- Consorzio Nazionale
Interuniversitario per le Scienze Fisiche della Materia (CNISM), c/o
Dipartimento di Fisica, Università di Bologna, 40127 Bologna, Italy
| |
Collapse
|
8
|
Picosecond dynamics in haemoglobin from different species: A quasielastic neutron scattering study. Biochim Biophys Acta Gen Subj 2014; 1840:2989-99. [DOI: 10.1016/j.bbagen.2014.06.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Revised: 06/10/2014] [Accepted: 06/11/2014] [Indexed: 11/22/2022]
|
9
|
Frontzek AV, Strokov SV, Embs JP, Lushnikov SG. Does a dry protein undergo a glass transition? J Phys Chem B 2014; 118:2796-802. [PMID: 24559377 DOI: 10.1021/jp4104905] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Bovine serum albumin (BSA) with extremely low hydration level 0.04, which is usually defined as dry, has been investigated in the temperature range between 200 and 340 K by incoherent inelastic neutron scattering using the neutron time-of-flight spectrometer FOCUS (PSI, Switzerland). Anomalous temperature behavior has been revealed for relaxational and low-frequency vibrational dynamics of BSA in the vicinity of 250 K. The mean-square atomic displacement has been shown to exhibit a change in the slope of temperature dependence near the same temperature. The presented results point out that the glass-like transition occurs in the dry protein.
Collapse
Affiliation(s)
- Anna V Frontzek
- A.F. Ioffe Physical Technical Institute , ul. Politekhnicheskaya 26, 194032 Saint-Petersburg, Russian Federation
| | | | | | | |
Collapse
|
10
|
Nickels JD, García Sakai V, Sokolov AP. Dynamics in Protein Powders on the Nanosecond–Picosecond Time Scale Are Dominated by Localized Motions. J Phys Chem B 2013; 117:11548-55. [DOI: 10.1021/jp4058884] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jonathan D. Nickels
- Joint
Institute for Neutron Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee 37831, United States
- Department
of Chemistry, University of Tennessee, 552 Buehler Hall, Knoxville, Tennessee 37996, United States
| | - Victoria García Sakai
- ISIS Neutron and Muon Facility, Science & Technology Facilities Council, Rutherford Appleton Laboratory, Didcot, OX11 0QX, United Kingdom
| | - Alexei P. Sokolov
- Joint
Institute for Neutron Sciences, Oak Ridge National Lab, Oak Ridge, Tennessee 37831, United States
- Department
of Chemistry, University of Tennessee, 552 Buehler Hall, Knoxville, Tennessee 37996, United States
| |
Collapse
|
11
|
Zhao L, Li W, Tian P. Reconciling mediating and slaving roles of water in protein conformational dynamics. PLoS One 2013; 8:e60553. [PMID: 23593243 PMCID: PMC3623917 DOI: 10.1371/journal.pone.0060553] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 02/27/2013] [Indexed: 11/18/2022] Open
Abstract
Proteins accomplish their physiological functions with remarkably organized dynamic transitions among a hierarchical network of conformational substates. Despite the essential contribution of water molecules in shaping functionally important protein dynamics, their exact role is still controversial. Water molecules were reported either as mediators that facilitate or as masters that slave protein dynamics. Since dynamic behaviour of a given protein is ultimately determined by the underlying energy landscape, we systematically analysed protein self energies and protein-water interaction energies obtained from extensive molecular dynamics simulation trajectories of barstar. We found that protein-water interaction energy plays the dominant role when compared with protein self energy, and these two energy terms on average have negative correlation that increases with increasingly longer time scales ranging from 10 femtoseconds to 100 nanoseconds. Water molecules effectively roughen potential energy surface of proteins in the majority part of observed conformational space and smooth in the remaining part. These findings support a scenario wherein water on average slave protein conformational dynamics but facilitate a fraction of transitions among different conformational substates, and reconcile the controversy on the facilitating and slaving roles of water molecules in protein conformational dynamics.
