Combining Neutron Scattering, Deuteration Technique, and Molecular Dynamics Simulations to Study Dynamics of Protein and Its Surface Water Molecules

Li-Rong Zheng Liang Hong

Citation:  Li-Rong Zheng, Liang Hong. Combining Neutron Scattering, Deuteration Technique, and Molecular Dynamics Simulations to Study Dynamics of Protein and Its Surface Water Molecules[J]. Chinese Journal of Polymer Science, 2019, 37(11): 1083-1091. doi: 10.1007/s10118-019-2312-2 shu

Combining Neutron Scattering, Deuteration Technique, and Molecular Dynamics Simulations to Study Dynamics of Protein and Its Surface Water Molecules

English


    1. [1]

      Johs, A.; Harwood, I. M.; Parks, J. M.; Nauss, R. E.; Smith, J. C.; Liang, L.; Miller, S. M. Structural characterization of intramolecular Hg2+ transfer between flexibly linked domains of mercuric ion reductase. J. Mol. Biol. 2011, 413 (3), 639-656. doi: 10.1016/j.jmb.2011.08.042

    2. [2]

      Martin, G. S. The hunting of the Src. Nat. Rev. Mol. Cell. Biol. 2001, 2 (5), 47-47. doi: 10.1038/35073094

    3. [3]

      Banks, R. D.; Blake, C. C.; Evans, P. R.; Haser, R., .; Rice, D. W.; Hardy, G. W.; Merrett, M., .; Phillips, A. W. Sequence, structure and activity of phosphoglycerate kinase: a possible hinge-bending enzyme. Nature 1979, 279 (5716), 773-777. doi: 10.1038/279773a0

    4. [4]

      Rupley, J. A.; Careri, G. Protein hydration and function. In Advances in protein chemistry. Elsevier, 1991, Vol. 41, p. 37−172

    5. [5]

      Bellissent-Funel, M. C.; Hassanali, A.; Havenith, M.; Henchman, R.; Pohl, P.; Sterpone, F.; Van, d. S. D.; Xu, Y.; Garcia, A. E. Water determines the structure and dynamics of proteins. Chem. Rev. 2016, 116 (13), 7673-7679. doi: 10.1021/acs.chemrev.5b00664

    6. [6]

      Hans, F.; Guo, C.; Joel, B.; Fenimore, P. W.; Helén, J.; Mcmahon, B. H.; Stroe, I. R.; Jan, S.; Young, R. D. A unified model of protein dynamics. Proc. Natl. Acad. Sci. USA 2009, 106 (13), 5129-5134. doi: 10.1073/pnas.0900336106

    7. [7]

      Biman, B. Water dynamics in the hydration layer around proteins and micelles. Chem. Rev. 2005, 105 (9), 3197-3219. doi: 10.1021/cr020661+

    8. [8]

      Philip, B. Water and life: seeking the solution. Nature 2005, 436 (7054), 1084. doi: 10.1038/4361084a

    9. [9]

      Pocker, Y. Water in enzyme reactions: Biophysical aspects of hydration-dehydration processes. CMLS, Cell. Mol. Life Sci. 2000, 57 (7), 1008-1017. doi: 10.1007/PL00000741

    10. [10]

      Jian, P.; Todd, S.; Ning, Z.; Catterall, W. A. The crystal structure of a voltage-gated sodium channel. Nature 2011, 475 (7356), 353-358. doi: 10.1038/nature10238

    11. [11]

      Pawlus, S.; Khodadadi, S.; Sokolov, A. P. Conductivity in hydrated proteins: no signs of the fragile-to-strong crossover. Phys. Rev. Lett. 2008, 100 (10), 2197-2204.

    12. [12]

      Otting, G.; Liepinsh, E.; Wuthrich, K. Protein hydration in aqueous solution. Science 1991, 254 (5034), 974-980. doi: 10.1126/science.1948083

    13. [13]

      Valeria, C. N.; Martina, H. New insights into the role of water in biological function: studying solvated biomolecules using terahertz absorption spectroscopy in conjunction with molecular dynamics simulations. J. Am. Chem. Soc. 2014, 136 (37), 12800-12807. doi: 10.1021/ja504441h

    14. [14]

      Yang, J.; Wang, Y.; Wang, L.; Zhong, D. Mapping hydration dynamics around a β-barrel protein. J. Am. Chem. Soc. 2017, 139 (12), 4399-4408. doi: 10.1021/jacs.6b12463

