1
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Tavagnacco L, Zanatta M, Buratti E, Bertoldo M, Chiessi E, Appel M, Natali F, Orecchini A, Zaccarelli E. Water slowing down drives the occurrence of the low temperature dynamical transition in microgels. Chem Sci 2024; 15:9249-9257. [PMID: 38903230 PMCID: PMC11186305 DOI: 10.1039/d4sc02650k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 06/22/2024] Open
Abstract
The protein dynamical transition marks an increase in atomic mobility and the onset of anharmonic motions at a critical temperature (T d), which is considered relevant for protein functionality. This phenomenon is ubiquitous, regardless of protein composition, structure and biological function and typically occurs at large protein content, to avoid water crystallization. Recently, a dynamical transition has also been reported in non-biological macromolecules, such as poly(N-isopropyl acrylamide) (PNIPAM) microgels, bearing many similarities to proteins. While the generality of this phenomenon is well-established, the role of water in the transition remains a subject of debate. In this study, we use atomistic molecular dynamics (MD) simulations and elastic incoherent neutron scattering (EINS) experiments with selective deuteration to investigate the microscopic origin of the dynamical transition and distinguish water and PNIPAM roles. While a standard analysis of EINS experiments would suggest that the dynamical transition occurs in PNIPAM and water at a similar temperature, simulations reveal a different perspective, also qualitatively supported by experiments. From room temperature down to about 180 K, PNIPAM exhibits only modest changes of dynamics, while water, being mainly hydration water under the probed extreme confinement, significantly slows down and undergoes a mode-coupling transition from diffusive to activated. Our findings therefore challenge the traditional view of the dynamical transition, demonstrating that it occurs in proximity of the water mode-coupling transition, shedding light on the intricate interplay between polymer and water dynamics.
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Affiliation(s)
- Letizia Tavagnacco
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
| | - Marco Zanatta
- Department of Physics, University of Trento Via Sommarive 14 38123 Trento Italy
| | - Elena Buratti
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Monica Bertoldo
- Department of Chemical, Pharmaceutical and Agricultural Sciences, University of Ferrara Via L. Borsari 46 44121 Ferrara Italy
| | - Ester Chiessi
- Department of Chemical Science and Technologies, University of Rome Tor Vergata Via della Ricerca Scientifica I 00133 Rome Italy
| | - Markus Appel
- Institut Laue-Langevin 71 avenue des Martyrs, CS 20156 38042 Grenoble Cedex 9 France
| | - Francesca Natali
- CNR-IOM, Operative Group Grenoble (OGG), Institut Laue Langevin F-38042 Grenoble France
| | - Andrea Orecchini
- Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
- CNR-IOM c/o Dipartimento di Fisica e Geologia, Università di Perugia Via Alessandro Pascoli 06123 Perugia Italy
| | - Emanuela Zaccarelli
- CNR Institute of Complex Systems, Uos Sapienza Piazzale Aldo Moro 2 00185 Rome Italy
- Department of Physics, Sapienza University of Rome Piazzale Aldo Moro 2 00185 Rome Italy
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2
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Kölbel J, Anuschek ML, Stelzl I, Santitewagun S, Friess W, Zeitler JA. Dynamical Transition in Dehydrated Proteins. J Phys Chem Lett 2024; 15:3581-3590. [PMID: 38527099 PMCID: PMC11000241 DOI: 10.1021/acs.jpclett.3c03584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/16/2024] [Accepted: 03/19/2024] [Indexed: 03/27/2024]
Abstract
Terahertz time-domain spectroscopy and differential scanning calorimetry were used to study the role of the dynamics of biomolecules decoupled from solvent effects. Lyophilized sucrose exhibited steadily increasing absorption with temperature as anharmonic excitations commenced as the system emerged from a deep minimum of the potential energy landscape where harmonic vibrations dominate. The polypeptide bacitracin and two globular proteins, lysozyme and human serum albumin, showed a more complex temperature dependence. Further analysis focused on the spectral signature below and above the boson peak. We found evidence of the onset of anharmonic motions that are characteristic for partial unfolding and molecular jamming in the dry biomolecules. The activation of modes of the protein molecules at temperatures comparable to the protein dynamical transition temperature was observed in the absence of hydration. No evidence of Fröhlich coherence, postulated to facilitate biological function, was found in our experiments.