Collapse
Affiliation(s)
- Li Zhao
- College of Life Science, Jilin University, Changchun, China
| | - Wenzhao Li
- College of Life Science, Jilin University, Changchun, China
| | - Pu Tian
- College of Life Science and MOE Key Laboratory of Molecular Enzymology and Engineering, Jilin University, Changchun, China
- * E-mail:
| |
Collapse
|
12
|
GhattyVenkataKrishna PK, Carri GA. The effect of complex solvents on the structure and dynamics of protein solutions: The case of Lysozyme in trehalose/water mixtures. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2013; 36:14. [PMID: 23404569 DOI: 10.1140/epje/i2013-13014-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/15/2012] [Accepted: 01/17/2013] [Indexed: 06/01/2023]
Abstract
We present a Molecular Dynamics simulation study of the effect of trehalose concentration on the structure and dynamics of individual proteins immersed in trehalose/water mixtures. Hen egg-white Lysozyme is used in this study and trehalose concentrations of 0%, 10%, 20%, 30% and 100% by weight are explored. Surprisingly, we have found that changes in trehalose concentration do not change the global structural characteristics of the protein as measured by standard quantities like the mean square deviation, radius of gyration, solvent accessible surface area, inertia tensor and asphericity. Only in the limit of pure trehalose these metrics change significantly. Specifically, we found that the protein is compressed by 2% when immersed in pure trehalose. At the amino acid level there is noticeable rearrangement of the surface residues due to the change in polarity of the surrounding environment with the addition of trehalose. From a dynamic perspective, our computation of the Incoherent Intermediate Scattering Function shows that the protein slows down with increasing trehalose concentration; however, this slowdown is not monotonic. Finally, we also report in-depth results for the hydration layer around the protein including its structure, hydrogen-bonding characteristics and dynamic behavior at different length scales.
Collapse
|
13
|
Pieper J, Trapp M, Skomorokhov A, Natkaniec I, Peters J, Renger G. Temperature-dependent vibrational and conformational dynamics of photosystem II membrane fragments from spinach investigated by elastic and inelastic neutron scattering. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2012; 1817:1213-9. [PMID: 22465855 DOI: 10.1016/j.bbabio.2012.03.020] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Revised: 03/07/2012] [Accepted: 03/16/2012] [Indexed: 11/27/2022]
Abstract
Vibrational and conformational protein dynamics of photosystem II (PS II) membrane fragments from spinach were investigated by elastic and inelastic incoherent neutron scattering (EINS and IINS). As to the EINS experiments, the average atomic mean square displacement values of PS II membrane fragments hydrated at a relative humidity of 57% exhibit a dynamical transition at ~230K. In contrast, the dynamical transition was absent at a relative humidity of 44%. These findings are in agreement with previous studies which reported a "freezing" of protein mobility due to dehydration (Pieper et al. (2008) Eur. Biophys. J. 37: 657-663) and its correlation with an inhibition of electron transfer from Q(A)(-) to Q(B) (Kaminskaya et al. (2003) Biochemistry 42, 8119-8132). IINS spectra of a sample hydrated at a relative humidity of 57% show a distinct Boson peak at ~7.5meV at 20K, which shifts towards lower energy values upon temperature increase to 250K. This unexpected effect is interpreted in terms of a "softening" of the protein matrix along with the onset of conformational protein dynamics as revealed by the EINS experiments. Information on the density of vibrational states of pigment-protein complexes is important for a realistic calculation of excitation energy transfer kinetics and spectral lineshapes and is often routinely obtained by optical line-narrowing spectroscopy at liquid helium temperature. The data presented here demonstrate that IINS is a valuable experimental tool in determining the density of vibrational states not only at cryogenic, but also at nearly physiological temperatures up to 250K. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial.
Collapse
Affiliation(s)
- Jörg Pieper
- Institute of Physics, University of Tartu, Tartu, Estonia.
| | | | | | | | | | | |
Collapse
|
14
|
Laurati M, Sotta P, Long DR, Fillot LA, Arbe A, Alegrı̀a A, Embs JP, Unruh T, Schneider GJ, Colmenero J. Dynamics of Water Absorbed in Polyamides. Macromolecules 2012. [DOI: 10.1021/ma202368x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. Laurati
- Laboratoire Polymères et Matériaux Avancés (LPMA), UMR5268, CNRS and Rhodia, CRTL, 85 Rue des frères Perret, 69192 Saint-Fons, France
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - P. Sotta
- Laboratoire Polymères et Matériaux Avancés (LPMA), UMR5268, CNRS and Rhodia, CRTL, 85 Rue des frères Perret, 69192 Saint-Fons, France
| | - D. R. Long
- Laboratoire Polymères et Matériaux Avancés (LPMA), UMR5268, CNRS and Rhodia, CRTL, 85 Rue des frères Perret, 69192 Saint-Fons, France
| | - L.-A. Fillot
- Laboratoire Polymères et Matériaux Avancés (LPMA), UMR5268, CNRS and Rhodia, CRTL, 85 Rue des frères Perret, 69192 Saint-Fons, France
| | - A. Arbe
