Citation: YANG Kecheng, CUI Fengchao, LI Yunqi. Distribution and Dynamics of Water and Urea in Hydration Shell of Ribonuclease Sa: A Molecular Dynamics Simulation Study[J]. Chinese Journal of Applied Chemistry, ;2018, 35(10): 1243-1248. doi: 10.11944/j.issn.1000-0518.2018.10.170342 shu

Distribution and Dynamics of Water and Urea in Hydration Shell of Ribonuclease Sa: A Molecular Dynamics Simulation Study

YANG Kecheng ^a,b ,
CUI Fengchao ^a,, ,
LI Yunqi ^a,,

a.
Key Laboratory of Synthetic Rubber, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
b.
University of Chinese Academy of Sciences, Beijing 100049, China

Corresponding author: CUI Fengchao, fccui@ciac.ac.cn LI Yunqi, yunqi@ciac.ac.cn
Received Date: 18 September 2017
Revised Date: 16 October 2017
Accepted Date: 24 November 2017

Fund Project: the National Natural Science Foundation of China 21504092the National Natural Science Foundation of China 21374117Supported by the National Natural Science Foundation of China(No.21374117, No.21504092), the One Hundred Person Project of the Chinese Academy of Sciences

Figures(3)

Extensive molecular dynamics simulations were performed to study the distribution and dynamics of water and urea in the hydration shell of ribonuclease Sa(RNase Sa) under different urea concentrations. It is found that urea molecules have stronger interactions with protein than water molecules and are enriched on the surface of RNase Sa by displacing water molecules. Urea molecules prefer to interact with hydrophobic residues and form hydrogen bonds with the backbone of RNase Sa. The transitional and rotational dynamics of urea molecules are much slower than those of water molecules. Besides, the increased urea concentrations can slow down the transitional and rotational dynamics of water molecules, but have no regular influences on the dynamics of urea molecules. Our results can help understanding the different influences of urea and water molecules on the stability of proteins.
- ribonuclease Sa,
- survival time correlation function,
- rotational time correlation function,
- molecular dynamics simulations
1. [1]
  Biedermannová L, Schneider B. Hydration of Proteins and Nucleic Acids:Advances in Experiment and Theory. A Review[J]. Biochim Biophys Acta, 2016,1860(9):1821-1835. doi: 10.1016/j.bbagen.2016.05.036
2. [2]
  Hu J, Cao Z X. Water Science on the Molecular Scale:New Insights into the Characteristics of Water[J]. Natl Sci Rev, 2014,1(2):179-181. doi: 10.1093/nsr/nwt015
3. [3]
  Dill K A, MacCallum J L. The Protein-Folding Problem, 50 Years On[J]. Science, 2012,338(6110):1042-1046. doi: 10.1126/science.1219021
4. [4]
  Walters J, Milam S L, Clark A C. (2009)Practical Approaches to Protein Folding and Assembly: Spectroscopic Strategies in Thermodynamics and Kinetics[M]//Michael L Johnson, Jo M Holt, Gary K Ackers. Methods in Enzymology. Academic Press, 2009, 8: 1-39.
5. [5]
  Bellissent-Funel M C, Hassanali A, Havenith M. Water Determines the Structure and Dynamics of Proteins[J]. Chem Rev, 2016,116(13):7673-7697. doi: 10.1021/acs.chemrev.5b00664
6. [6]
  Doster W, Cusack S, Petry W. Dynamical Transition of Myoglobin Revealed by Inelastic Neutron Scattering[J]. Nature, 1989,337(6209):754-756. doi: 10.1038/337754a0
7. [7]
  Qvist J, Ortega G, Tadeo X. Hydration Dynamics of a HalophilicProtein in Folded and Unfolded States[J]. J Phys Chem B, 2012,116(10):3436-3444. doi: 10.1021/jp3000569
8. [8]
  Canchi D R, García A E. Cosolvent Effects on Protein Stability[J]. Annu Rev Phys Chem, 2013,64(1):273-293. doi: 10.1146/annurev-physchem-040412-110156
9. [9]
  Frank H S, Franks F. Structural Approach to the Solvent Power of Water for Hydrocarbons; Urea as a Structure Breaker[J]. J Chem Phys, 1968,48(10):4746-4757. doi: 10.1063/1.1668057
10. [10]
  Hua L, Zhou R, Thirumalai D. Urea Denaturation by Stronger Dispersion Interactions with Proteins than Water Implies a 2-Stage Unfolding[J]. Proc Natl Acad Sci USA, 2008,105(44):16928-16933. doi: 10.1073/pnas.0808427105
11. [11]
  Candotti M, Esteban-Martín S, Salvatella X. Toward an Atomistic Description of the Urea-Denatured State of Proteins[J]. Proc Natl Acad Sci USA, 2013,110(15):5933-5938. doi: 10.1073/pnas.1216589110
12. [12]
  Canchi D R, García A E. Backbone and Side-Chain Contributions in Protein Denaturation by Urea[J]. Biophys J, 2011,100(6):1526-1533. doi: 10.1016/j.bpj.2011.01.028
13. [13]
  Candotti M, Pérez A, Ferrer-Costa C. Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale[J]. PLoS Comput Biol, 2013,9(12)e1003393. doi: 10.1371/journal.pcbi.1003393
14. [14]
  Laurents D, Perez-Canadillas J M, Santoro J. Solution Structure and Dynamics of Ribonuclease Sa[J]. Proteins:Struct Funct Bioinf, 2001,44(3):200-211. doi: 10.1002/prot.v44:3
15. [15]
  Phillips J C, Braun R, Wang W. Scalable Molecular Dynamics with Namd[J]. J Comput Chem, 2005,26(16):1781-1802. doi: 10.1002/(ISSN)1096-987X
16. [16]
  Mackerell A D, Feig M, Brooks C L. Extending the Treatment of Backbone Energetics in Protein Force Fields:Limitations of Gas-Phase Quantum Mechanics in Reproducing Protein Conformational Distributions in Molecular Dynamics Simulations[J]. J Comput Chem, 2004,25(11):1400-1415. doi: 10.1002/jcc.v25:11
17. [17]
  MacKerell A D, Bashford D, Bellott M. All-atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins[J]. J Phys Chem B, 1998,102(18):3586-3616. doi: 10.1021/jp973084f
18. [18]
  Vanommeslaeghe K, Hatcher E, Acharya C. Charmm General Force Field:A Force Field for Drug-Like Molecules Compatible with the Charmm All-atom Additive Biological Force Fields[J]. J Comput Chem, 2010,31(4):671-690.
19. [19]
  Berman H M, Westbrook J, Feng Z. The Protein Data Bank[J]. Nucl Acids Res, 2000,28(1):235-242. doi: 10.1093/nar/28.1.235
20. [20]
  Humphrey W, Dalke A, Schulten K. Vmd:Visual molecular dynamics[J]. J Mol Graph, 1996,14(1):33-38. doi: 10.1016/0263-7855(96)00018-5
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