    15. [15]

      Chen, C.; Stevens, B.; Kaur, J.; Cabral, D.; Liu, H.; Wang, Y.; Zhang, H.; Rosenblum, G.; Smilansky, Z.; Goldman, Y. E. Single-molecule fluorescence measurements of ribosomal translocation dynamics. Mol. Cell 2011, 42 (3), 367-377. doi: 10.1016/j.molcel.2011.03.024

    16. [16]

      Hong, L.; Jain, N.; Cheng, X.; Bernal, A.; Tyagi, M.; Smith, J. C. Determination of functional collective motions in a protein at atomic resolution using coherent neutron scattering. Sci. Adv. 2016, 2 (10), e1600886. doi: 10.1126/sciadv.1600886

    17. [17]

      Hong, L.; Sharp, M. A.; Poblete, S.; Biehl, R.; Zamponi, M.; Szekely, N.; Appavou, M. S.; Winkler, R. G.; Nauss, R. E.; Johs, A.; Parks, J. M.; Yi, Z.; Cheng, X.; Liang, L.; Ohl, M.; Miller, S. M.; Richter, D.; Gompper, G.; Smith, J. C. Structure and dynamics of a compact state of a multidomain protein, the mercuric ion reductase. Biophys. J. 2014, 107 (2), 393-400. doi: 10.1016/j.bpj.2014.06.013

    18. [18]

      Hong, L.; Smolin, N.; Lindner, B.; Sokolov, A. P.; Smith, J. C. Three classes of motion in the dynamic neutron-scattering susceptibility of a globular protein. Phys. Rev. Lett. 2011, 107 (14), 148102. doi: 10.1103/PhysRevLett.107.148102

    19. [19]

      Hong, L.; Smolin, N.; Smith, J. C. de Gennes narrowing describes the relative motion of protein domains. Phys. Rev. Lett. 2014, 112 (15), 158102. doi: 10.1103/PhysRevLett.112.158102

    20. [20]

      Liu, Z.; Huang, J.; Tyagi, M.; O'Neill, H.; Zhang, Q.; Mamontov, E.; Jain, N.; Wang, Y.; Zhang, J.; Smith, J. C.; Hong, L. Dynamical transition of collective motions in dry proteins. Phys. Rev. Lett. 2017, 119 (4), 048101. doi: 10.1103/PhysRevLett.119.048101

    21. [21]

      Nickels, J. D.; O'Neill, H.; Hong, L.; Tyagi, M.; Ehlers, G.; Weiss, K. L.; Zhang, Q.; Yi, Z.; Mamontov, E.; Smith, J. C.; Sokolov, A. P. Dynamics of protein and its hydration water: neutron scattering studies on fully deuterated GFP. Biophys. J. 2012, 103 (7), 1566-1575. doi: 10.1016/j.bpj.2012.08.046

    22. [22]

      Tan, P.; Liang, Y.; Xu, Q.; Mamontov, E.; Li, J.; Xing, X.; Hong, L. Gradual crossover from subdiffusion to normal diffusion: a many-body effect in protein surface water. Phys. Rev. Lett. 2018, 120 (24), 248101. doi: 10.1103/PhysRevLett.120.248101

    23. [23]

      Hong, L.; Cheng, X.; Glass, D. C.; Smith, J. C. Surface hydration amplifies single-well protein atom diffusion propagating into the macromolecular core. Phys. Rev. Lett. 2012, 108 (23), 238102. doi: 10.1103/PhysRevLett.108.238102

    24. [24]

      Hong, L.; Glass, D. C.; Nickels, J. D.; Perticaroli, S.; Yi, Z.; Tyagi, M.; O'Neill, H.; Zhang, Q.; Sokolov, A. P.; Smith, J. C. Elastic and conformational softness of a globular protein. Phys. Rev. Lett. 2013, 110 (2), 028104. doi: 10.1103/PhysRevLett.110.028104

    25. [25]

      Liu, Z.; Yang, C.; Huang, J.; Ciampalini, G.; Li, J.; García Sakai, V.; Tyagi, M.; O’Neill, H.; Zhang, Q.; Capaccioli, S.; Ngai, K. L.; 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 (43), 9956-9961. doi: 10.1021/acs.jpcb.8b09355

    26. [26]