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Affiliation(s)
- Johanna Kölbel
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
| | - Moritz L. Anuschek
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
- Department
of Pharmacy - Center for Drug Research, Pharmaceutical Technology
and Biopharmaceutics, Ludwig-Maximilians
Universität, Butenandtstrasse
5, 81377 Munich, Germany
| | - Ivonne Stelzl
- Department
of Pharmacy - Center for Drug Research, Pharmaceutical Technology
and Biopharmaceutics, Ludwig-Maximilians
Universität, Butenandtstrasse
5, 81377 Munich, Germany
| | - Supawan Santitewagun
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
| | - Wolfgang Friess
- Department
of Pharmacy - Center for Drug Research, Pharmaceutical Technology
and Biopharmaceutics, Ludwig-Maximilians
Universität, Butenandtstrasse
5, 81377 Munich, Germany
| | - J. Axel Zeitler
- Department
of Chemical Engineering, University of Cambridge, Cambridge CB3 0AS, U.K.
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3
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Ye Y, Zheng L, Hong L, García Sakai V, de Souza NR, Teng D, Wu B, Xu Y, Cai J, Liu Z. Direct Observation of the Mutual Coupling Effect in the Protein-Water-Glycerol Mixture by Combining Neutron Scattering and Selective Deuteration. J Phys Chem B 2024; 128:405-414. [PMID: 38183282 DOI: 10.1021/acs.jpcb.3c05135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2024]
Abstract
Numerous studies have discussed the impact of cosolvents on the structure, dynamics, and stability of proteins in aqueous solutions. However, the dynamics of cosolvents in the protein-water-cosolvent ternary system is largely unexplored in experiments due to technical difficulty. Consequently, a comprehensive understanding of the interplay among proteins, water, and cosolvents is still lacking. Here, we employed selective deuteration and neutron scattering techniques to characterize the individual motions of each component in the protein/water/glycerol (GLY) mixture across various temperatures. The consistent dynamic onset temperatures and the correlation between the MSD of the protein and the viscosity of solvents revealed the mutual coupling effects among the three components. Furthermore, our experimental and simulation results showed that the hydrogen bond relaxation energy barrier in the ternary system is ∼43 kJ/mol, whereas in the protein-water binary system it is merely ∼35 kJ/mol. Therefore, we suggest that GLY can enhance hydrogen bond interactions in the ternary system through the mutual coupling effect, thereby serving as one of the protective mechanisms of protein preservation by GLY.
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Affiliation(s)
- Yongfeng Ye
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - 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
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Centre for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - Victoria García Sakai
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, U.K
| | - Nicolas R de Souza
- Australian Nuclear Science and Technology (ANSTO), Locked Bag 2001, Kirrawee DC, New South Wales 2232, Australia
| | - Dahong Teng
- Organ Transplantation Center, Fujian Medical University Union Hospital, Fuzhou 350000, China
| | - Bin Wu
- Organ Transplantation Center, Fujian Medical University Union Hospital, Fuzhou 350000, China
| | - Yichao Xu
- Organ Transplantation Center, Fujian Medical University Union Hospital, Fuzhou 350000, China
| | - Jinzhen Cai
- Organ Transplantation Center, Fujian Medical University Union Hospital, Fuzhou 350000, China
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai National Centre for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- Zhangjiang Institute for Advanced Study, Shanghai Jiao Tong University, Shanghai 201203, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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4
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Jiang F, Bian J, Liu H, Li S, Bai X, Zheng L, Jin S, Liu Z, Yang GY, Hong L. Creatinase: Using Increased Entropy to Improve the Activity and Thermostability. J Phys Chem B 2023; 127:2671-2682. [PMID: 36926920 DOI: 10.1021/acs.jpcb.2c08062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
Improving protein thermostability in mutagenesis-based enzyme engineering was often achieved by enhancing interresidue interactions via mutation to increase the enthalpy penalty of unfolding. However, this approach may trade off the functional activity due to the loss of structural flexibility of the biomolecule. Here, by performing X-ray crystallography, enzymatic kinetic experiments, neutron scattering, and thermodynamical measurements, we compared the structures, catalytic behaviors, dynamics, and thermostability between a wild-type creatinase and its four-point mutant. We found that the mutant is an entropy-driven thermostable protein with higher structural flexibility, i.e., higher conformational entropy, in the folded state compared to the wild type. The increased conformational entropy of the mutant in the folded state can reduce the entropy gain during unfolding and thus renders it greater thermostability. Moreover, the increased structural flexibility, particularly around the catalytic site, can broaden the mutant's working temperature range and considerably improve its activity at ambient conditions, which is crucial for its application in diagnosing kidney diseases. Complementary all-atom molecular dynamics simulations indicated that the four mutations replaced several of the strong interresidue interactions (electrostatic interactions and hydrogen bonds) with weak hydrophobic interactions. These substitutions not only release the structural flexibility to promote the thermostability and enzymatic activity of the protein but they also preserve the protein structure from collapsing. Our findings may pave a route for the entropy-driven strategy to design proteins with high thermostability and activity.