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
| | - A. Alegrı̀a
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Departamento de Física
de Materiales, University of the Basque Country (UPV/EHU), Paseo Manuel de Lardizabal 3, E-20018 San Sebastián, Spain
| | - J. P. Embs
- Laboratory for Neutron Scattering, Paul Scherrer Institut, Villigen, Switzerland
| | - T. Unruh
- Forschungsneutronenquelle Heinz Maier-Leibnitz, Lichtenbergstrasse 1, D-85747
Garching, Germany
| | - G. J. Schneider
- Jülich
Centre for Neutron Science at FRM II, Forschungszentrum Jülich
GmbH, Institut für Festkörperforschung, Lichtenbergstrasse 1, D-85747 Garching, Germany
| | - J. Colmenero
- Centro de Física de Materiales (CSIC, UPV/EHU) and Materials Physics Center (MPC), Paseo Manuel de Lardizabal 5, E-20018 San Sebastián, Spain
- Departamento de Física
de Materiales, University of the Basque Country (UPV/EHU), Paseo Manuel de Lardizabal 3, E-20018 San Sebastián, Spain
| |
Collapse
|
15
|
Capponi S, Arbe A, Cerveny S, Busselez R, Frick B, Embs JP, Colmenero J. Quasielastic neutron scattering study of hydrogen motions in an aqueous poly(vinyl methyl ether) solution. J Chem Phys 2011; 134:204906. [PMID: 21639476 DOI: 10.1063/1.3592560] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a quasielastic neutron scattering (QENS) investigation of the component dynamics in an aqueous Poly(vinyl methyl ether) (PVME) solution (30% water content in weight). In the glassy state, an important shift in the Boson peak of PVME is found upon hydration. At higher temperatures, the diffusive-like motions of the components take place with very different characteristic times, revealing a strong dynamic asymmetry that increases with decreasing T. For both components, we observe stretching of the scattering functions with respect to those in the bulk and non-Gaussian behavior in the whole momentum transfer range investigated. To explain these observations we invoke a distribution of mobilities for both components, probably originated from structural heterogeneities. The diffusive-like motion of PVME in solution takes place faster and apparently in a more continuous way than in bulk. We find that the T-dependence of the characteristic relaxation time of water changes at T ≲ 225 K, near the temperature where a crossover from a low temperature Arrhenius to a high temperature cooperative behavior has been observed by broadband dielectric spectroscopy (BDS) [S. Cerveny, J. Colmenero and A. Alegría, Macromolecules, 38, 7056 (2005)]. This observation might be a signature of the onset of confined dynamics of water due to the freezing of the PVME dynamics, that has been selectively followed by these QENS experiments. On the other hand, revisiting the BDS results on this system we could identify an additional "fast" process that can be attributed to water motions coupled with PVME local relaxations that could strongly affect the QENS results. Both kinds of interpretations, confinement effects due to the increasing dynamic asymmetry and influence of localized motions, could provide alternative scenarios to the invoked "strong-to-fragile" transition.
Collapse
Affiliation(s)
- S Capponi
- Donostia International Physics Center, Paseo Manuel de Lardizabal 4, 20018 San Sebastián, Spain.
| | | | | | | | | | | | | |
Collapse
|
16
|
Renger G, Pieper J, Theiss C, Trostmann I, Paulsen H, Renger T, Eichler HJ, Schmitt FJ. Water soluble chlorophyll binding protein of higher plants: a most suitable model system for basic analyses of pigment-pigment and pigment-protein interactions in chlorophyll protein complexes. JOURNAL OF PLANT PHYSIOLOGY 2011; 168:1462-1472. [PMID: 21256622 DOI: 10.1016/j.jplph.2010.12.005] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Revised: 12/08/2010] [Accepted: 12/08/2010] [Indexed: 05/30/2023]
Abstract
This short review paper describes spectroscopic studies on pigment-pigment and pigment-protein interactions of chlorophyll (Chl) a and b bound to the recombinant protein of class IIa water soluble chlorophyll protein (WSCP) from cauliflower. Two Chls form a strongly excitonically coupled open sandwich dimer within the tetrameric protein matrix. In marked contrast to the mode of excitonic coupling of Chl and bacterio-Chl molecules in light harvesting complexes and reaction centers of all photosynthetic organisms, the unique structural pigment array in the Chl dimer of WSCP gives rise to an upper excitonic state with a large oscillator strength. This property opens the way for thorough investigations on exciton relaxation processes in Chl-protein complexes. Lifetime measurements of excited singlet states show that the unusual stability towards photodamage of Chls bound to WSCP, which lack any protective carotenoid molecule, originates from a high diffusion barrier to interaction of molecular dioxygen with Chl triplets. Site selective spectroscopic methods provide a wealth of information on the interactions of the Chls with the protein matrix and on the vibronic structure of the pigments. The presented data and discussions illustrate the great potential of WSCP as a model system for systematic experimental and theoretical studies on the functionalizing of Chls by the protein matrix. It opens the way for further detailed analyses and a deeper understanding of the properties of pigment protein complexes.