      Liu, Z.; Lemmonds, S.; Huang, J.; Tyagi, M.; Hong, L.; Jain, N. Entropic contribution to enhanced thermal stability in the thermostable P450 CYP119. Proc. Natl. Acad. Sci. USA 2018, 115 (43), E10049-E10058. doi: 10.1073/pnas.1807473115

    27. [27]

      Buchenau, U.; Wischnewski, A.; Richter, D.; Frick, B. Is the fast process at the glass transition mainly due to long wavelength excitations? Phys. Rev. Lett. 1996, 77 (19), 4035-4038. doi: 10.1103/PhysRevLett.77.4035

    28. [28]

      Nickels, J. D.; Perticaroli, S.; O'Neill, H.; Zhang, Q.; Ehlers, G.; Sokolov, A. P. Coherent neutron scattering and collective dynamics in the protein, GFP. Biophys. J. 2013, 105 (9), 2182-2187. doi: 10.1016/j.bpj.2013.09.029

    29. [29]

      Carpenter, J. M.; Pelizzari, C. A. Inelastic neutron scattering from amorphous solids. I. Calculation of the scattering law for model structures. Phys. Rev. B 1975, 12, 2391. doi: 10.1103/PhysRevB.12.2391

    30. [30]

      Suhre, K.; Sanejouand, Y. H. ElNemo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement. Nucleic Acids Res. 2004, 32 (suppl_2, 1), W610-W614.

    31. [31]

      Khodadadi, S.; Pawlus, S.; Sokolov, A. P. Influence of hydration on protein dynamics: Combining dielectric and neutron scattering spectroscopy data. J. Phys. Chem. B 2008, 112 (45), 14273-14280. doi: 10.1021/jp8059807

    32. [32]

      Modig, K.; Liepinsh, E.; Otting, G.; Halle, B. Dynamics of protein and peptide hydration. J. Am. Chem. Soc. 2004, 126 (1), 102-114. doi: 10.1021/ja038325d

    33. [33]

      Ebbinghaus, S.; Kim, S. J.; Heyden, M.; Yu, X.; Heugen, U.; Gruebele, M.; Leitner, D. M.; Havenith, M. An extended dynamical hydration shell around proteins. Proc. Natl. Acad. Sci. USA 2007, 104 (52), 20749-20752. doi: 10.1073/pnas.0709207104

    34. [34]

      King, J. T.; Kubarych, K. J. Site-specific coupling of hydration water and protein flexibility studied in solution with ultrafast 2D-IR spectroscopy. J. Am. Chem. Soc. 2012, 134 (45), 18705-18712. doi: 10.1021/ja307401r

    35. [35]

      Vitkup, D.; Ringe, D.; Petsko, G. A.; Karplus, M. Solvent mobility and the protein 'glass' transition. Nat. Struct. Biol. 2000, 7 (1), 34-38. doi: 10.1038/71231

    36. [36]

      Roh, J. H.; Curtis, J. E.; Azzam, S.; Novikov, V. N.; Peral, I.; Chowdhuri, Z.; Gregory, R. B.; Sokolov, A. P. Influence of hydration on the dynamics of lysozyme. Biophys. J. 2006, 91 (7), 2573-2588. doi: 10.1529/biophysj.106.082214

    37. [37]

      Rasmussen, B. F.; Stock, A. M.; Ringe, D.; Petsko, G. A. Crystalline ribonuclease-a Loses function below the dynamic transition at 220 K. Nature 1992, 357 (6377), 423-424. doi: 10.1038/357423a0

    38. [38]

      He, Y.; Ku, P. I.; Knab, J. R.; Chen, J. Y.; Markelz, A. G. Protein dynamical transition does not require protein structure. Phys. Rev. Lett. 2008, 101 (17), 178103. doi: 10.1103/PhysRevLett.101.178103

    39. [39]

      Ferrand, M.; Dianoux, A. J.; Petry, W.; Zaccaï, G. Thermal motions and function of bacteriorhodopsin in purple membranes: effects of temperature and hydration studied by neutron scattering. Proc. Natl. Acad. Sci. USA 1993, 90 (20), 9668-9672. doi: 10.1073/pnas.90.20.9668

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  • 发布日期:  2019-11-01
  • 收稿日期:  2019-04-14
  • 修回日期:  2019-05-18
  • 网络出版日期:  2019-09-02
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