1
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Shiraga K, Urabe M, Matsui T, Kikuchi S, Ogawa Y. Highly precise characterization of the hydration state upon thermal denaturation of human serum albumin using a 65 GHz dielectric sensor. Phys Chem Chem Phys 2020; 22:19468-19479. [PMID: 32761010 DOI: 10.1039/d0cp02265a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The biological functions of proteins depend on harmonization with hydration water surrounding them. Indeed, the dynamical transition of proteins, such as thermal denaturation, is dependent on the changes in the mobility of hydration water. However, the role of hydration water during dynamical transition is yet to be fully understood due to technical limitations in precisely characterizing the amount of hydration water. A state-of-the-art CMOS dielectric sensor consisting of 65 GHz LC resonators addressed this issue by utilizing the feature that oscillation frequency sensitively shifts in response to the complex dielectric constant at 65 GHz with extremely high precision. This study aimed to establish an analytical algorithm to derive the hydration number from the measured frequency shift and to demonstrate the transition of hydration number upon the thermal denaturation of human serum albumin. The determined hydration number in the native state drew a "global" hydration picture beyond the first solvation shell, with substantially reduced uncertainty of the hydration number (about ±1%). This allowed the detection of a rapid increase in the hydration number at about 55 °C during the heating process, which was in excellent phase with the irreversible rupture of the α-helical structure into solvent-exposed extended chains, whereas the hydration number did not trace the forward path in the subsequent cooling process. Our result indicates that the weakening of water hydrogen bonds trigger the unfolding of the protein structure first, followed by the changes in the number of hydration water as a consequence of thermal denaturation.
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Affiliation(s)
- Keiichiro Shiraga
- RIKEN Center for Integrative Medical Sciences (IMS), Tsurumi, Yokohama, Kanagawa 230-0045, Japan.
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2
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Robertson LA, Li Z, Cao Y, Shkrob IA, Tyagi M, Smith KC, Zhang L, Moore JS, Z Y. Observation of Microheterogeneity in Highly Concentrated Nonaqueous Electrolyte Solutions. J Am Chem Soc 2019; 141:8041-8046. [PMID: 31074276 DOI: 10.1021/jacs.9b02323] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of models to describe structure and dynamics of nonaqueous electrolyte solutions is challenging, and experimental observations are needed to form a foundation. Here, neutron scattering is used to probe molecular dynamics in nonaqueous organic electrolytes. Two solutions were compared: one contained symmetrical electrolyte molecules prone to crystallize, and one contained desymmetrized electrolyte molecules preferring disordered states. For the latter, calorimetry and neutron data show that a disordered fluid persists to very low temperatures at high concentrations. Upon heating, localized cold crystallization occurs, leading to burst nucleation of microcrystalline solids within fluid phases. Our findings indicate molecular clustering and point to solvation inhomogeneities and molecular crowding in these concentrated fluids.
