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Zheng L, Zhou B, Wu B, Tan Y, Huang J, Tyagi M, García Sakai V, Yamada T, O'Neill H, Zhang Q, Hong L. Decoupling of the onset of anharmonicity between a protein and its surface water around 200 K. eLife 2024; 13:RP95665. [PMID: 39158544 PMCID: PMC11333040 DOI: 10.7554/elife.95665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024] Open
Abstract
The protein dynamical transition at ~200 K, where the biomolecule transforms from a harmonic, non-functional form to an anharmonic, functional state, has been thought to be slaved to the thermal activation of dynamics in its surface hydration water. Here, by selectively probing the dynamics of protein and hydration water using elastic neutron scattering and isotopic labeling, we found that the onset of anharmonicity in the two components around 200 K is decoupled. The one in protein is an intrinsic transition, whose characteristic temperature is independent of the instrumental resolution time, but varies with the biomolecular structure and the amount of hydration, while the one of water is merely a resolution effect.
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Affiliation(s)
- Lirong Zheng
- Institute of Natural Sciences, Shanghai Jiao Tong UniversityShanghaiChina
- Department of Cell and Developmental Biology & Michigan Neuroscience Institute, University of Michigan Medical SchoolAnn ArborUnited States
| | - Bingxin Zhou
- Institute of Natural Sciences, Shanghai Jiao Tong UniversityShanghaiChina
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong UniversityShanghaiChina
| | - Banghao Wu
- Institute of Natural Sciences, Shanghai Jiao Tong UniversityShanghaiChina
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiChina
| | - Yang Tan
- Institute of Natural Sciences, Shanghai Jiao Tong UniversityShanghaiChina
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong UniversityShanghaiChina
| | - Juan Huang
- Institute of Natural Sciences, Shanghai Jiao Tong UniversityShanghaiChina
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong UniversityShanghaiChina
| | - Madhusudan Tyagi
- Department of Materials Science and Engineering, University of MarylandCollege ParkUnited States
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST)GaithersburgUnited States
| | - Victoria García Sakai
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities CouncilDidcotUnited Kingdom
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and SocietyIbarakiJapan
| | - Hugh O'Neill
- Biology and Soft Matter Division, Oak Ridge National LaboratoryOak RidgeUnited States
| | - Qiu Zhang
- Biology and Soft Matter Division, Oak Ridge National LaboratoryOak RidgeUnited States
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong UniversityShanghaiChina
- Shanghai National Center for Applied Mathematics (SJTU Center), Shanghai Jiao Tong UniversityShanghaiChina
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong UniveristyShanghaiChina
- Shanghai Artificial Intelligence LaboratoryShanghaiChina
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2
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Bertini L, Libera V, Ripanti F, Natali F, Paolantoni M, Orecchini A, Nucara A, Petrillo C, Comez L, Paciaroni A. Polymorphism and Ligand Binding Modulate Fast Dynamics of Human Telomeric G-Quadruplexes. Int J Mol Sci 2023; 24:ijms24054280. [PMID: 36901712 PMCID: PMC10001961 DOI: 10.3390/ijms24054280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
Telomeric G-quadruplexes (G4s) are promising targets in the design and development of anticancer drugs. Their actual topology depends on several factors, resulting in structural polymorphism. In this study, we investigate how the fast dynamics of the telomeric sequence AG3(TTAG3)3 (Tel22) depends on the conformation. By using Fourier transform Infrared spectroscopy, we show that, in the hydrated powder state, Tel22 adopts parallel and mixed antiparallel/parallel topologies in the presence of K+ and Na+ ions, respectively. These conformational differences are reflected in the reduced mobility of Tel22 in Na+ environment in the sub-nanosecond timescale, as probed by elastic incoherent neutron scattering. These findings are consistent with the G4 antiparallel conformation being more stable than the parallel one, possibly due to the presence of ordered hydration water networks. In addition, we study the effect of Tel22 complexation with BRACO19 ligand. Despite the quite similar conformation in the complexed and uncomplexed state, the fast dynamics of Tel22-BRACO19 is enhanced compared to that of Tel22 alone, independently of the ions. We ascribe this effect to the preferential binding of water molecules to Tel22 against the ligand. The present results suggest that the effect of polymorphism and complexation on the G4 fast dynamics is mediated by hydration water.