Collapse
Affiliation(s)
- G Renger
- Max Volmer Laboratory for Biophysical Chemistry, Berlin Institute of Technology, Berlin, Germany.
| | | | | | | | | | | | | | | |
Collapse
|
17
|
Jankowiak R, Reppert M, Zazubovich V, Pieper J, Reinot T. Site Selective and Single Complex Laser-Based Spectroscopies: A Window on Excited State Electronic Structure, Excitation Energy Transfer, and Electron–Phonon Coupling of Selected Photosynthetic Complexes. Chem Rev 2011; 111:4546-98. [DOI: 10.1021/cr100234j] [Citation(s) in RCA: 122] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ryszard Jankowiak
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Mike Reppert
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Valter Zazubovich
- Department of Physics, Concordia University, Montreal H4B1R6 Quebec, Canada
| | - Jörg Pieper
- Max-Volmer-Laboratories for Biophysical Chemistry, Technical University of Berlin, Germany
- Institute of Physics, University of Tartu, Riia 142, 51014 Tartu, Estonia
| | - Tonu Reinot
- Department of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| |
Collapse
|
18
|
Pieper J, Rätsep M, Trostmann I, Paulsen H, Renger G, Freiberg A. Excitonic Energy Level Structure and Pigment−Protein Interactions in the Recombinant Water-Soluble Chlorophyll Protein. I. Difference Fluorescence Line-Narrowing. J Phys Chem B 2011; 115:4042-52. [DOI: 10.1021/jp111455g] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Pieper
- Max-Volmer-Laboratories for
Biophysical Chemistry, Berlin Institute of Technology, Berlin, Germany
| | - M. Rätsep
- Institute of Physics, University of Tartu, Tartu, Estonia
| | - I. Trostmann
- Institute of General Botany, Johannes Gutenberg University Mainz, Germany
| | - H. Paulsen
- Institute of General Botany, Johannes Gutenberg University Mainz, Germany
| | - G. Renger
- Max-Volmer-Laboratories for
Biophysical Chemistry, Berlin Institute of Technology, Berlin, Germany
| | - A. Freiberg
- Institute of Physics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell
Biology, University of Tartu, Tartu, Estonia
| |
Collapse
|
19
|
Combet S, Zanotti JM, Bellissent-Funel MC. Temperature- and hydration-dependent internal dynamics of stripped human erythrocyte vesicles studied by incoherent neutron scattering. Biochim Biophys Acta Gen Subj 2010; 1810:202-10. [PMID: 21059380 DOI: 10.1016/j.bbagen.2010.10.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Revised: 10/08/2010] [Accepted: 10/26/2010] [Indexed: 11/29/2022]
Abstract
BACKGROUND We focus on temperature- and hydration-dependence of internal molecular motions in stripped human red blood cell (RBC) vesicles, widely used as a model system for more complex biomembranes. METHODS We singled out picosecond local motions of the non-exchangeable hydrogen atoms of RBC vesicles by performing elastic and quasielastic incoherent neutron scattering measurements in dry and heavy water (D₂O)-hydrated RBC powders. RESULTS In dry stripped RBCs, hydrogen motions remained harmonic all along the measured temperature range (100-310K) and mean-square displacements (MSDs) exhibited no temperature transition up to 310K. In contrast, MSDs of hydrated stripped RBCs (h ≈ 0.38g D₂O/g dry powder) exhibited a pronounced transition near 260K, with the sharp rise of anharmonic diffusive motions of hydrogen atoms. This transition at ~260K was correlated with both the onset of nonvibrational (harmonic and nonharmonic) motions and the melting of crystallized hydration water. GENERAL SIGNIFICANCE In conclusion, we have shown that MSDs in human RBC vesicles are temperature-and hydration-dependent. These results provide insight into biomembrane internal dynamics at picosecond timescale and nanometer length scale. Such motions have been shown to act as the "lubricant" of larger conformational changes on a slower, millisecond timescale that are necessary for important biological processes.