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Affiliation(s)
- Lily A Robertson
- Joint Center for Energy Storage Research , Argonne National Laboratory, 9700 S. Cass Avenue , Lemont , Illinois 60439 , United States.,Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Zhixia Li
- Joint Center for Energy Storage Research , Argonne National Laboratory, 9700 S. Cass Avenue , Lemont , Illinois 60439 , United States.,Department of Nuclear, Plasma, and Radiological Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Yu Cao
- Joint Center for Energy Storage Research , Argonne National Laboratory, 9700 S. Cass Avenue , Lemont , Illinois 60439 , United States.,Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Ilya A Shkrob
- Joint Center for Energy Storage Research , Argonne National Laboratory, 9700 S. Cass Avenue , Lemont , Illinois 60439 , United States.,Chemical Sciences and Engineering Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Madhusudan Tyagi
- NIST Center for Neutron Research , National Institute for Standards and Technology, Gaithersburg , Maryland 20899 , United States.,Department of Materials Science and Engineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Kyle C Smith
- Joint Center for Energy Storage Research , Argonne National Laboratory, 9700 S. Cass Avenue , Lemont , Illinois 60439 , United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Mechanical Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Lu Zhang
- Joint Center for Energy Storage Research , Argonne National Laboratory, 9700 S. Cass Avenue , Lemont , Illinois 60439 , United States.,Chemical Sciences and Engineering Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
| | - Jeffrey S Moore
- Joint Center for Energy Storage Research , Argonne National Laboratory, 9700 S. Cass Avenue , Lemont , Illinois 60439 , United States.,Department of Chemistry , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
| | - Y Z
- Joint Center for Energy Storage Research , Argonne National Laboratory, 9700 S. Cass Avenue , Lemont , Illinois 60439 , United States.,Department of Nuclear, Plasma, and Radiological Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Materials Science and Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States.,Department of Electrical and Computer Engineering , University of Illinois at Urbana-Champaign , Urbana , Illinois 61801 , United States
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3
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Mallamace D, Fazio E, Mallamace F, Corsaro C. The Role of Hydrogen Bonding in the Folding/Unfolding Process of Hydrated Lysozyme: A Review of Recent NMR and FTIR Results. Int J Mol Sci 2018; 19:ijms19123825. [PMID: 30513664 PMCID: PMC6321052 DOI: 10.3390/ijms19123825] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/23/2018] [Accepted: 11/24/2018] [Indexed: 02/07/2023] Open
Abstract
The biological activity of proteins depends on their three-dimensional structure, known as the native state. The main force driving the correct folding mechanism is the hydrophobic effect and when this folding kinetics is altered, aggregation phenomena intervene causing the occurrence of illnesses such as Alzheimer and Parkinson’s diseases. The other important effect is performed by water molecules and by their ability to form a complex network of hydrogen bonds whose dynamics influence the mobility of protein amino acids. In this work, we review the recent results obtained by means of spectroscopic techniques, such as Fourier Transform Infrared (FTIR) and Nuclear Magnetic Resonance (NMR) spectroscopies, on hydrated lysozyme. In particular, we explore the Energy Landscape from the thermal region of configurational stability up to that of the irreversible denaturation. The importance of the coupling between the solute and the solvent will be highlighted as well as the different behaviors of hydrophilic and hydrophobic moieties of protein amino acid residues.
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Affiliation(s)
- Domenico Mallamace
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra (MIFT), Università di Messina, 98166 Messina, Italy.
| | - Enza Fazio
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra (MIFT), Università di Messina, 98166 Messina, Italy.
| | - Francesco Mallamace
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.
- Istituto dei Sistemi Complessi (ISC)-CNR, 00185 Rome, Italy.
| | - Carmelo Corsaro
- Dipartimento di Scienze Matematiche e Informatiche, Scienze Fisiche e Scienze della Terra (MIFT), Università di Messina, 98166 Messina, Italy.
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4
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Grimaldo M, Roosen-Runge F, Hennig M, Zanini F, Zhang F, Jalarvo N, Zamponi M, Schreiber F, Seydel T. Hierarchical molecular dynamics of bovine serum albumin in concentrated aqueous solution below and above thermal denaturation. Phys Chem Chem Phys 2016; 17:4645-55. [PMID: 25587698 DOI: 10.1039/c4cp04944f] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of proteins in solution is a complex and hierarchical process, affected by the aqueous environment as well as temperature. We present a comprehensive study on nanosecond time and nanometer length scales below, at, and above the denaturation temperature Td. Our experimental data evidence dynamical processes in protein solutions on three distinct time scales. We suggest a consistent physical picture of hierarchical protein dynamics: (i) self-diffusion of the entire protein molecule is confirmed to agree with colloid theory for all temperatures where the protein is in its native conformational state. At higher temperatures T > Td, the self-diffusion is strongly obstructed by cross-linking or entanglement. (ii) The amplitude of backbone fluctuations grows with increasing T, and a transition in its dynamics is observed above Td. (iii) The number of mobile side-chains increases sharply at Td while their average dynamics exhibits only little variations. The combination of quasi-elastic neutron scattering and the presented analytical framework provides a detailed microscopic picture of the protein molecular dynamics in solution, thereby reflecting the changes of macroscopic properties such as cluster formation and gelation.