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Affiliation(s)
- Luca Bertini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Francesca Ripanti
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Correspondence: (F.R.); (L.C.)
| | - Francesca Natali
- CNR-IOM and INSIDE@ILL c/o OGG, 71 avenue des Martyrs, CEDEX 9, 38042 Grenoble, France
| | - Marco Paolantoni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Via Elce di Sotto 6, 06123 Perugia, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Alessandro Nucara
- Department of Physics, Sapienza University of Rome, P.le Aldo Moro 5, 00185 Roma, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
| | - Lucia Comez
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
- Correspondence: (F.R.); (L.C.)
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, Via Alessandro Pascoli, 06123 Perugia, Italy
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Capaccioli S, Zheng L, Kyritsis A, Paciaroni A, Vogel M, Ngai KL. The Dynamics of Hydrated Proteins Are the Same as Those of Highly Asymmetric Mixtures of Two Glass-Formers. ACS OMEGA 2021; 6:340-347. [PMID: 33458485 PMCID: PMC7807739 DOI: 10.1021/acsomega.0c04655] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/08/2020] [Indexed: 05/31/2023]
Abstract
Customarily, the studies of dynamics of hydrated proteins are focused on the fast hydration water ν-relaxation, the slow structural α-relaxation responsible for a single glass transition, and the protein dynamic transition (PDT). Guided by the analogy with the dynamics of highly asymmetric mixtures of molecular glass-formers, we explore the possibility that the dynamics of hydrated proteins are richer than presently known. By providing neutron scattering, dielectric relaxation, calorimetry, and deuteron NMR data in two hydrated globular proteins, myoglobin and BSA, and the fibrous elastin, we show the presence of two structural α-relaxations, α1 and α2, and the hydration water ν-relaxation, all coupled together with interconnecting properties. There are two glass transition temperatures T g α1and T g α2 corresponding to vitrification of the α1 and α2 processes. Relaxation time τα2(T) of the α2-relaxation changes its Arrhenius temperature dependence to super-Arrhenius on crossing T g α1 from below. The ν-relaxation responds to the two vitrifications by changing the T-dependence of its relaxation time τν(T) on crossing consecutively T g α2 and T g α1. It generates the PDT at T d where τν(T d) matches about five times the experimental instrument timescale τexp, provided that T d > T g α1. This condition is satisfied by the hydrated globular proteins considered in this paper, and the ν-relaxation is in the liquid state with τν(T) having the super-Arrhenius temperature dependence. However, if T d < T g α1, the ν-relaxation fails to generate the PDT because it is in the glassy state and τν(T) has Arrhenius T-dependence, as in the case of hydrated elastin. Overall, the dynamics of hydrated proteins are the same as the dynamics of highly asymmetric mixtures of glass-formers. The results from this study have expanded the knowledge of the dynamic processes and their properties in hydrated proteins, and impact on research in this area is expected.
