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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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Marques MPM, Santos IP, Batista de Carvalho ALM, Mamede AP, Martins CB, Figueiredo P, Sarter M, Sakai VG, Batista de Carvalho LAE. Water dynamics in human cancer and non-cancer tissues. Phys Chem Chem Phys 2022; 24:15406-15415. [PMID: 35704895 DOI: 10.1039/d2cp00621a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Normal-to-malignant transformation is a poorly understood process associated with cellular biomechanical properties. These are strongly dependent on the dynamical behaviour of water, known to play a fundamental role in normal cellular activity and in the maintenance of the three-dimensional architecture of the tissue and the functional state of biopolymers. In this study, quasi-elastic neutron scattering was used to probe the dynamical behaviour of water in human cancer specimens and their respective surrounding normal tissue from breast and tongue, as an innovative approach for identifying particular features of malignancy. This methodology has been successfully used by the authors in human cells and was the first study of human tissues by neutron scattering techniques. A larger flexibility was observed for breast versus tongue tissues. Additionally, different dynamics were found for malignant and non-malignant specimens, depending on the tissue: higher plasticity for breast invasive cancer versus the normal, and an opposite effect for tongue. The data were interpreted in the light of two different water populations within the samples: one displaying bulk-like dynamics (extracellular and intracellular/cytoplasmic) and another with constrained flexibility (extracellular/interstitial and intracellular/hydration layers).
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Affiliation(s)
- M P M Marques
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal. .,University of Coimbra, Department of Life Sciences, 3000-456 Coimbra, Portugal
| | - I P Santos
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - A L M Batista de Carvalho
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - A P Mamede
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - C B Martins
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
| | - P Figueiredo
- Oncology Institute of Coimbra Francisco Gentil, 3000-075 Coimbra, Portugal
| | - M Sarter
- ISIS Neutron and Muon Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
| | - V García Sakai
- ISIS Neutron and Muon Facility, STFC Rutherford Appleton Laboratory, Chilton, Didcot, OX11 0QX, UK
| | - L A E Batista de Carvalho
- University of Coimbra, Molecular Physical-Chemistry R&D Unit, Department of Chemistry, 3004-535 Coimbra, Portugal.
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Tan P, Huang J, Mamontov E, García Sakai V, Merzel F, Liu Z, Ye Y, Hong L. Decoupling between the translation and rotation of water in the proximity of a protein molecule. Phys Chem Chem Phys 2020; 22:18132-18140. [PMID: 32761039 DOI: 10.1039/d0cp02416c] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The interaction between water and biomacromolecules is of fundamental interest in biophysics, biochemistry and physical chemistry. By combining neutron scattering and molecular dynamics simulations on a perdeuterated protein at a series of hydration levels, we demonstrated that the translational motion of water is slowed down more significantly than its rotation, when water molecules approach the protein molecule. Further analysis of the simulation trajectories reveals that the observed decoupling results from the fact that the translational motion of water is more correlated over space and more retarded by the charged/polar residues and spatial confinement on the protein surface, than the rotation. Moreover, around the stable protein residues (with smaller atomic fluctuations), water exhibits more decoupled dynamics, indicating a connection between the observed translation-rotation decoupling in hydration water and the local stability of the protein molecule.
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Affiliation(s)
- Pan Tan
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Eugene Mamontov
- Spallation Neutron Source, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Victoria García Sakai
- ISIS Neutron and Muon Source, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, UK
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, SI 1000 Ljubljana, Slovenia
| | - Zhuo Liu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yiyang Ye
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China. and Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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Li R, Liu Z, Li L, Huang J, Yamada T, Sakai VG, Tan P, Hong L. Anomalous sub-diffusion of water in biosystems: From hydrated protein powders to concentrated protein solution to living cells. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2020; 7:054703. [PMID: 33094127 PMCID: PMC7556885 DOI: 10.1063/4.0000036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 09/22/2020] [Indexed: 06/11/2023]
Abstract
Water is essential to life and its translational motion in living systems mediates various biological processes, including transportation of function-required ingredients and facilitating the interaction between biomacromolecules. By combining neutron scattering and isotopic labeling, the present work characterizes translational motion of water on a biomolecular surface, in a range of systems: a hydrated protein powder, a concentrated protein solution, and in living Escherichia coli (E. coli) cells. Anomalous sub-diffusion of water is observed in all samples, which is alleviated upon increasing the water content. Complementary molecular dynamics simulations and coarse-grained numerical modeling demonstrated that the sub-diffusive behavior results from the heterogeneous distribution of microscopic translational mobility of interfacial water. Moreover, by comparing the experimental results measured on E. coli cells with those from a concentrated protein solution with the same amount of water, we show that water in the two samples has a similar average mobility, however the underlying distribution of motion is more heterogeneous in the living cell.
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Affiliation(s)
| | | | - Like Li
- Zhiyuan College, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Juan Huang
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Takeshi Yamada
- Neutron Science and Technology Center, Comprehensive Research Organization for Science and Society, Ibaraki 319-1106, Japan
| | - Victoria García Sakai
- ISIS Facility, Rutherford Appleton Laboratory, Chilton, Didcot OX11 0QX, United Kingdom
| | - Pan Tan
- Authors to whom correspondence should be addressed: and
| | - Liang Hong
- Authors to whom correspondence should be addressed: and
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