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Affiliation(s)
- Marco Grimaldo
- Institut Max von Laue - Paul Langevin (ILL), CS 20156, F-38042 Grenoble, France.
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5
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Mallamace F, Corsaro C, Mallamace D, Vasi S, Vasi C, Stanley HE, Chen SH. Some thermodynamical aspects of protein hydration water. J Chem Phys 2015; 142:215103. [DOI: 10.1063/1.4921897] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Francesco Mallamace
- Dipartimento di Fisica e Scienze della Terra, Università di Messina and CNISM, I-98168 Messina, Italy
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
| | - Carmelo Corsaro
- Dipartimento di Fisica e Scienze della Terra, Università di Messina and CNISM, I-98168 Messina, Italy
- CNR-IPCF, Viale F. Stagno D’Alcontres 37, I-98158 Messina, Italy
| | | | - Sebastiano Vasi
- Dipartimento di Fisica e Scienze della Terra, Università di Messina and CNISM, I-98168 Messina, Italy
| | - Cirino Vasi
- CNR-IPCF, Viale F. Stagno D’Alcontres 37, I-98158 Messina, Italy
| | - H. Eugene Stanley
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
| | - Sow-Hsin Chen
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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6
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Mallamace F, Corsaro C, Mallamace D, Vasi S, Vasi C, Stanley HE. Thermodynamic properties of bulk and confined water. J Chem Phys 2015; 141:18C504. [PMID: 25399169 DOI: 10.1063/1.4895548] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The thermodynamic response functions of water display anomalous behaviors. We study these anomalous behaviors in bulk and confined water. We use nuclear magnetic resonance (NMR) to examine the configurational specific heat and the transport parameters in both the thermal stable and the metastable supercooled phases. The data we obtain suggest that there is a behavior common to both phases: that the dynamics of water exhibit two singular temperatures belonging to the supercooled and the stable phase, respectively. One is the dynamic fragile-to-strong crossover temperature (T(L) ≃ 225 K). The second, T* ∼ 315 ± 5 K, is a special locus of the isothermal compressibility K(T)(T, P) and the thermal expansion coefficient α(P)(T, P) in the P-T plane. In the case of water confined inside a protein, we observe that these two temperatures mark, respectively, the onset of protein flexibility from its low temperature glass state (T(L)) and the onset of the unfolding process (T*).
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Affiliation(s)
- Francesco Mallamace
- Dipartimento di Fisica e Scienza della Terra Università di Messina and CNISM, I-98168 Messina, Italy
| | - Carmelo Corsaro
- Dipartimento di Fisica e Scienza della Terra Università di Messina and CNISM, I-98168 Messina, Italy
| | - Domenico Mallamace
- Dipartimento di Scienze dell'Ambiente, della Sicurezza, del Territorio, degli Alimenti e della Salute, Università di Messina, I-98166 Messina, Italy
| | | | | | - H Eugene Stanley
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, USA
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7
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Mallamace F, Corsaro C, Mallamace D, Vasi S, Vasi C, Dugo G. The role of water in protein's behavior: The two dynamical crossovers studied by NMR and FTIR techniques. Comput Struct Biotechnol J 2014; 13:33-7. [PMID: 25750698 PMCID: PMC4348435 DOI: 10.1016/j.csbj.2014.11.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Revised: 11/10/2014] [Accepted: 11/12/2014] [Indexed: 12/01/2022] Open
Abstract
The role the solvent plays in determining the biological activity of proteins is of primary importance. Water is the solvent of life and proteins need at least a water monolayer covering their surface in order to become biologically active. We study how the properties of water and the effect of its coupling with the hydrophilic moieties of proteins govern the regime of protein activity. In particular we follow, by means of Fourier Transform Infrared spectroscopy, the thermal evolution of the amide vibrational modes of hydrated lysozyme in the temperature interval 180 K < T < 350 K. In such a way we are able to observe the thermal limit of biological activity characterizing hydrated lysozyme. Finally we focus on the region of lysozyme thermal denaturation by following the evolution of the proton Nuclear Magnetic Resonance (NMR) spectra for 298 K < T < 366 K with the High-Resolution Magic Angle Spinning probe. Our data suggest that the hydrogen bond coupling between hydration water and protein hydrophilic groups is crucial in triggering the main mechanisms that define the enzymatic activity of proteins.