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Affiliation(s)
- Simone Capaccioli
- Dipartimento
di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
- CNR-IPCF, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| | - Lirong Zheng
- School
of Physics and Astronomy, Shanghai Jiao
Tong University, Shanghai 200240, China
- Institute
of Natural Sciences, Shanghai Jiao Tong
University, Shanghai 200240, China
| | - Apostolos Kyritsis
- Department
of Physics, National Technical University
of Athens, 157 80 Athens, Greece
| | | | - Michael Vogel
- Institute
of Condensed Matter Physics, Technische
Universität Darmstadt, Hochschulstr. 6, 64289 Darmstadt, Germany
| | - Kia L. Ngai
- CNR-IPCF, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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4
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Batens M, Shmool TA, Massant J, Zeitler JA, Van den Mooter G. Advancing predictions of protein stability in the solid state. Phys Chem Chem Phys 2020; 22:17247-17254. [PMID: 32685957 DOI: 10.1039/d0cp00341g] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The β-relaxation associated with the sub-glass transition temperature (Tg,β) is attributed to fast, localised molecular motions which can occur below the primary glass transition temperature (Tg,α). Consistent with Tg,β being observed well-below storage temperatures, the β-relaxation associated motions have been hypothesised to influence protein stability in the solid state and could thus impact the quality of e.g. protein powders for inhalation or reconstitution and injection. Why then do distinct solid state protein formulations with similar aggregation profiles after drying and immediate reconstitution, display different profiles when reconstituted following prolonged storage? Is the value of Tg,β, associated with the β-relaxation process of the system, a reliable parameter for characterising the behaviour of proteins in the solid state? Bearing this in mind, in this work we further explore the different relaxation dynamics of glassy solid state monoclonal antibody formulations using terahertz time-domain spectroscopy and dynamical mechanical analysis. By conducting a 52 week stability study on a series of multi-component spray-dried formulations, an approach for characterising and analysing the solid state dynamics and how these relate to protein stability is outlined.
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Affiliation(s)
- Maarten Batens
- Drug Delivery and Disposition, KU Leuven, Leuven, Belgium.
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5
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Kämpf K, Demuth D, Zamponi M, Wuttke J, Vogel M. Quasielastic neutron scattering studies on couplings of protein and water dynamics in hydrated elastin. J Chem Phys 2020; 152:245101. [PMID: 32610976 DOI: 10.1063/5.0011107] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Performing quasielastic neutron scattering measurements and analyzing both elastic and quasielasic contributions, we study protein and water dynamics of hydrated elastin. At low temperatures, hydration-independent methyl group rotation dominates the findings. It is characterized by a Gaussian distribution of activation energies centered at about Em = 0.17 eV. At ∼195 K, coupled protein-water motion sets in. The hydration water shows diffusive motion, which is described by a Gaussian distribution of activation energies with Em = 0.57 eV. This Arrhenius behavior of water diffusion is consistent with previous results for water reorientation, but at variance with a fragile-to-strong crossover at ∼225 K. The hydration-related elastin backbone motion is localized and can be attributed to the cage rattling motion. We speculate that its onset at ∼195 K is related to a secondary glass transition, which occurs when a β relaxation of the protein has a correlation time of τβ ∼ 100 s. Moreover, we show that its temperature-dependent amplitude has a crossover at the regular glass transition Tg = 320 K of hydrated elastin, where the α relaxation of the protein obeys τα ∼ 100 s. By contrast, we do not observe a protein dynamical transition when water dynamics enters the experimental time window at ∼240 K.
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Affiliation(s)
- Kerstin Kämpf
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
| | - Dominik Demuth
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
| | - Michaela Zamponi
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Joachim Wuttke
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science at Heinz Maier-Leibnitz Zentrum, Lichtenbergstraße 1, 85747 Garching, Germany
| | - Michael Vogel
- Institute of Condensed Matter Physics, Technische Universität Darmstadt, Hochschulstraße 6, 64289 Darmstadt, Germany
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6
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Capaccioli S, Ngai KL, Ancherbak S, Bertoldo M, Ciampalini G, Thayyil MS, Wang LM. The JG β-relaxation in water and impact on the dynamics of aqueous mixtures and hydrated biomolecules. J Chem Phys 2019; 151:034504. [DOI: 10.1063/1.5100835] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- S. Capaccioli
- CNR-IPCF, Dipartimento di Fisica, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
- Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
| | - K. L. Ngai
- CNR-IPCF, Dipartimento di Fisica, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
- State Key Lab of Metastable Materials Science and Technology, and College of Materials Science and Engineering, Yanshan University, Qinhuangdao, Hebei, 066004, China
| | - S. Ancherbak
- Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
| | - M. Bertoldo
- ISOF - CNR Area della Ricerca di Bologna, Via P. Gobetti 101, 40129 Bologna, Italy
| | - G. Ciampalini
- Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127, Pisa, Italy
| | | | - Li-Min Wang
- State Key Lab of Metastable Materials Science and Technology, and College of Materials Science and Engineering, Yanshan University, Qinhuangdao, Hebei, 066004, China
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7
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Ngai K, Hong L, Capaccioli S, Paciaroni A. Uncovering a novel transition in the dynamics of proteins in the dry state. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2019.04.087] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Vural D, Smith JC, Petridis L. Dynamics of the lignin glass transition. Phys Chem Chem Phys 2018; 20:20504-20512. [DOI: 10.1039/c8cp03144d] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Despite lignin being a heterogenous polyphenolic, its glass transition obeys well-established polymer theory concepts.