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Affiliation(s)
- Fan Jiang
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jiahao Bian
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Liu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Song Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - 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
| | - Sha Jin
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China.,Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China.,Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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5
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Pathak AK, Bandyopadhyay T. Heat-induced transitions of an empty minute virus of mice capsid in explicit water: all-atom MD simulation. J Biomol Struct Dyn 2022; 40:11900-11913. [PMID: 34459706 DOI: 10.1080/07391102.2021.1969283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The capsid-like structure of the virus-based protein nanoparticles (NPs) can serve as bionanomaterials, with applications in biomedicines and nanotechnology. Release of packaged material from these nanocontainers is associated with subtle conformational changes of the NP structure, which in vitro, is readily accomplished by heating. Characterizing the structural changes as a function of temperature may provide fresh insights into nanomaterial/antiviral strategies. Here, we have calculated heat induced changes in the properties of an empty minute virus of mice particle using large-scale ≈ 3.0 × 106 all-atom molecular dynamics simulations. We focus on two heat induced structural changes of the NP, namely, dynamical transition (DT) and breathing transition (BT), both characterized by sudden and sharp change of measured parameters at temperatures, TDT and TBT, respectively. While DT is assessed by mean-square fluctuation of hydrogen atoms of the NP, BT is monitored through internal volume and permeation rate of water molecules through the NP. Both the transitions, resulting primarily from collective atomistic motion, are found to occur at temperatures widely separated from one another (TBT>TDT). The breathing motions, responsible for the translocation events of the packaged materials through the NP to kick off, are further probed by computing atomic resolution stresses from NVE simulations. Distribution of equilibrium atomistic stresses on the NP reveals a largely asymmetric nature and suggests structural breathing may actually represent large dynamic changes in the hotspot regions, far from the NP pores, which is in remarkable resemblance with recently conducted hydrogen-deuterium exchange coupled to mass spectrometry experiment. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section, Chemistry Division, Bhabha Atomic Research Centre, Mumbai, India.,Homi Bhabha National Institute, Mumbai, India
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6
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Li Y, Han Z, Ma C, Hong L, Ding Y, Chen Y, Zhao J, Liu D, Sun G, Zuo T, Cheng H, Han CC. Structure and dynamics of supercooled water in the hydration layer of poly(ethylene glycol). STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2022; 9:054901. [PMID: 36090796 PMCID: PMC9462885 DOI: 10.1063/4.0000158] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
The statics and dynamics of supercooled water in the hydration layer of poly(ethylene glycol) (PEG) were studied by a combination of quasi-elastic neutron scattering (QENS) and molecular dynamics (MD) simulations. Two samples, that is, hydrogenated PEG/deuterated water (h-PEG/D2O) and fully deuterated PEG/hydrogenated water (d-PEG/H2O) with the same molar ratio of ethylene glycol (EG) monomer to water, 1:1, are compared. The QENS data of h-PEG/D2O show the dynamics of PEG, and that of d-PEG/H2O reveals the motion of water. The temperature-dependent elastic scattering intensity of both samples has shown transitions at supercooled temperature, and these transition temperatures depend on the energy resolution of the instruments. Therefore, neither one is a phase transition, but undergoes dynamic process. The dynamic of water can be described as an Arrhenius to super-Arrhenius transition, and it reveals the hydrogen bonding network relaxation of hydration water around PEG at supercooled temperature. Since the PEG-water hydrogen bond structural relaxation time from MD is in good agreement with the average relaxation time from QENS (d-PEG/H2O), MD may further reveal the atomic pictures of the supercooled hydration water. It shows that hydration water molecules form a series of pools around the hydrophilic oxygen atom of PEG. At supercooled temperature, they have a more bond ordered structure than bulk water, proceed a trapping sites diffusion on the PEG surface, and facilitate the structural relaxation of PEG backbone.