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Affiliation(s)
- Francesco Mallamace
- Dipartimento di Fisica e Scienze della Terra, Università di Messina, Viale F. Stagno D'Alcontres 31, 98166 Messina, Italy ; CNR-IPCF, Istituto per i Processi Chimico-Fisici, Viale F. Stagno D'Alcontres 37, 98158 Messina, Italy
| | - Carmelo Corsaro
- Dipartimento di Fisica e Scienze della Terra, Università di Messina, Viale F. Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Domenico Mallamace
- Dipartimento di Scienze dell'Ambiente, della Sicurezza, del Territorio, degli Alimenti edella Salute, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Sebastiano Vasi
- Dipartimento di Fisica e Scienze della Terra, Università di Messina, Viale F. Stagno D'Alcontres 31, 98166 Messina, Italy
| | - Cirino Vasi
- CNR-IPCF, Istituto per i Processi Chimico-Fisici, Viale F. Stagno D'Alcontres 37, 98158 Messina, Italy
| | - Giacomo Dugo
- Dipartimento di Scienze dell'Ambiente, della Sicurezza, del Territorio, degli Alimenti edella Salute, Università di Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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8
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Dhindsa GK, Tyagi M, Chu XQ. Temperature-dependent dynamics of dry and hydrated β-casein studied by quasielastic neutron scattering. J Phys Chem B 2014; 118:10821-9. [PMID: 25144497 DOI: 10.1021/jp504548w] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
β-Casein is a component of casein micelle with amphillic nature and is recognized as a "natively disordered" protein that lacks secondary structures. In this study, the temperature and hydration effects on the dynamics of β-casein are explored by quasielastic neutron scattering (QENS). An upturn in the mean square displacement (MSD) of hydrated β-casein indicates an increase of protein flexibility at a temperature of ~225 K. Another increase in MSD at ~100 K, observed in both dry and hydrated β-casein, is ascribed to the methyl group rotations, which are not sensitive to hydration. QENS analysis in the energy domain reveals that the fraction of hydrogen atoms participating in motion in a sphere of diffusion is highly hydration dependent and increases with temperature. In the time domain analysis, a logarithmic-like decay is observed in the range of picosecond to nanosecond (β-relaxation time) in the dynamics of hydrated β-casein. This dynamical behavior has been observed in hydrated globular and oligomeric proteins. Our temperature-dependent QENS experiments provide evidence that lack of a secondary structure in β-casein results in higher flexibility in its dynamics and easier reversible thermal unfolding compared to other rigid biomolecules.
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Affiliation(s)
- Gurpreet K Dhindsa
- Department of Physics and Astronomy, Wayne State University , Detroit, Michigan 48201, United States
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9
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Fluorescence Investigation of Interactions Between Novel Benzanthrone Dyes and Lysozyme Amyloid Fibrils. J Fluoresc 2013; 24:493-504. [DOI: 10.1007/s10895-013-1318-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 11/07/2013] [Indexed: 10/25/2022]
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10
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Abramo MC, Caccamo C, Cavero M, Costa D, Pellicane G, Ruberto R, Wanderlingh U. Effective protein-protein interaction from structure factor data of a lysozyme solution. J Chem Phys 2013; 139:054904. [DOI: 10.1063/1.4817191] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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11
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Chu XQ, Mamontov E, O'Neill H, Zhang Q. Temperature Dependence of Logarithmic-like Relaxational Dynamics of Hydrated tRNA. J Phys Chem Lett 2013; 4:936-942. [PMID: 26291359 DOI: 10.1021/jz400128u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The dynamics of RNA within the β-relaxation region of 10 ps to 1 ns is crucial to its biological function. Because of its simpler chemical building blocks and the lack of the side methyl groups, faster relaxational dynamics of RNA compared to proteins can be expected. However, the situation is actually opposite. In this work, the relaxational dynamics of tRNA is measured by quasielastic neutron scattering and analyzed using the mode coupling theory, originally developed for glass-forming liquids. Our results reveal that the dynamics of tRNA follows a log-decay within the β-relaxation region, which is an important trait demonstrated by the dynamics of proteins. The dynamics of hydrated tRNA and lysozyme compared in the time domain further demonstrate that the slower dynamics of tRNA relative to proteins originates from the difference in the folded states of tRNA and proteins, as well as the influence of their hydration water.
