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Molecular Insight into Different Denaturing Efficiency of Urea, Guanidinium, and Methanol: A Comparative Simulation Study

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    Molecular Insight into Different Denaturing Efficiency of Urea, Guanidinium, and Methanol: A Comparative Simulation Study
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    † Department of Applied Physics, University of Fukui, 3-9-1 Bunkyo,Fukui 910-8507, Japan
    ‡ Department of Mechanical Engineering, Keio University, Yokohama 223-8522, Japan
    § Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, South Korea
    ∥ International Institute for Carbon-Neutral Energy Research (WPI-I2CNER), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
    ⊥ Department of Chemistry, University of Nebraska, Lincoln, Nebraska 68588, United States
    *E-mail: [email protected], [email protected]
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    Journal of Chemical Theory and Computation

    Cite this: J. Chem. Theory Comput. 2013, 9, 6, 2540–2551
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    https://doi.org/10.1021/ct3010968
    Published April 17, 2013
    Copyright © 2013 American Chemical Society
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    Abstract

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    We have designed various nanoslit systems, whose opposing surfaces can be either hydrophobic, hydrophilic, or simply a water-vapor interface, for the molecular dynamics simulation of confined water with three different protein denaturants, i.e., urea, guanidinium chloride (GdmCl), and methanol, respectively. Particular attention is placed on the preferential adsorption of the denaturant molecules onto the opposing surfaces and associated resident time in the vicinal layer next to the surfaces, as well as their implication in the denaturing efficiency of different denaturant molecules. Our simulation results show that among the three denaturants, the occupancy of methanol in the vicinal layer is the highest while the residence time of Gdm is the longest. Although the occupancy and the residence time of urea in the vicinal layer is less than those of the other two denaturant molecules, urea entails “all-around” properties for being a highly effective denaturant. The distinct characteristics of three denaturants may suggest a different molecular mechanism for the protein denaturation. This comparative simulation by design allows us to gain additional insights, on the molecular level, into the denaturation effect and related hydrophobic effect.

    Copyright © 2013 American Chemical Society

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    Supporting Information

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    Movies for urea, GdmCl, and methanol with the hydrophobic and hydrophilic plates in the 1% systems; local mole fraction and number density profiles with the hydrophobic and the hydrophilic plate for urea, Gdm, and methanol in 5% and 10% systems; and local mole fraction and number density profiles including the liquid–vapor surface for Gdm and methanol systems. These materials are available free of charge via the Internet at http://pubs.acs.org.

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    This article is cited by 18 publications.