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Affiliation(s)
| | | | | | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yanwei Ding
- Department of Chemical Physics, University of Science and Technology of China, Hefei 230026, China
| | - Ye Chen
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Junpeng Zhao
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Dong Liu
- Key Laboratory of Neutron Physics, Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999, China
| | - Guangai Sun
- Key Laboratory of Neutron Physics, Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621999, China
| | | | - He Cheng
- Author to whom correspondence should be addressed: . Tel.: +86-769-8915-6445. Fax: +86-769-8915-6441
| | - Charles C. Han
- Institute for Advanced Study, Shenzhen University, Shenzhen 508060, China
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7
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Zheng L, Liu Z, Zhang Q, Li S, Huang J, Zhang L, Zan B, Tyagi M, Cheng H, Zuo T, Sakai VG, Yamada T, Yang C, Tan P, Jiang F, Chen H, Zhuang W, Hong L. Universal dynamical onset in water at distinct material interfaces. Chem Sci 2022; 13:4341-4351. [PMID: 35509458 PMCID: PMC9006901 DOI: 10.1039/d1sc04650k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Interfacial water remains liquid and mobile much below 0 °C, imparting flexibility to the encapsulated materials to ensure their diverse functions at subzero temperatures. However, a united picture that can describe the dynamical differences of interfacial water on different materials and its role in imparting system-specific flexibility to distinct materials is lacking. By combining neutron spectroscopy and isotope labeling, we explored the dynamics of water and the underlying substrates independently below 0 °C across a broad range of materials. Surprisingly, while the function-related anharmonic dynamical onset in the materials exhibits diverse activation temperatures, the surface water presents a universal onset at a common temperature. Further analysis of the neutron experiment and simulation results revealed that the universal onset of water results from an intrinsic surface-independent relaxation: switching of hydrogen bonds between neighboring water molecules with a common energy barrier of ∼35 kJ mol−1. We demonstrated that the dynamical onset of interfacial water is an intrinsic property of water itself, resulting from a surface independent relaxation process in water with an approximately universal energy barrier of ∼35 kJ mol−1.![]()
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Affiliation(s)
- Lirong Zheng
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Zhuo Liu
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qiang Zhang
- College of Chemistry and Materials Science, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia 028043, China
| | - Song Li
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lei Zhang
- School of Materials Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Zan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, Maryland 20899, USA
- Department of Materials Science and Engineering, University of Maryland, College Park, Maryland 20742, USA
| | - He Cheng
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Taisen Zuo
- China Spallation Neutron Source (CSNS), Institute of High Energy Physics (IHEP), Chinese Academy of Science (CAS), Dongguan 523803, China
- Dongguan Institute of Neutron Science (DINS), Dongguan 523808, China
| | - Victoria García Sakai
- ISIS Pulsed Neutron and Muon Source, Rutherford Appleton Laboratory, Science & Technology Facilities Council, Didcot OX11 0QX, UK
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, 162-1 Shirakata, Tokai, Naka, Ibaraki 319-1106, Japan
| | - Chenxing Yang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Pan Tan
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Fan Jiang
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hao Chen
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
| | - Wei Zhuang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou, Fujian 35000, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, Fujian 361021, China
| | - Liang Hong
- School of Physics and Astronomy, Institute of Natural Sciences, Shanghai National Center for Applied Mathematics (SJTU Center), MOE-LSC, Shanghai Jiao Tong University, Shanghai 200240, China
- Shanghai Artificial Intelligence Laboratory, Shanghai 200232, China
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8
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Huang J, Xu Q, Liu Z, Jain N, Tyagi M, Wei DQ, Hong L. Controlling the Substrate Specificity of an Enzyme through Structural Flexibility by Varying the Salt-Bridge Density. Molecules 2021; 26:5693. [PMID: 34577164 PMCID: PMC8470667 DOI: 10.3390/molecules26185693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 09/03/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022] Open
Abstract
Many enzymes, particularly in one single family, with highly conserved structures and folds exhibit rather distinct substrate specificities. The underlying mechanism remains elusive, the resolution of which is of great importance for biochemistry, biophysics, and bioengineering. Here, we performed a neutron scattering experiment and molecular dynamics (MD) simulations on two structurally similar CYP450 proteins; CYP101 primarily catalyzes one type of ligands, then CYP2C9 can catalyze a large range of substrates. We demonstrated that it is the high density of salt bridges in CYP101 that reduces its structural flexibility, which controls the ligand access channel and the fluctuation of the catalytic pocket, thus restricting its selection on substrates. Moreover, we performed MD simulations on 146 different kinds of CYP450 proteins, spanning distinct biological categories including Fungi, Archaea, Bacteria, Protista, Animalia, and Plantae, and found the above mechanism generally valid. We demonstrated that, by fine changes of chemistry (salt-bridge density), the CYP450 superfamily can vary the structural flexibility of its member proteins among different biological categories, and thus differentiate their substrate specificities to meet the specific biological needs. As this mechanism is well-controllable and easy to be implemented, we expect it to be generally applicable in future enzymatic engineering to develop proteins of desired substrate specificities.