Collapse
Affiliation(s)
- S Combet
- Laboratoire Léon-Brillouin, UMR 12 CEA/CNRS, Gif-sur-Yvette Cedex, France.
| | | | | |
Collapse
|
20
|
Kealley C, Sokolova A, Kearley G, Kemner E, Russina M, Faraone A, Hamilton W, Gilbert E. Dynamical transition in a large globular protein: Macroscopic properties and glass transition. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2010; 1804:34-40. [DOI: 10.1016/j.bbapap.2009.06.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2009] [Revised: 06/12/2009] [Accepted: 06/29/2009] [Indexed: 10/20/2022]
|
21
|
Malardier-Jugroot C, Bowron DT, Soper AK, Johnson ME, Head-Gordon T. Structure and water dynamics of aqueous peptide solutions in the presence of co-solvents. Phys Chem Chem Phys 2010; 12:382-92. [DOI: 10.1039/b915346b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
22
|
Pieper J, Renger G. Protein dynamics investigated by neutron scattering. PHOTOSYNTHESIS RESEARCH 2009; 102:281-293. [PMID: 19763874 DOI: 10.1007/s11120-009-9480-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2009] [Accepted: 07/19/2009] [Indexed: 05/28/2023]
Abstract
This contribution describes incoherent quasielastic neutron scattering (QENS) as a suitable tool for investigations of protein dynamics with special emphasis on applications in photosynthesis research. QENS characterizes protein dynamics via the measurement of energy and momentum exchange between sample system and incident low-energy neutrons (1 meV<E<20 meV). This method is especially sensitive for picosecond motions of hydrogen atoms because it makes use of the exceptionally large incoherent neutron scattering cross section of protons and their almost homogeneous distribution in proteins. After a short introduction into the basic principles of neutron scattering, a more detailed description of QENS will be presented including a short overview on instrumentation and theory. Recent QENS results will be discussed for the antenna complex LHC II and PS II membrane fragments. It is shown that diffusive protein dynamics is indispensable for enabling Q(A)(-·) reoxidation by Q(B) at temperatures above 240 K, which explains the strong dependence of this electron transfer step on temperature and hydration level of the sample. Finally, a new laser-QENS pump-probe technique will be introduced which permits in situ monitoring of protein dynamics correlated with a change of the functional state of the sample, i.e. a direct observation of structure-dynamics-function relationships in real time.
Collapse
Affiliation(s)
- Jörg Pieper
- Max-Volmer-Laboratorium für Biophysikalische Chemie, Technische Universität Berlin, Strasse des 17. Juni 135, 10623, Berlin, Germany.
| | | |
Collapse
|
23
|
|
24
|
Jasnin M. Atomic-scale dynamics inside living cells explored by neutron scattering. J R Soc Interface 2009; 6 Suppl 5:S611-7. [PMID: 19586955 DOI: 10.1098/rsif.2009.0144.focus] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Single-particle neutron spectroscopy has contributed important experimental data on molecular dynamics in biological systems. The technique provides information on atomic and molecular motions in macromolecules on the picosecond to the nanosecond time scale, which are essential to biological function. Here, we report on recent neutron measurements performed directly in living cells by using isotope labelling to explore the dynamics of specific cellular components. The paper proposes an integrated view of results on atomic-scale cell water dynamics, internal and global macromolecular motions and solvent isotope effect on macromolecular dynamics. The work established the specific usefulness of the neutron scattering technique to get insight into biologically relevant dynamical features, in particular through comparative measurements. The method developed can now be applied to look for dynamical signatures related to cell characteristics in many different cell types and organelles.
Collapse
Affiliation(s)
- Marion Jasnin
- Institut Laue-Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9, France.
| |
Collapse
|
25
|
Pieper J, Buchsteiner A, Dencher NA, Lechner RE, Hauß T. Light-induced Modulation of Protein Dynamics During the Photocycle of Bacteriorhodopsin. Photochem Photobiol 2009; 85:590-7. [DOI: 10.1111/j.1751-1097.2008.00501.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
26
|
Isaev NP, Dzuba SA. Fast Stochastic Librations and Slow Rotations of Spin Labeled Stearic Acids in a Model Phospholipid Bilayer at Cryogenic Temperatures. J Phys Chem B 2008; 112:13285-91. [DOI: 10.1021/jp805794c] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Nikolay P. Isaev
- Institute of Chemical Kinetics and Combustion, Institutskaya-3, 630090 Novosibirsk, Russia, and Novosibirsk State University, 630090, Pirogova-2, Novosibirsk, Russia
| | - Sergei A. Dzuba
- Institute of Chemical Kinetics and Combustion, Institutskaya-3, 630090 Novosibirsk, Russia, and Novosibirsk State University, 630090, Pirogova-2, Novosibirsk, Russia
| |
Collapse
|
27
|
Surovtsev NV, Salnikov ES, Malinovsky VK, Sveshnikova LL, Dzuba SA. On the Low-Temperature Onset of Molecular Flexibility in Lipid Bilayers Seen by Raman Scattering. J Phys Chem B 2008; 112:12361-5. [DOI: 10.1021/jp801575d] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nikolay V. Surovtsev
- Institute of Automatics and Electrometry, Ak. Koptyuga 1, 630090, Novosibirsk, Russia, Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090, Novosibirsk, Russia, and Institute of Semiconductor Physics, Lavrent’eva 13, 630090, Novosibirsk, Russia