    1. Jian Zhu, Jing Huang. Methylguanidinium at the Air/Water Interface: A Simulation Study with the Drude Polarizable Force Field. The Journal of Physical Chemistry B 2021, 125 (1) , 393-405. https://doi.org/10.1021/acs.jpcb.0c08556
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    3. Biswajit Biswas, Aswathy N. Muttathukattil, Govardhan Reddy, Prashant Chandra Singh. Contrasting Effects of Guanidinium Chloride and Urea on the Activity and Unfolding of Lysozyme. ACS Omega 2018, 3 (10) , 14119-14126. https://doi.org/10.1021/acsomega.8b01911
    4. S. Strazdaite, J. Versluis, N. Ottosson, and Huib J. Bakker . Orientation of Methylguanidinium Ions at the Water–Air Interface. The Journal of Physical Chemistry C 2017, 121 (42) , 23398-23405. https://doi.org/10.1021/acs.jpcc.7b03752
    5. Pan Chen, Yoshiharu Nishiyama, Jakob Wohlert, Ang Lu, Karim Mazeau, and Ahmed E. Ismail . Translational Entropy and Dispersion Energy Jointly Drive the Adsorption of Urea to Cellulose. The Journal of Physical Chemistry B 2017, 121 (10) , 2244-2251. https://doi.org/10.1021/acs.jpcb.6b11914
    6. Di Cui, Shu-Ching Ou, and Sandeep Patel . Protein Denaturants at Aqueous–Hydrophobic Interfaces: Self-Consistent Correlation between Induced Interfacial Fluctuations and Denaturant Stability at the Interface. The Journal of Physical Chemistry B 2015, 119 (1) , 164-178. https://doi.org/10.1021/jp507203g
    7. Carolyn N. Kingsley, Jan C. Bierma, Vyvy Pham, and Rachel W. Martin . γS-Crystallin Proteins from the Antarctic Nototheniid Toothfish: A Model System for Investigating Differential Resistance to Chemical and Thermal Denaturation. The Journal of Physical Chemistry B 2014, 118 (47) , 13544-13553. https://doi.org/10.1021/jp509134d
    8. Richard J. Cooper, Sven Heiles, Matthew J. DiTucci, and Evan R. Williams . Hydration of Guanidinium: Second Shell Formation at Small Cluster Size. The Journal of Physical Chemistry A 2014, 118 (30) , 5657-5666. https://doi.org/10.1021/jp506429a
    9. Ishai Strauss, Henry Chan, and Petr Král . Ultralong Polarization Chains Induced by Ions Solvated in Confined Water Monolayers. Journal of the American Chemical Society 2014, 136 (4) , 1170-1173. https://doi.org/10.1021/ja4087962
    10. Shuching Ou, Di Cui, and Sandeep Patel . Liquid–Vapor Interfacial Properties of Aqueous Solutions of Guanidinium and Methyl Guanidinium Chloride: Influence of Molecular Orientation on Interface Fluctuations. The Journal of Physical Chemistry B 2013, 117 (39) , 11719-11731. https://doi.org/10.1021/jp405862p
    11. Yu Yamamori, Nobuyuki Matubayasi. Interaction-component analysis of the effects of urea and its alkylated derivatives on the structure of T4-lysozyme. The Journal of Chemical Physics 2017, 146 (22) https://doi.org/10.1063/1.4985222
    12. Zhaoqian Su, Cristiano L. Dias. Molecular interactions accounting for protein denaturation by urea. Journal of Molecular Liquids 2017, 228 , 168-175. https://doi.org/10.1016/j.molliq.2016.10.022
    13. Li-Yuan Zhu, Xin-Gen Hu, Hua-Qin Wang, Nan Chen. Enthalpic pairwise self-interactions of urea and its four derivatives in (dimethylformamide + water) mixtures rich in water at T = 298.15 K. The Journal of Chemical Thermodynamics 2016, 93 , 200-204. https://doi.org/10.1016/j.jct.2015.10.010
    14. Ryan D. Macdonald, Mazdak Khajehpour. Effects of the protein denaturant guanidinium chloride on aqueous hydrophobic contact-pair interactions. Biophysical Chemistry 2015, 196 , 25-32. https://doi.org/10.1016/j.bpc.2014.08.006
    15. Jun Zhang, Jie Zhong, Wen Li, Muhan Wang, Bing Liu, Zhen Li, Youguo Yan. Molecular insight into the dynamical adsorption behavior of nanoscale water droplets on a heterogeneous surface. RSC Advances 2015, 5 (65) , 52322-52329. https://doi.org/10.1039/C5RA09296E
    16. Sven Heiles, Richard J. Cooper, Matthew J. DiTucci, Evan R. Williams. Hydration of guanidinium depends on its local environment. Chemical Science 2015, 6 (6) , 3420-3429. https://doi.org/10.1039/C5SC00618J
    17. Subrat Kumar Pattanayak, Snehasis Chowdhuri. Effects of methanol on the hydrogen bonding structure and dynamics in aqueous N-methylacetamide solution. Journal of Molecular Liquids 2014, 194 , 141-148. https://doi.org/10.1016/j.molliq.2014.01.012
    18. Manoj Mandal, Chaitali Mukhopadhyay. Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin. Phys. Chem. Chem. Phys. 2014, 16 (39) , 21706-21716. https://doi.org/10.1039/C4CP01657B
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    Journal of Chemical Theory and Computation

    Cite this: J. Chem. Theory Comput. 2013, 9, 6, 2540–2551
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ct3010968
    Published April 17, 2013
    Copyright © 2013 American Chemical Society
    Request reuse permissions

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