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Affiliation(s)
- Juan Huang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Qin Xu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
| | - Zhuo Liu
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute for Advanced Study, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Nitin Jain
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA;
| | - Madhusudan Tyagi
- NIST Center for Neutron Research, National Institute of Standards and Technology (NIST), Gaithersburg, MD 20899, USA;
- Department of Materials Science and Engineering, University of Maryland, College Park, MD 20742, USA
| | - Dong-Qing Wei
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China;
- Peng Cheng Laboratory, Shenzhen 518055, China
| | - Liang Hong
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China;
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
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9
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Benedetto A, Kearley GJ. Experimental demonstration of the novel "van-Hove integral method (vHI)" for measuring diffusive dynamics by elastic neutron scattering. Sci Rep 2021; 11:14093. [PMID: 34238981 PMCID: PMC8266890 DOI: 10.1038/s41598-021-93463-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/24/2021] [Indexed: 11/09/2022] Open
Abstract
Quasi-elastic neutron scattering (QENS)-based on the seminal work of Nobel Laureate Brockhouse-has been one of the major methods for studying pico-second to nano-second diffusive dynamics over the past 70 years. This is regarded as an "inelastic" method for dynamics. In contrast, we recently proposed a new neutron-scattering method for dynamics, which uses the elastic line of the scattering to access system dynamics directly in the time domain (Benedetto and Kearley in Sci Rep 9:11284, 2019). This new method has been denoted "vHI" that stands for "van Hove Integral". The reason is that, under certain conditions, the measured elastic intensity corresponds to the running-time integral of the intermediate scattering function, [Formula: see text], up to a time that is inversely proportional to the energy band-width incident on the sample. As a result, [Formula: see text] is accessed from the time derivative of the measured vHI profile. vHI has been supported by numerical and Monte-Carlo simulations, but has been difficult to validate experimentally due to the lack of a suitable instrument. Here we show that vHI works in practice, which we achieved by using a simple modification to the standard QENS backscattering spectrometer methodology. Basically, we varied the neutron-energy band-widths incident at the sample via a step-wise variation of the frequency of the monochromator Doppler-drive. This provides a measurement of the vHI profile at the detectors. The same instrument and sample were also used in standard QENS mode for comparison. The intermediate scattering functions, [Formula: see text], obtained by the two methods-vHI and QENS-are strikingly similar providing a direct experimental validation of the vHI method. Perhaps surprisingly, the counting statistics of the two methods are comparable even though the instrument used was expressly designed for QENS. This shows that the methodology modification adopted here can be used in practice to access vHI profiles at many of the backscattering spectrometers worldwide. We also show that partial integrations of the measured QENS spectrum cannot provide the vHI profile, which clarifies a common misconception. At the same time, we show a novel approach which does access [Formula: see text] from QENS spectra.
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Affiliation(s)
- Antonio Benedetto
- School of Physics, University College Dublin, Dublin 4, Ireland.
- Conway Institute, University College Dublin, Dublin 4, Ireland.
- Department of Sciences, University of Roma Tre, Rome, Italy.
- Laboratory for Neutron Scattering, Paul Scherrer Institute, Villigen, Switzerland.
| | - Gordon J Kearley
- School of Physics, University College Dublin, Dublin 4, Ireland
- School of Chemistry, University College Dublin, Dublin 4, Ireland
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10
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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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11
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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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12
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Schirò G, Weik M. Role of hydration water in the onset of protein structural dynamics. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:463002. [PMID: 31382251 DOI: 10.1088/1361-648x/ab388a] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Proteins are the molecular workhorses in a living organism. Their 3D structures are animated by a multitude of equilibrium fluctuations and specific out-of-equilibrium motions that are required for proteins to be biologically active. When studied as a function of temperature, functionally relevant dynamics are observed at and above the so-called protein dynamical transition (~240 K) in hydrated, but not in dry proteins. In this review we present and discuss the main experimental and computational results that provided evidence for the dynamical transition, with a focus on the role of hydration water dynamics in sustaining functional protein dynamics. The coupling and mutual influence of hydration water dynamics and protein dynamics are discussed and the hypotheses illustrated that have been put forward to explain the physical origin of their onsets.
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Affiliation(s)
- Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CNRS, CEA, Grenoble, France
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13
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Combining Neutron Scattering, Deuteration Technique, and Molecular Dynamics Simulations to Study Dynamics of Protein and Its Surface Water Molecules. CHINESE JOURNAL OF POLYMER SCIENCE 2019. [DOI: 10.1007/s10118-019-2312-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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14
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Pathak AK, Bandyopadhyay T. Temperature Induced Dynamical Transition of Biomolecules in Polarizable and Nonpolarizable TIP3P Water. J Chem Theory Comput 2019; 15:2706-2718. [PMID: 30849227 DOI: 10.1021/acs.jctc.9b00005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Temperature induced dynamical transition (DT), associated with a sharp rise in molecular flexibility, is well-known to be exhibited between 270 and 280 K in glycerol to 200-230 K in hydrated biomolecules and is controlled by diffusivity (viscosity) of the solvation layer. In the molecular dynamics (MD) community, especially for water as a solvent, this has been an intense area of research despite decades of investigations. However, in general, water in these studies is described by empirical nonpolarizable force fields in which electronic polarizability is treated implicitly with effective charges and related parameters. This might have led to the present trait of discovery that DTs of biomolecules, irrespective of the potential functions for water models used, occur within a narrow band of temperature variation (30-40 K). Whereas a water molecule in a biomolecular surface and one in bulk are polarized differently, therefore explicit treatment of water polarizability would be a powerful approach toward the treatment of hydration water, believed to cause the DT manifestation. Using MD simulations, we investigated the effects of polarizable water on the DT of biomolecules and the dynamic properties of hydration water. We chose two types of solutes: globular protein (lysozyme) and more open and flexible RNAs (a hairpin and a riboswitch) with different natures of hydrophilic sites than proteins in general. We found that the characteristic temperature of DT ( TDT) for the solutes in polarizable water is always higher than that in its nonpolarizable counterpart. In particular, for RNAs, the variations are found to be ∼45 K between the two water models, whereas for the more compact lysozyme, it is only ∼4 K. The results are discussed in light of the enormous increase in relaxation times of a liquid upon cooling in the paradigm of dynamic switchover in hydration water with liquid-liquid phase transition, derived from the existence of the second critical point. Our result supports the idea that structures of biomolecules and their interactions with the hydration water determines TDT and provides evidence for the decisive role of polarizable water on the onset of DT, which has been hitherto ignored.