| | - Evgeniy S. Salnikov
- Institute of Automatics and Electrometry, Ak. Koptyuga 1, 630090, Novosibirsk, Russia, Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090, Novosibirsk, Russia, and Institute of Semiconductor Physics, Lavrent’eva 13, 630090, Novosibirsk, Russia
| | - Valeriy K. Malinovsky
- Institute of Automatics and Electrometry, Ak. Koptyuga 1, 630090, Novosibirsk, Russia, Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090, Novosibirsk, Russia, and Institute of Semiconductor Physics, Lavrent’eva 13, 630090, Novosibirsk, Russia
| | - Larisa L. Sveshnikova
- Institute of Automatics and Electrometry, Ak. Koptyuga 1, 630090, Novosibirsk, Russia, Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090, Novosibirsk, Russia, and Institute of Semiconductor Physics, Lavrent’eva 13, 630090, Novosibirsk, Russia
| | - Sergey A. Dzuba
- Institute of Automatics and Electrometry, Ak. Koptyuga 1, 630090, Novosibirsk, Russia, Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia, Institute of Chemical Kinetics and Combustion, Institutskaya 3, 630090, Novosibirsk, Russia, and Institute of Semiconductor Physics, Lavrent’eva 13, 630090, Novosibirsk, Russia
| |
Collapse
|
28
|
Spinozzi F, Ortore MG, Sinibaldi R, Mariani P, Esposito A, Cinelli S, Onori G. Microcalorimetric study of thermal unfolding of lysozyme in water/glycerol mixtures: An analysis by solvent exchange model. J Chem Phys 2008; 129:035101. [DOI: 10.1063/1.2945303] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
|
29
|
Abstract
To understand the effect of hydration on protein dynamics, inelastic neutron-scattering experiments were performed on staphylococcal nuclease samples at differing hydration levels: dehydrated, partially hydrated, and hydrated. At cryogenic temperatures, hydration affected the collective motions with energies lower than 5 meV, whereas the high-energy localized motions were independent of hydration. The prominent change was a shift of boson peak toward higher energy by hydration, suggesting a hardening of harmonic potential at local minima on the energy landscape. The 240 K transition was observed only for the hydrated protein. Significant quasielastic scattering at 300 K was observed only for the hydrated sample, indicating that the origin of the transition is the motion activated by hydration water. The neutron-scattering profile of the partially hydrated sample was quite similar to that of the hydrated sample at 100 K and 200 K, whereas it was close to the dehydrated sample at 300 K, indicating that partial hydration is sufficient to affect the harmonic nature of protein dynamics, and that there is a threshold hydration level to activate anharmonic motions. Thus, hydration water controls both harmonic and anharmonic protein dynamics by differing means.
Collapse
|
30
|
Pieper J, Buchsteiner A, Dencher NA, Lechner RE, Hauss T. Transient protein softening during the working cycle of a molecular machine. PHYSICAL REVIEW LETTERS 2008; 100:228103. [PMID: 18643463 DOI: 10.1103/physrevlett.100.228103] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Indexed: 05/26/2023]
Abstract
Proper functioning of proteins usually requires a certain internal flexibility provided by stochastic structural fluctuations on the picosecond time scale. In contrast with conventional steady-state experiments, we report on a novel type of (laser-neutron) pump-probe experiment combining in situ activation of protein function with a time-dependent test of protein dynamics using quasielastic neutron scattering. A "transient protein softening" is shown to occur during the photocycle of bacteriorhodopsin as a direct proof for the functional significance of protein flexibility.
Collapse
Affiliation(s)
- Jörg Pieper
- Max-Volmer-Laboratories for Biophysical Chemistry, Technische Universität Berlin, Strasse des 17. Juni 135, 10623 Berlin, Germany.
| | | | | | | | | |
Collapse
|
31
|
Abstract
We present direct quasielastic neutron scattering measurements, in vivo, of macromolecular dynamics in Escherichia coli. The experiments were performed on a wide range of timescales to cover the large panel of internal and self-diffusion motions. Three major internal processes were extracted at physiological temperature: a fast picosecond process that corresponded to restricted jump diffusion motions and two slower processes that resulted from reorientational motions occurring in approximately 40 ps and 90 ps, respectively. The analysis of the fast process revealed that the cellular environment leads to an appreciable increase in internal molecular flexibility and diffusive motion rates compared with those evaluated in fully hydrated powders. The result showed that the amount of cell water plays a decisive role in internal molecular dynamics. Macromolecular interactions and confinement, however, attenuate slightly the lubricating effect of water, as revealed by the decrease of the in vivo parameters compared with those measured in solution. The study demonstrated that standard sample preparations do not mimic accurately the physiological environment and suggested that intracellular complexity participates in functional dynamics necessary for biological activity. Furthermore, the method allowed the extraction of the self-diffusion of E. coli macromolecules, which presented similar parameters as those extracted for hemoglobin in red blood cells.