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Affiliation(s)
- Derya Vural
- UT/ORNL Center for Molecular Biophysics
- Oak Ridge National Laboratory
- Tennessee 37831
- USA
- Department of Physics, Giresun University
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics
- Oak Ridge National Laboratory
- Tennessee 37831
- USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics
- Oak Ridge National Laboratory
- Tennessee 37831
- USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee
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9
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Martin DR, Forsmo JE, Matyushov DV. Complex Dynamics of Water in Protein Confinement. J Phys Chem B 2017; 122:3418-3425. [PMID: 29206460 DOI: 10.1021/acs.jpcb.7b10448] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper studies single-molecule and collective dynamics of water confined in protein powders by means of molecular dynamics simulations. The single-particle dynamics show a modest retardation compared to the bulk but become highly stretched in the powder, with the stretching exponent of ≃0.2. The collective dynamics of the total water dipole are affected by intermolecular correlations inside water and by cross-correlations between the water and the protein. The dielectric spectrum of water in the powder has two nearly equal-amplitude peaks: a Debye peak with ≃16 ps relaxation time and a highly stretched peak with the relaxation time of ≃13 ns and a stretching exponent of ≃0.12. The slower relaxation component is not seen in the single-molecule correlation functions and can be assigned to elastic protein motions displacing water in the powder. The loss spectrum of the intermediate scattering function reported by neutron-scattering experiments is also highly stretched, with the high-frequency wing scaling according to a power law. Translational dynamics can become much slower in the powder than in the bulk but are overshadowed by the rotational loss in the overall loss spectrum of neutron scattering.
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Affiliation(s)
| | - James E Forsmo
- College of Engineering , Georgia Institute of Technology , 225 North Avenue , Atlanta , Georgia 30332 , United States
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10
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Seyedi S, Matyushov DV. Ergodicity breaking of iron displacement in heme proteins. SOFT MATTER 2017; 13:8188-8201. [PMID: 29082406 DOI: 10.1039/c7sm01561e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present a model of the dynamical transition of atomic displacements in proteins. Increased mean-square displacement at higher temperatures is caused by the softening of the force constant for atomic/molecular displacements by electrostatic and van der Waals forces from the protein-water thermal bath. Displacement softening passes through a nonergodic dynamical transition when the relaxation time of the force-force correlation function enters, with increasing temperature, the instrumental observation window. Two crossover temperatures are identified. The lower crossover, presently connected to the glass transition, is related to the dynamical unfreezing of rotations of water molecules within nanodomains polarized by charged surface residues of the protein. The higher crossover temperature, usually assigned to the dynamical transition, marks the onset of water translations. All crossovers are ergodicity breaking transitions depending on the corresponding observation windows. Allowing stretched exponential relaxation of the protein-water thermal bath significantly improves the theory-experiment agreement when applied to solid protein samples studied by Mössbauer spectroscopy.