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Affiliation(s)
- Xiang-Qiang Chu
- †Department of Physics and Astronomy, Wayne State University, Detroit, Michigan 48201, United States
- ‡Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eugene Mamontov
- §Chemical and Engineering Materials Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- ‡Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- ‡Biology and Soft Matter Division, Neutron Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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12
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Li H, Fratini E, Chiang WS, Baglioni P, Mamontov E, Chen SH. Dynamic behavior of hydration water in calcium-silicate-hydrate gel: a quasielastic neutron scattering spectroscopy investigation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:061505. [PMID: 23367956 DOI: 10.1103/physreve.86.061505] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Indexed: 06/01/2023]
Abstract
The translational dynamics of hydration water confined in calcium-silicate-hydrate (C-S-H) gel was studied by quasielastic neutron scattering spectroscopy in the temperature range from 280 to 230 K. The stretch exponent β, the self-diffusion constant D, the average translational relaxation time {τ}, and the temperature dependence of confinement radius α extracted from the elastic fraction of immobile water molecules p(Q) were obtained from the analyses of the low-Q spectra according to the relaxing cage model. Measurements were made using C-S-H of three different water contents, 10%, 17%, and 30%. Among the three samples of C-S-H gel with different water contents, the values of β decrease with increasing water contents, while α increases. The values of D and {τ} are insensitive to temperature for the two lower water contents, as opposed to the 30% case where a slight variation is observed. The trend for violation of the Stokes-Einstein relation is only visible in the case of 30% water content.
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Affiliation(s)
- Hua Li
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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13
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Chu XQ, Gajapathy M, Weiss KL, Mamontov E, Ng JD, Coates L. Dynamic behavior of oligomeric inorganic pyrophosphatase explored by quasielastic neutron scattering. J Phys Chem B 2012; 116:9917-21. [PMID: 22804561 DOI: 10.1021/jp303127w] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The purpose of this investigation is to determine whether a large oligomeric protein, inorganic pyrophosphatase (IPPase) from Thermococcus thioreducens with quaternary structural complexity, would have distinguishable dynamic characteristics compared to those of the small simple monomeric model protein, lysozyme. In this study, the β-relaxational dynamics of the two proteins, IPPase and lysozyme, are compared in the 10 ps to 0.5 ns time interval using quasi-elastic neutron scattering (QENS). Both of the protein dynamics show a characteristic logarithmic-like decay in the intermediate scattering function (ISF) of the hydrogen atoms. Distinguishable dynamical behavior found between two proteins reveals local flexibility and conformational substates unique to oligomeric structures. Moreover, the temperature dependence of the mean square displacement (MSD) of the hydrogen atoms in protein molecules, which is a traditional way to determine the "softness" of the protein molecule, is measured and shows no difference for the two proteins.
