Influence of Disulfide Bridge on the Structural Stability of Human Neuroglobin: A Molecular Dynamics Simulation Using Latest Data Entry
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DOI:
https://doi.org/10.15625/0868-3166/26/2/8618Keywords:
molecular dynamics simulation, neuroglobin, crystal structure of proteinAbstract
In this paper, we investigated the role of the disulfide bridge in the structural stability of wild-type human neuroglobin. The classical simulation of the neuroglobin without the disulfide bridge was performed for a long simulation run of 240~ns using a new parameter set of Gromos96 force field and the latest data entry as the initial topologies. We used the analyzed data of original neuroglobin with the remained disulfide bridge to compare to the ones from this simulation. Our results showed that, the structure of neuroglobin was still very stable although the disulfide bridge was absent. There was only a few residues in B and C helices having a higher mobility. The most interesting result we obtained was that the increasing distance between the distal histidine and heme group could allow oxygen to bind more easily.Downloads
References
T. Burmester, B. Weich, S. Reinhardt, and T. Hankeln, Nature 407 (2000) 520.
M. Brunori and B. Vallone, FASEB J. 20 (2006) 2192.
M. Brunori and B. Vallone, Cell. Mol. Life Sci. 64 (2007) 1259.
K. Nienhaus and G. U. Nienhaus, IUBMB Life 59 (2007) 490.
T. Burmester and T. Hankeln, J. Exp. Biol. 212 (2009) 1423.
S. Dewilde, L. Kiger, T. Burmester, T. Hankeln, V. Baudin-Creuza, T. Aerts, M. C. Marden, R. Caubergs and L.
Moens, J. Biol. Chem. 276 (2001) 38949.
A. Pesce, S. Dewilde, M. Nardini, L. Moens, P. Ascenzi, T. Hankeln, T. Burmester, and M. Bolognesi, Structure
(2003) 1087-1095.
A. Pesce, S. Dewilde, M. Nardini, S. Dewilde, L. Moens, T. Hankeln, T. Burmester, P. Ascenzi and M. Bolognesi,
IUBMB Life 56 (2004) 657.
B.Vallone, K. Nienhaus, M. Brunori, and G. U. Nienhaus, Proteins 56 (2004) 85-92.
A. Bocahut, S. Bernad, P. Sebban and S. Sacquin-Mora, J. Phys Chem B 113 (2009) 16257.
F. Hoppe-Seyler, U¨ ber die oxydation in lebendem blute Med-chem Untersuch Lab 1 (1866) 133.
M. Brunori, Rend. Fis. Acc. Lincei 21 (2010) 335.
N. Kawada, D. B. Kristensen, K. Asahina, K. Nakatani, Y. Minamiyama, S. Seki and K. Yoshizato, The Journal
of Biological Chemistry 276 (2001) 25318.
T. Burmester, B. Ebner, B. Weich and T. Hankeln, Molecular Biology and Evolution 19 (2002) 416.
D. Hamdane et al., J. Biol. Chem. 278 (2003) 51713.
D. Hamdane, L. Kiger, S. Dewilde, B.N. Green, A. Pesce, J. Uzan, T. Burmester, T. Hankeln, M. Bolognesi, L.
Moens and M.C. Marden, Micron 35 (2004) 59.
E. Vinck, S. Van Doorslaer, S. Dewilde and L. Moens, J. Am. Chem. Soc. 126 (2004) 4516.
L. Astudillo, S. Bernad, V. Derrien, P. Sebban and J. Miksovska, Biophys. J. 99 (2010) L16-L18.
D. Hamdane et. al., J. Biol. Chem. 278 (2003) 51713.
B. G. Guimar˜aes, D. Hamdane, C. Lechauve, M. C. Marden and B. Golinelli-Pimpaneau, Acta Cryst. D 70
(2014) 1005.
N. Guex and M.C. Peitsch, Electrophoresis 18 (1997) 2714.
W. Humphrey, A. Dalke and K. Schulten, J. Molec. Graphics, 14 (1996) 33-38.
S. Pronk, S. P´all, R. Schulz, P. Larsson, P. Bjelkmar, R. Apostolov, M.R. Shirts, J.C. Smith, P.M. Kasson,
D. van der Spoel, B. Hess, E. Lindahl, Bioinformatics 29(7), 845854 (2013); M.J. Abraham, D. van der
Spoel, E. Lindahl, B. Hess, and the GROMACS development team, ”GROMACS User Manual version 5.1”,
www.gromacs.org (2015).
N. Schmid, A.P. Eichenberger, A. Choutko, S. Riniker, M. Winger, A.E. Mark and W.F. van Gunsteren, Eur.
Biophys. J. 40 (2011) 843-856.
H. J. C. Berendsen, J. R. Grigera and T. P. Straatsma, J. Phys. Chem. 91 (1987) 62696271.
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