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Affiliation(s)
- Salman Seyedi
- Department of Physics, Arizona State University, PO Box 871504, Tempe, Arizona 85287, USA
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11
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Li J, Koshnick C, Diallo SO, Ackling S, Huang DM, Jacobs IE, Harrelson TF, Hong K, Zhang G, Beckett J, Mascal M, Moulé AJ. Quantitative Measurements of the Temperature-Dependent Microscopic and Macroscopic Dynamics of a Molecular Dopant in a Conjugated Polymer. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b00672] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
| | | | | | - Sophia Ackling
- Department
of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
| | - David M. Huang
- Department
of Chemistry, School of Physical Sciences, The University of Adelaide, Adelaide, SA 5005, Australia
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12
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Ngai KL, Capaccioli S, Paciaroni A. Dynamics of hydrated proteins and bio-protectants: Caged dynamics, β-relaxation, and α-relaxation. Biochim Biophys Acta Gen Subj 2016; 1861:3553-3563. [PMID: 27155356 DOI: 10.1016/j.bbagen.2016.04.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND The properties of the three dynamic processes, α-relaxation, ν-relaxation, and caged dynamics in aqueous mixtures and hydrated proteins are analogous to corresponding processes found in van der Waals and polymeric glass-formers apart from minor differences. METHODS Collection of various experimental data enables us to characterize the structural α-relaxation of the protein coupled to hydration water (HW), the secondary or ν-relaxation of HW, and the caged HW process. RESULTS From the T-dependence of the ν-relaxation time of hydrated myoglobin, lysozyme, and bovine serum albumin, we obtain Ton at which it enters the experimental time windows of Mössbauer and neutron scattering spectroscopies, coinciding with protein dynamical transition (PDT) temperature Td. However, for all systems considered, the α-relaxation time at Ton or Td is many orders of magnitude longer. The other step change of the mean-square-displacement (MSD) at Tg_alpha originates from the coupling of the nearly constant loss (NCL) of caged HW to density. The coupling of the NCL to density is further demonstrated by another step change at the secondary glass temperature Tg_beta in two bio-protectants, trehalose and sucrose. CONCLUSIONS The structural α-relaxation plays no role in PDT. Since PDT is simply due to the ν-relaxation of HW, the term PDT is a misnomer. NCL of caged dynamics is coupled to density and show transitions at lower temperature, Tg_beta and Tg_alpha. GENERAL SIGNIFICANCE The so-called protein dynamical transition (PDT) of hydrated proteins is not caused by the structural α-relaxation of the protein but by the secondary ν-relaxation of hydration water. "This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo".
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Affiliation(s)
- K L Ngai
- CNR-IPCF, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy.
| | - S Capaccioli
- CNR-IPCF, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy; Dipartimento di Fisica, Università di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| | - A Paciaroni
- Dipartimento di Fisica, Università degli Studi di Perugia, Via A Pascoli 1, 06123 Perugia, Italy
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13
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Sebastiani F, Longo M, Orecchini A, Comez L, De Francesco A, Muthmann M, Teixeira SCM, Petrillo C, Sacchetti F, Paciaroni A. Hydration-dependent dynamics of human telomeric oligonucleotides in the picosecond timescale: A neutron scattering study. J Chem Phys 2015; 143:015102. [DOI: 10.1063/1.4923213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Affiliation(s)
- F. Sebastiani
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - M. Longo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Elettra—Sincrotrone Trieste, 34149 Basovizza, Trieste, Italy
| | - A. Orecchini
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - L. Comez
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. De Francesco
- CNR-IOM OGG c/o Institut Laue-Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - M. Muthmann
- Jülich Centre for Neutron Science, Forschungszentrum Jülich GmbH, Outstation at Heinz Maier-Leibnitz Zentrum, Lichtenbergstrasse 1, 85747 Garching, Germany
| | - S. C. M. Teixeira
- EPSAM, Keele University, Staffordshire ST5 5BG, United Kingdom
- Institut Laue–Langevin, 71 Avenue des Martyrs, CS20156, 38042 Grenoble Cedex 9, France
| | - C. Petrillo
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - F. Sacchetti
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR, Istituto Officina dei Materiali, Unità di Perugia, c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - A. Paciaroni
- Dipartimento di Fisica e Geologia, Università degli Studi di Perugia, Via A. Pascoli, 06123 Perugia, Italy
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14
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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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15
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Translational diffusion of hydration water correlates with functional motions in folded and intrinsically disordered proteins. Nat Commun 2015; 6:6490. [PMID: 25774711 PMCID: PMC4382692 DOI: 10.1038/ncomms7490] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 02/02/2015] [Indexed: 12/12/2022] Open
Abstract
Hydration water is the natural matrix of biological macromolecules and is essential for their activity in cells. The coupling between water and protein dynamics has been intensively studied, yet it remains controversial. Here we combine protein perdeuteration, neutron scattering and molecular dynamics simulations to explore the nature of hydration water motions at temperatures between 200 and 300 K, across the so-called protein dynamical transition, in the intrinsically disordered human protein tau and the globular maltose binding protein. Quasi-elastic broadening is fitted with a model of translating, rotating and immobile water molecules. In both experiment and simulation, the translational component markedly increases at the protein dynamical transition (around 240 K), regardless of whether the protein is intrinsically disordered or folded. Thus, we generalize the notion that the translational diffusion of water molecules on a protein surface promotes the large-amplitude motions of proteins that are required for their biological activity. Hydration water plasticizes protein structures and is essential for their biological functions, such as enzymatic catalysis. Here, the authors use neutron scattering and molecular dynamics simulations to study hydration water at the dynamical transition of folded and disordered proteins.