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Affiliation(s)
- Arup Kumar Pathak
- Theoretical Chemistry Section , Bhabha Atomic Research Centre , Mumbai 400 085 , India.,Homi Bhabha National Institute , Mumbai 400094 , India
| | - Tusar Bandyopadhyay
- Theoretical Chemistry Section , Bhabha Atomic Research Centre , Mumbai 400 085 , India.,Homi Bhabha National Institute , Mumbai 400094 , India
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15
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Tavagnacco L, Chiessi E, Zanatta M, Orecchini A, Zaccarelli E. Water-Polymer Coupling Induces a Dynamical Transition in Microgels. J Phys Chem Lett 2019; 10:870-876. [PMID: 30735054 PMCID: PMC6416711 DOI: 10.1021/acs.jpclett.9b00190] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/08/2019] [Indexed: 06/09/2023]
Abstract
The long debated protein dynamical transition was recently found also in nonbiological macromolecules, such as poly- N-isopropylacrylamide (PNIPAM) microgels. Here, by using atomistic molecular dynamics simulations, we report a description of the molecular origin of the dynamical transition in these systems. We show that PNIPAM and water dynamics below the dynamical transition temperature T d are dominated by methyl group rotations and hydrogen bonding, respectively. By comparing with bulk water, we unambiguously identify PNIPAM-water hydrogen bonding as mainly responsible for the occurrence of the transition. The observed phenomenology thus crucially depends on the water-macromolecule coupling, being relevant to a wide class of hydrated systems, independently from the biological function.
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Affiliation(s)
- Letizia Tavagnacco
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
| | - Ester Chiessi
- Department
of Chemical Sciences and Technologies, University
of Rome Tor Vergata, Via della Ricerca Scientica I, 00133 Rome, Italy
| | - Marco Zanatta
- Department
of Computer Science, University of Verona, Strada Le Grazie 15, 37138 Verona, Italy
| | - Andrea Orecchini
- Department
of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM
c/o Department of Physics and Geology, University
of Perugia, Via A. Pascoli, 06123 Perugia, Italy
| | - Emanuela Zaccarelli
- CNR-ISC
and Department of Physics, Sapienza University
of Rome, Piazzale A.
Moro 2, 00185 Rome, Italy
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16
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Zeller D, Telling MTF, Zamponi M, García Sakai V, Peters J. Analysis of elastic incoherent neutron scattering data beyond the Gaussian approximation. J Chem Phys 2018; 149:234908. [PMID: 30579322 DOI: 10.1063/1.5049938] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
This work addresses the use of the Gaussian approximation as a common tool to extract atomic motions in proteins from elastic incoherent neutron scattering and whether improvements in data analysis and additional information can be obtained when going beyond that. We measured alpha-lactalbumin with different levels of hydration on three neutron backscattering spectrometers, to be able to resolve a wide temporal and spatial range for dynamics. We demonstrate that the Gaussian approximation gives qualitatively similar results to models that include heterogeneity, if one respects a certain procedure to treat the intercept of the elastic intensities with the momentum transfer axis. However, the inclusion of motional heterogeneity provides better fits to the data. Our analysis suggests an approach of limited heterogeneity, where including only two kinds of motions appears sufficient to obtain more quantitative results for the mean square displacement. Finally, we note that traditional backscattering spectrometers pose a limit on the lowest accessible momentum transfer. We therefore suggest that complementary information about the spatial evolution of the elastic intensity close to zero momentum transfer can be obtained using other neutron methods, in particular, neutron spin-echo together with polarization analysis.