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Affiliation(s)
- Xiang-qiang Chu
- Neutron Scattering Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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14
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Peter E, Dick B, Baeurle SA. A novel computer simulation method for simulating the multiscale transduction dynamics of signal proteins. J Chem Phys 2012; 136:124112. [DOI: 10.1063/1.3697370] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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15
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Oleinikova A, Brovchenko I. Hydrogen-bonded network of hydration water around model solutes. Phys Chem Chem Phys 2012; 14:5686-94. [DOI: 10.1039/c2cp00062h] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Mallamace F, Corsaro C, Mallamace D, Baglioni P, Stanley HE, Chen SH. A Possible Role of Water in the Protein Folding Process. J Phys Chem B 2011; 115:14280-94. [DOI: 10.1021/jp205285t] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Francesco Mallamace
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Dipartimento di Fisica and CNISM, Università di Messina, I-98166 Messina, Italy
| | - Carmelo Corsaro
- Dipartimento di Fisica and CNISM, Università di Messina, I-98166 Messina, Italy
- Fondazione F. Frisone, Via Etnea 73, Catania I-95125, Italy
| | - Domenico Mallamace
- Dipartimento di Scienze degli Alimenti e dellˈAmbiente “G. Stagno DˈAlcontres”, Università di Messina, I-98166 Messina, Italy
| | - Piero Baglioni
- Department of Chemistry and CSGI, University of Florence, Florence 50019, Italy
| | - H. Eugene Stanley
- Center for Polymer Studies and Department of Physics, Boston University, Boston, Massachusetts 02215, United States
| | - Sow-Hsin Chen
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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17
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Meersman F, Atilgan C, Miles AJ, Bader R, Shang W, Matagne A, Wallace BA, Koch MHJ. Consistent picture of the reversible thermal unfolding of hen egg-white lysozyme from experiment and molecular dynamics. Biophys J 2011; 99:2255-63. [PMID: 20923660 DOI: 10.1016/j.bpj.2010.07.060] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 07/15/2010] [Accepted: 07/23/2010] [Indexed: 11/19/2022] Open
Abstract
Synchrotron radiation circular dichroism, Fourier transform infrared, and nuclear magnetic resonance spectroscopies, and small-angle x-ray scattering were used to monitor the reversible thermal unfolding of hen egg white lysozyme. The results were compared with crystal structures and high- and low-temperature structures derived from molecular-dynamics calculations. The results of both experimental and computational methods indicate that the unfolding process starts with the loss of β-structures followed by the reversible loss of helix content from ∼40% at 20°C to 27% at 70°C and ∼20% at 77°C, beyond which unfolding becomes irreversible. Concomitantly there is a reversible increase in the radius of gyration of the protein from 15 Å to 18 Å. The reversible decrease in forward x-ray scattering demonstrates a lack of aggregation upon unfolding, suggesting the change is due to a larger dilation of hydration water than of bulk water. Molecular-dynamics simulations suggest a similar sequence of events and are in good agreement with the (1)H(N) chemical shift differences in nuclear magnetic resonance. This study demonstrates the power of complementary methods for elucidating unfolding/refolding processes and the nature of both the unfolded structure, for which there is no crystallographic data, and the partially unfolded forms of the protein that can lead to fibril formation and disease.
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Affiliation(s)
- Filip Meersman
- Department of Chemistry, Katholieke Universiteit Leuven, Leuven, Belgium.
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18
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Reátegui E, Aksan A. Effects of water on the structure and low/high temperature stability of confined proteins. Phys Chem Chem Phys 2010; 12:10161-72. [PMID: 20689888 DOI: 10.1039/c003517c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this study well-characterized model proteins were confined in silica nanoporous matrices. Confinement of the proteins in silica matrices allowed us to explore the role of water hydrogen bonding on the structures of the proteins in a broad range of temperatures (-120 degrees C to 95 degrees C). At low temperatures confinement suppressed freezing of water, which remained in the liquid state. We obtained direct evidence that the changes in the hydrogen bonding of water induced changes in the structure of confined proteins. At high temperatures, a reduction of hydrogen bonding of water facilitated protein-silica interactions and the confined proteins underwent denaturation. However, the incorporation of the osmolyte, trehalose, reduced protein-silica interactions, and altered the hydrogen bonding of water. As a result, the high temperature thermal stability of the confined proteins was greatly improved.
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Affiliation(s)
- Eduardo Reátegui
- Biostabilization Laboratory, Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN, USA
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