Collapse
|
32
|
The effect of hydration on protein flexibility in photosystem II of green plants studied by quasielastic neutron scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2008; 37:657-63. [PMID: 18351332 DOI: 10.1007/s00249-008-0297-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Revised: 02/14/2008] [Accepted: 02/26/2008] [Indexed: 10/22/2022]
Abstract
The effect of hydration on protein dynamics in photosystem II (PS II) membrane fragments from spinach has been investigated by using the method of quasielastic neutron scattering (QENS) at room temperature. The QENS data obtained indicate that the protein dynamics is strongly dependent on the extent of hydration. In particular, the hydration-induced activation of localized diffusive protein motions and QA- reoxidation by QB in PS II appear to be correlated in their onset at a hydration value of about 45% relative humidity (r.h.). These findings underline the crucial functional relevance of localized diffusive protein motions on the picosecond-timescale for the reactions of light-induced photosynthetic water splitting under formation of plastoquinol and molecular oxygen in PS II of green plants.
Collapse
|
33
|
Sinibaldi R, Ortore MG, Spinozzi F, Carsughi F, Frielinghaus H, Cinelli S, Onori G, Mariani P. Preferential hydration of lysozyme in water/glycerol mixtures: A small-angle neutron scattering study. J Chem Phys 2007; 126:235101. [PMID: 17600444 DOI: 10.1063/1.2735620] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
In solution small-angle neutron scattering has been used to study the solvation properties of lysozyme dissolved in water/glycerol mixtures. To detect the characteristics of the protein-solvent interface, 35 different experimental conditions (i.e., protein concentration, water/glycerol fraction in the solvent, content of deuterated compounds) have been considered and a suitable software has been developed to fit simultaneously the whole set of scattering data. The average composition of the solvent in the close vicinity of the protein surface at each experimental condition has been derived. In all the investigated conditions, glycerol resulted especially excluded from the protein surface, confirming that lysozyme is preferentially hydrated. By considering a thermodynamic hydration model based on an equilibrium exchange between water and glycerol from the solvation layer to the bulk, the preferential binding coefficient and the excess solvation number have been estimated. Results were compared with data previously derived for ribonuclease A in the same mixed solvent: even if the investigated solvent compositions were very different, the agreement between data is noticeable, suggesting that a unique mechanism presides over the preferential hydration process. Moreover, the curve describing the excess solvation number as a function of the solvent composition shows the occurrence of a region of maximal hydration, which probably accounts for the changes in protein stability detected in the presence of cosolvents.
Collapse
Affiliation(s)
- Raffaele Sinibaldi
- Dipartimento di Scienze Applicate ai Sistemi Complessi, Università Politecnica delle Marche, Ancona 60131, Italy
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Cornicchi E, Marconi M, Onori G, Paciaroni A. Controlling the protein dynamical transition with sugar-based bioprotectant matrices: a neutron scattering study. Biophys J 2006; 91:289-97. [PMID: 16617083 PMCID: PMC1479059 DOI: 10.1529/biophysj.106.081752] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Accepted: 03/20/2006] [Indexed: 11/18/2022] Open
Abstract
Through elastic neutron scattering we measured the mean-square displacements of the hydrogen atoms of lysozyme embedded in a glucose-water glassy matrix as a function of the temperature and at various water contents. The elastic intensity of all the samples has been interpreted in terms of the double-well model in the whole temperature range. The dry sample shows an onset of anharmonicity at approximately 100 K, which can be attributed to the activation of methyl group reorientations. Such a protein intrinsic dynamics is decoupled from the external environment on the whole investigated temperature range. In the hydrated samples an additional and larger anharmonic contribution is provided by the protein dynamical transition, which appears at a higher temperature Td. As hydration increases the coupling between the protein internal dynamics and the surrounding matrix relaxations becomes more effective. The behavior of Td that, as a function of the water content, diminishes by approximately 60 K, supports the picture of the protein dynamics as driven by solvent relaxations. A possible connection between the protein dynamical response versus T and the thermal stability in glucose-water bioprotectant matrices is proposed.