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Affiliation(s)
- D Zeller
- Université Grenoble Alpes, CNRS, LiPhy, 140 av. de la Physique, 38000 Grenoble, France
| | - M T F Telling
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 0QX, United Kingdom
| | - M Zamponi
- Forschungszentrum Jülich GmbH, Jülich Centre for Neutron Science (JCNS) at Heinz Maier-Leibnitz Zentrum (MLZ), Lichtenbergstr. 1, 85748 Garching, Germany
| | - V García Sakai
- ISIS Pulsed Neutron and Muon Source, STFC Rutherford Appleton Laboratory, Chilton, Oxfordshire OX11 0QX, United Kingdom
| | - J Peters
- Université Grenoble Alpes, CNRS, LiPhy, 140 av. de la Physique, 38000 Grenoble, France
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17
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Liu Z, Yang C, Huang J, Ciampalini G, Li J, García Sakai V, Tyagi M, O'Neill H, Zhang Q, Capaccioli S, Ngai KL, Hong L. Direct Experimental Characterization of Contributions from Self-Motion of Hydrogen and from Interatomic Motion of Heavy Atoms to Protein Anharmonicity. J Phys Chem B 2018; 122:9956-9961. [PMID: 30295486 DOI: 10.1021/acs.jpcb.8b09355] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
One fundamental challenge in biophysics is to understand the connection between protein dynamics and its function. Part of the difficulty arises from the fact that proteins often present local atomic motions and collective dynamics on the same time scales, and challenge the experimental identification and quantification of different dynamic modes. Here, by taking lyophilized proteins as the example, we combined deuteration technique and neutron scattering to separate and characterize the self-motion of hydrogen and the collective interatomic motion of heavy atoms (C, O, N) in proteins on the pico-to-nanosecond time scales. We found that hydrogen atoms present an instrument-resolution-dependent onset for anharmonic motions, which can be ascribed to the thermal activation of local side-group motions. However, the protein heavy atoms exhibit an instrument-resolution-independent anharmonicity around 200 K, which results from unfreezing of the relaxation of the protein structures on the laboratory equilibrium time (100-1000 s), softening of the entire bio-macromolecules.
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Affiliation(s)
| | | | | | - Gaia Ciampalini
- Dipartimento di Fisica "E. Fermi" , Università di Pisa and Istituto per Processi Chimico-Fisici-Consiglio Nazionale delle Ricerche , Largo Pontecorvo 3 , Pisa 56127 , Italy
| | | | - Victoria García Sakai
- ISIS Neutron and Muon Facility , Rutherford Appleton Laboratory, Science & Technology Facilities Council , Didcot OX11 0QX , United Kingdom
| | - Madhusudan Tyagi
- National Institute of Standards and Technology (NIST) , NIST Center for Neutron Research , Gaithersburg , Maryland 20899 , United States.,Department of Materials Science and Engineering , University of Maryland , College Park , Maryland 20742 , United States
| | - Hugh O'Neill
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37931 , United States
| | - Qiu Zhang
- Biology and Soft Matter Division , Oak Ridge National Laboratory , Oak Ridge , Tennessee 37931 , United States
| | - Simone Capaccioli
- Dipartimento di Fisica "E. Fermi" , Università di Pisa and Istituto per Processi Chimico-Fisici-Consiglio Nazionale delle Ricerche , Largo Pontecorvo 3 , Pisa 56127 , Italy
| | - K L Ngai
- Dipartimento di Fisica "E. Fermi" , Università di Pisa and Istituto per Processi Chimico-Fisici-Consiglio Nazionale delle Ricerche , Largo Pontecorvo 3 , Pisa 56127 , Italy
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18
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Dynamical properties of myoglobin in an ultraviscous water-glycerol solvent investigated with elastic neutron scattering and FTIR spectroscopy. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.07.050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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19
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Zanatta M, Tavagnacco L, Buratti E, Bertoldo M, Natali F, Chiessi E, Orecchini A, Zaccarelli E. Evidence of a low-temperature dynamical transition in concentrated microgels. SCIENCE ADVANCES 2018; 4:eaat5895. [PMID: 30276264 PMCID: PMC6162076 DOI: 10.1126/sciadv.aat5895] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 08/21/2018] [Indexed: 05/07/2023]
Abstract
A low-temperature dynamical transition has been reported in several proteins. We provide the first observation of a "protein-like" dynamical transition in nonbiological aqueous environments. To this aim, we exploit the popular colloidal system of poly-N-isopropylacrylamide (PNIPAM) microgels, extending their investigation to unprecedentedly high concentrations. Owing to the heterogeneous architecture of the microgels, water crystallization is avoided in concentrated samples, allowing us to monitor atomic dynamics at low temperatures. By elastic incoherent neutron scattering and molecular dynamics simulations, we find that a dynamical transition occurs at a temperature T d ~ 250 K, independently from PNIPAM mass fraction. However, the transition is smeared out on approaching dry conditions. The quantitative agreement between experiments and simulations provides evidence that the transition occurs simultaneously for PNIPAM and water dynamics. The similarity of these results with hydrated protein powders suggests that the dynamical transition is a generic feature in complex macromolecular systems, independently from their biological function.