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16
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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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17
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Surovtsev NV, Dzuba SA. Flexibility of phospholipids with saturated and unsaturated chains studied by Raman scattering: The effect of cholesterol on dynamical and phase transitions. J Chem Phys 2014; 140:235103. [DOI: 10.1063/1.4883237] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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18
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Hill JJ, Shalaev EY, Zografi G. The importance of individual protein molecule dynamics in developing and assessing solid state protein preparations. J Pharm Sci 2014; 103:2605-2614. [PMID: 24867196 DOI: 10.1002/jps.24021] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/05/2014] [Accepted: 05/06/2014] [Indexed: 11/09/2022]
Abstract
Processing protein solutions into the solid state is a common approach for generating stable amorphous protein mixtures that are suitable for long-term storage. Great care is typically given to protecting the protein native structure during the various drying steps that render it into the amorphous solid state. However, many studies illustrate that chemical and physical degradations still occur in spite of this amorphous material having good glassy properties and it being stored at temperatures below its glass transition temperature (Tg). Because of these persistent issues and recent biophysical studies that have refined the debate ascribing meaning to the molecular dynamical transition temperature and Tg of protein molecules, we provide an updated discussion on the impact of assessing and managing localized, individual protein molecule nondiffusive motions in the context of proteins being prepared into bulk amorphous mixtures. Our aim is to bridge the pharmaceutical studies addressing bulk amorphous preparations and their glassy behavior, with the biophysical studies historically focused on the nondiffusive internal protein dynamics and a protein's activity, along with their combined efforts in assessing the impact of solvent hydrogen-bonding networks on local stability. We also provide recommendations for future research efforts in solid-state formulation approaches.
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Affiliation(s)
- John J Hill
- Department of Bioengineering, University of Washington, Seattle, WA 98195.
| | | | - George Zografi
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705-2222
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19
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Schirò G, Fomina M, Cupane A. Communication: Protein dynamical transition vs. liquid-liquid phase transition in protein hydration water. J Chem Phys 2014; 139:121102. [PMID: 24089711 DOI: 10.1063/1.4822250] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we compare experimental data on myoglobin hydrated powders from elastic neutron scattering, broadband dielectric spectroscopy, and differential scanning calorimetry. Our aim is to obtain new insights on the connection between the protein dynamical transition, a fundamental phenomenon observed in proteins whose physical origin is highly debated, and the liquid-liquid phase transition (LLPT) possibly occurring in protein hydration water and related to the existence of a low temperature critical point in supercooled water. Our results provide a consistent thermodynamic/dynamic description which gives experimental support to the LLPT hypothesis and further reveals how fundamental properties of water and proteins are tightly related.
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Affiliation(s)
- Giorgio Schirò
- Department of Physics and Chemistry, University of Palermo, Via Archirafi 36, 90123 Palermo, Italy
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20
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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.