Collapse
Affiliation(s)
- E Cornicchi
- Dipartimento di Fisica dell'Università di Perugia, CEMIN (Centro di Eccellenza per i Materiali Innovativi Nanostrutturati) and INFM CRS-SOFT, 06123 Perugia, Italy
| | | | | | | |
Collapse
|
35
|
Paciaroni A, Cornicchi E, De Francesco A, Marconi M, Onori G. Conditioning action of the environment on the protein dynamics studied through elastic neutron scattering. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2006; 35:591-9. [PMID: 16761157 DOI: 10.1007/s00249-006-0073-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2006] [Revised: 04/19/2006] [Accepted: 05/04/2006] [Indexed: 11/25/2022]
Abstract
The dynamics of lysozyme in the picosecond timescale has been studied when it is in dry and hydrated powder form and when it is embedded in glycerol, glycerol-water, glucose and glucose-water matrices. The investigation has been undertaken through elastic neutron scattering technique on the backscattering spectrometer IN13. The dynamics of dry powder and embedded-in-glucose lysozyme can be considered purely vibrational up to 100 K, where the onset of an anharmonic contribution takes place. This contribution can be attributed to the activation of methyl group reorientations and is described with an Arrhenius trend. An additional source of anharmonic dynamics appears at higher temperatures for lysozyme in hydrated powders and embedded in glycerol, glycerol-water and glucose-water matrices. This second process, also represented with an Arrhenius trend, corresponds to the so-called protein dynamical transition. Both the temperature where such a transition takes place and the magnitude of the protein mean square displacements depend on the environment. The dynamical response of the protein to temperature is put in relationship with its thermal stability.
Collapse
Affiliation(s)
- A Paciaroni
- Dipartimento di Fisica dell'Università di Perugia, CNR-INFM CRS SOFT, Via A. Pascoli, 06123, Perugia, Italy.
| | | | | | | | | |
Collapse
|
36
|
Affiliation(s)
- Biman Bagchi
- Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
| |
Collapse
|
37
|
De Francesco A, Marconi M, Cinelli S, Onori G, Paciaroni A. Picosecond internal dynamics of lysozyme as affected by thermal unfolding in nonaqueous environment. Biophys J 2004; 86:480-7. [PMID: 14695292 PMCID: PMC1303815 DOI: 10.1016/s0006-3495(04)74126-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
A neutron-scattering investigation of the internal picosecond dynamics of lysozyme solvated in glycerol as a function of temperature in the range 200-410 K has been undertaken. The inelastic contribution to the measured intensity is characterized by the presence of a bump generally known as "boson peak", clearly distinguishable at low temperature. When the temperature is increased the quasielastic component of the spectrum becomes more and more intrusive and progressively overwhelms the vibrational bump. This happens especially for T > 345 K when the protein goes through an unfolding process, which leads to the complete denaturation. The quasielastic term is the superposition of two components whose intensities and linewidths have been studied as a function of temperature. The slower component describes motions with characteristic times of approximately 4 ps corresponding to reorientations of polypeptide side chains. Both the intensity and linewidth of this kind of relaxations show two distinct regimes with a crossover in the temperature range where the melting process occurs, thus suggesting the presence of a dynamical transition correlated to the protein unfolding. Conversely the faster component might be ascribed to the local dynamics of hydrogen atoms caged by the nearest neighbors with characteristic time of approximately 0.3 ps.
Collapse
Affiliation(s)
- A De Francesco
- Istituto Nazionale per la Fisica della Materia, Dipartimento di Fisica dell'Università di Perugia, Perugia 06121, Italy
| | | | | | | | | |
Collapse
|
38
|
Pieper J, Irrgang KD, Renger G, Lechner RE. Density of Vibrational States of the Light-Harvesting Complex II of Green Plants Studied by Inelastic Neutron Scattering. J Phys Chem B 2004. [DOI: 10.1021/jp049341f] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J. Pieper
- Hahn-Meitner-Institut Berlin, Glienicker Str. 100, 14109 Berlin, Germany, and Max-Volmer-Laboratories for Biophysical Chemistry, Technical University, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - K.-D. Irrgang
- Hahn-Meitner-Institut Berlin, Glienicker Str. 100, 14109 Berlin, Germany, and Max-Volmer-Laboratories for Biophysical Chemistry, Technical University, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - G. Renger
- Hahn-Meitner-Institut Berlin, Glienicker Str. 100, 14109 Berlin, Germany, and Max-Volmer-Laboratories for Biophysical Chemistry, Technical University, Strasse des 17. Juni 135, 10623 Berlin, Germany
| | - R. E. Lechner
- Hahn-Meitner-Institut Berlin, Glienicker Str. 100, 14109 Berlin, Germany, and Max-Volmer-Laboratories for Biophysical Chemistry, Technical University, Strasse des 17. Juni 135, 10623 Berlin, Germany
| |
Collapse
|