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Affiliation(s)
- Marco Zanatta
- Department of Computer Science, University of Verona, Strada le Grazie 15, 37134 Verona, Italy
| | - Letizia Tavagnacco
- Consiglio Nazionale delle Ricerche (CNR)–Istituto dei Sistemi Complessi, Sede Sapienza, and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy
| | - Elena Buratti
- CNR–Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Area della Ricerca, via G. Moruzzi 1, 56124 Pisa, Italy
| | - Monica Bertoldo
- CNR–Istituto per i Processi Chimico-Fisici, Sede Secondaria di Pisa, Area della Ricerca, via G. Moruzzi 1, 56124 Pisa, Italy
- Corresponding author. (M.B.); (A.O.); (E.Z.)
| | - Francesca Natali
- CNR–Istituto Officina dei Materiali (IOM), Operative Group in Grenoble, c/o Institut Laue Langevin, 6 rue Jules Horowitz, BP 156, 38042 Grenoble Cedex 9, France
| | - Ester Chiessi
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata, Via della Ricerca Scientifica I, 00133 Rome, Italy
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, Via A. Pascoli, 06123 Perugia, Italy
- Corresponding author. (M.B.); (A.O.); (E.Z.)
| | - Emanuela Zaccarelli
- Consiglio Nazionale delle Ricerche (CNR)–Istituto dei Sistemi Complessi, Sede Sapienza, and Department of Physics, Sapienza University of Rome, Piazzale A. Moro 2, 00185 Rome, Italy
- Corresponding author. (M.B.); (A.O.); (E.Z.)
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20
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Chen P, Terenzi C, Furó I, Berglund LA, Wohlert J. Hydration-Dependent Dynamical Modes in Xyloglucan from Molecular Dynamics Simulation of 13C NMR Relaxation Times and Their Distributions. Biomacromolecules 2018; 19:2567-2579. [DOI: 10.1021/acs.biomac.8b00191] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Pan Chen
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Camilla Terenzi
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - István Furó
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Lars A. Berglund
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
| | - Jakob Wohlert
- Wallenberg Wood Science Center, KTH Royal Institute of Technology, SE-10044 Stockholm, Sweden
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21
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Abstract
Dynamic neutron scattering directly probes motions in biological systems on femtosecond to microsecond timescales. When combined with molecular dynamics simulation and normal mode analysis, detailed descriptions of the forms and frequencies of motions can be derived. We examine vibrations in proteins, the temperature dependence of protein motions, and concepts describing the rich variety of motions detectable using neutrons in biological systems at physiological temperatures. New techniques for deriving information on collective motions using coherent scattering are also reviewed.
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Affiliation(s)
- Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Pan Tan
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, USA; .,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Liang Hong
- School of Physics and Astronomy and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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22
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Abstract
Protein dynamics is characterized by fluctuations among different conformational substates, i.e. the different minima of their energy landscape. At temperatures above ~200 K, these fluctuations lead to a steep increase in the thermal dependence of all dynamical properties, phenomenon known as Protein Dynamical Transition. In spite of the intense studies, little is known about the effects of pressure on these processes, investigated mostly near room temperature. We studied by neutron scattering the dynamics of myoglobin in a wide temperature and pressure range. Our results show that high pressure reduces protein motions, but does not affect the onset temperature for the Protein Dynamical Transition, indicating that the energy differences and barriers among conformational substates do not change with pressure. Instead, high pressure values strongly reduce the average structural differences between the accessible conformational substates, thus increasing the roughness of the free energy landscape of the system.
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23
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Benedetto A. Low-Temperature Decoupling of Water and Protein Dynamics Measured by Neutron Scattering. J Phys Chem Lett 2017; 8:4883-4886. [PMID: 28937227 DOI: 10.1021/acs.jpclett.7b02273] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Water plays a major role in biosystems, greatly contributing to determine their structure, stability, and function. It is well known, for instance, that proteins require a minimum amount of water to be fully functional. Despite many years of intensive research, however, the detailed nature of protein-hydration water interactions is still partly unknown. The widely accepted "protein dynamical transition" scenario is based on perfect coupling between the dynamics of proteins and that of their hydration water, which has never been probed in depth experimentally. I present here high-resolution elastic neutron scattering measurements of the atomistic dynamics of lysozyme in water. The results show for the first time that the dynamics of proteins and of their hydration water are actually decoupled at low temperatures. This important result challenges the "protein dynamical transition" scenario and requires a new model to link protein dynamics to the dynamics of its hydration water.
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Affiliation(s)
- Antonio Benedetto
- School of Physics, University College Dublin , Dublin 4, Ireland
- Laboratory for Neutron Scattering, Paul Scherrer Institut , Villigen, Switzerland
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