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Affiliation(s)
- Anna V Frontzek
- A.F. Ioffe Physical Technical Institute , ul. Politekhnicheskaya 26, 194032 Saint-Petersburg, Russian Federation
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21
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Doster W, Nakagawa H, Appavou MS. Scaling analysis of bio-molecular dynamics derived from elastic incoherent neutron scattering experiments. J Chem Phys 2014; 139:045105. [PMID: 23902030 DOI: 10.1063/1.4816513] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Numerous neutron scattering studies of bio-molecular dynamics employ a qualitative analysis of elastic scattering data and atomic mean square displacements. We provide a new quantitative approach showing that the intensity at zero energy exchange can be a rich source of information of bio-structural fluctuations on a pico- to nano-second time scale. Elastic intensity scans performed either as a function of the temperature (back-scattering) and∕or by varying the instrumental resolution (time of flight spectroscopy) yield the activation parameters of molecular motions and the approximate structural correlation function in the time domain. The two methods are unified by a scaling function, which depends on the ratio of correlation time and instrumental resolution time. The elastic scattering concept is illustrated with a dynamic characterization of alanine-dipeptide, protein hydration water, and water-coupled protein motions of lysozyme, per-deuterated c-phycocyanin (CPC) and hydrated myoglobin. The complete elastic scattering function versus temperature, momentum exchange, and instrumental resolution is analyzed instead of focusing on a single cross-over temperature of mean square displacements at the apparent onset temperature of an-harmonic motions. Our method predicts the protein dynamical transition (PDT) at Td from the collective (α) structural relaxation rates of the solvation shell as input. By contrast, the secondary (β) relaxation enhances the amplitude of fast local motions in the vicinity of the glass temperature Tg. The PDT is specified by step function in the elastic intensity leading from elastic to viscoelastic dynamic behavior at a transition temperature Td.
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Affiliation(s)
- W Doster
- Physik-Department, Technische Universität München, D-85748 Garching, Germany.
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22
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Fomina M, Schirò G, Cupane A. Hydration dependence of myoglobin dynamics studied with elastic neutron scattering, differential scanning calorimetry and broadband dielectric spectroscopy. Biophys Chem 2013; 185:25-31. [PMID: 24309207 DOI: 10.1016/j.bpc.2013.11.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/07/2013] [Accepted: 11/07/2013] [Indexed: 11/18/2022]
Abstract
In this work we present a thorough investigation of the hydration dependence of myoglobin dynamics. The study is performed on D2O-hydrated protein powders in the hydration range 0<h<0.5 (h≡gr[D2O]/gr[protein]) and in the temperature range 20-300K. The protein equilibrium fluctuations are investigated with Elastic Neutron Scattering using the spectrometer IN13 at ILL (Grenoble), while the relaxations of the protein+hydration water system are investigated with Broadband Dielectric Spectroscopy; finally, Differential Scanning Calorimetry is used to obtain a thermodynamic description of the system. The effect of increasing hydration is to speed up the relaxations of the myoglobin+hydration water system and, thermodynamically, to decrease the glass transition temperature; these effects tend to saturate at h values greater than ~0.3. Moreover, the calorimetric scans put in evidence the occurrence of an endothermic peak whose onset temperature is located at ~230K independent of hydration. From the point of view of the protein equilibrium fluctuations, while the amplitude of anharmonic mean square displacements is found to increase with hydration, their onset temperature (i.e. the onset temperature of the well known "protein dynamical transition") is hydration independent. On the basis of the above results, the relevance of protein+hydration water relaxations and of the thermodynamic state of hydration water to the onset of the protein dynamical transition is discussed.
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Affiliation(s)
- Margarita Fomina
- Department of Physics and Chemistry, University of Palermo, via Archirafi 36, 90123 Palermo, Italy
| | - Giorgio Schirò
- Department of Physics and Chemistry, University of Palermo, via Archirafi 36, 90123 Palermo, Italy
| | - Antonio Cupane
- Department of Physics and Chemistry, University of Palermo, via Archirafi 36, 90123 Palermo, Italy.
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23
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Ngai K, Capaccioli S, Paciaroni A. Nature of the water specific relaxation in hydrated proteins and aqueous mixtures. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.05.018] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Tombari E, Johari GP. Specific heat of hydrated lysozyme, water's contribution to its dynamics, and criteria for glass formation of biomaterials. J Chem Phys 2013; 139:105102. [DOI: 10.1063/1.4819791] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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