Dynamics of water in the hydration layer of a partially unfolded structure of the protein HP-36

The Journal of Physical Chemistry. B
Sudip Chakraborty, Sanjoy Bandyopadhyay

Abstract

Atomistic molecular dynamics simulations of the folded native structure and a partially unfolded molten globule structure of the protein villin headpiece subdomain or HP-36 have been carried out with explicit solvent to explore the effects of unfolding on the dynamical behavior of water present in the hydration layers of different segments (three alpha-helices) of the protein. The calculations revealed that the unfolding of helix-2 influences the translational and rotational motions of water present in the hydration layers of the three helices in a heterogeneous manner. It is observed that a correlation exists between the unfolding of helix-2 and the microscopic kinetics of protein-water hydrogen bonds formed by its residues. This in turn has an influence on the rigidity of the hydration layers of the helices in the unfolded structure versus that in the folded native structure. These results should provide a microscopic explanation to recent solvation dynamics experiments on folded native and unfolded structures of proteins.

References

Jan 1, 1992·Annual Review of Physical Chemistry·R Pethig
Aug 7, 1990·Biochemistry·K A Dill
May 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·J D Honeycutt, D Thirumalai
Oct 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·M Levitt, R Sharon
Jan 1, 1986·Annals of the New York Academy of Sciences·H J BerendsenR G Geurtsen
Nov 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·J D Bryngelson, P G Wolynes
Mar 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·K A DillH S Chan
May 19, 1994·Nature·A SaliM Karplus
Feb 1, 1995·Current Opinion in Structural Biology·O B Ptitsyn
Jul 12, 1996·Journal of Molecular Biology·C J McKnightP S Kim
Mar 1, 1997·Nature Structural Biology·C J McKnightP S Kim
Mar 21, 1998·Proceedings of the National Academy of Sciences of the United States of America·F B Sheinerman, C L Brooks
Aug 26, 1998·Proceedings of the National Academy of Sciences of the United States of America·Y DuanP A Kollman
Feb 5, 1996·Physical Review Letters·A Luzar, D Chandler
Feb 14, 2002·Proceedings of the National Academy of Sciences of the United States of America·Samir Kumar PalAhmed H Zewail
Feb 16, 2002·Journal of Molecular Biology·C K ReddyB Jayaram
Apr 17, 2002·Physical Review Letters·M Tarek, D J Tobias
Apr 18, 2002·Proceedings of the National Academy of Sciences of the United States of America·Franci Merzel, Jeremy C Smith
Jun 6, 2002·Journal of the American Chemical Society·Massimo MarchiMatteo Ceccarelli
Aug 15, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jorge PeonAhmed H Zewail
Dec 6, 2002·Journal of the American Chemical Society·Christopher D SnowVijay S Pande
Feb 19, 2003·Accounts of Chemical Research·Kankan Bhattacharyya
May 3, 2003·Current Opinion in Structural Biology·Teresa Head-Gordon, Scott Brown
Dec 4, 2003·Journal of the American Chemical Society·Soonmin JangYoungshang Pak
Jan 8, 2004·Journal of the American Chemical Society·Kristofer ModigBertil Halle
Feb 28, 2004·Proceedings of the National Academy of Sciences of the United States of America·Garegin A PapoianPeter G Wolynes
Apr 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Young Min RheeVijay S Pande
Apr 23, 2004·Current Opinion in Structural Biology·José Nelson Onuchic, Peter G Wolynes
Jul 9, 2004·Biophysical Journal·Jose M BorregueroNikolay V Dokholyan
Aug 12, 2004·Chemical Reviews·Arthur G Palmer
Dec 8, 2004·Biochemistry·Bruno RizzutiLuigi Sportelli
Jun 22, 2005·Biochemistry·Soumi GuhaKankan Bhattacharyya
Jul 23, 2005·The Journal of Chemical Physics·Arnab MukherjeeBiman Bagchi
Sep 13, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ryan Day, Valerie Daggett
Sep 15, 2005·Chemical Reviews·Biman Bagchi
Nov 25, 2005·Journal of the American Chemical Society·Sanjoy BandyopadhyayBiman Bagchi
Dec 13, 2005·Journal of Molecular Biology·Yuefeng TangDaniel P Raleigh
Feb 14, 2006·The Journal of Physical Chemistry. B·Kalyanasis SahuKankan Bhattacharyya
Feb 24, 2006·The Journal of Physical Chemistry. B·Lan HuaB J Berne

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Citations

Oct 14, 2011·The Journal of Chemical Physics·Sudipta Kumar Sinha, Sanjoy Bandyopadhyay
Dec 24, 2013·The Journal of Chemical Physics·Somedatta Pal, Sanjoy Bandyopadhyay
Apr 10, 2014·Journal of Molecular Modeling·Li L DuanJohn Z H Zhang
Feb 11, 2015·The Journal of Chemical Physics·Somedatta PalSanjoy Bandyopadhyay
Jan 24, 2020·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Atanu MaityRajarshi Chakrabarti
Jun 1, 2010·The Journal of Physical Chemistry. B·Stefania PerticaroliAssunta Morresi
Jan 18, 2018·The Journal of Physical Chemistry. B·Madhulika GuptaSanjoy Bandyopadhyay

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