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

  • Corresponding author: Liang Hong, hongl3liang@sjtu.edu.cn
  • Received Date: 14 April 2019
    Revised Date: 18 May 2019
    Available Online: 2 September 2019

  • Protein internal dynamics is essential for its function. Exploring the internal dynamics of protein molecules as well as its connection to protein structure and function is a central topic in biophysics. However, the atomic motions in protein molecules exhibit a great degree of complexities. These complexities arise from the complex chemical composition and superposition of different types of atomic motions on the similar time scales, and render it challenging to explicitly understand the microscopic mechanism governing protein motions, functions, and their connections. Here, we demonstrate that, by using neutron scattering, molecular dynamics simulation, and deuteration technique, one can address this challenge to a large extent.
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    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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