Hydrogen bonding in helical polypeptides from molecular dynamics simulations and amide hydrogen exchange analysis: alamethicin and melittin in methanol

Biophysical Journal
R B SessionsC E Dempsey

Abstract

Molecular dynamics simulations of ion channel peptides alamethicin and melittin, solvated in methanol at 27 degrees C, were run with either regular alpha-helical starting structures (alamethicin, 1 ns; melittin 500 ps either with or without chloride counterions), or with the x-ray crystal coordinates of alamethicin as a starting structure (1 ns). The hydrogen bond patterns and stabilities were characterized by analysis of the dynamics trajectories with specified hydrogen bond angle and distance criteria, and were compared with hydrogen bond patterns and stabilities previously determined from high-resolution NMR structural analysis and amide hydrogen exchange measurements in methanol. The two alamethicin simulations rapidly converged to a persistent hydrogen bond pattern with a high level of 3(10) hydrogen bonding involving the amide NH's of residues 3, 4, 9, 15, and 18. The 3(10) hydrogen bonds stabilizing amide NH's of residues C-terminal to P2 and P14 were previously proposed to explain their high amide exchange stabilities. The absence, or low levels of 3(10) hydrogen bonds at the N-terminus or for A15 NH, respectively, in the melittin simulations, is also consistent with interpretations from amide exchange analysis. Perturb...Continue Reading

References

Sep 1, 1992·Journal of Molecular Graphics·D J Osguthorpe, P Dauber-Osguthorpe
Apr 9, 1991·FEBS Letters·C E DempseyI D Campbell
Jan 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·G R MarshallM T Leplawy
Feb 24, 1987·Biochemistry·G EspositoI D Campbell
Dec 5, 1989·Journal of Molecular Biology·R B SessionsD J Osguthorpe
Jan 1, 1985·Advances in Protein Chemistry·G D RoseJ A Smith
Jan 1, 1989·European Biophysics Journal : EBJ·A PastoreI D Campbell
Apr 5, 1988·European Journal of Biochemistry·R BazzoI D Campbell
Sep 1, 1987·Biopolymers·L PielaH A Scheraga
Jan 1, 1966·Advances in Protein Chemistry·A Hvidt, S O Nielsen
Nov 1, 1983·Quarterly Reviews of Biophysics·S W Englander, N R Kallenbach
Jan 1, 1984·Progress in Biophysics and Molecular Biology·E N Baker, R E Hubbard
Oct 27, 1995·Journal of Molecular Biology·D J TobiasS J Opella
Nov 1, 1993·Quarterly Reviews of Biophysics·M S Sansom
Jun 13, 1995·Biochemistry·J D Hirst, C L Brooks
Sep 1, 1993·Proteins·Y BaiS W Englander
Oct 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·D H KitsonA T Hagler
May 1, 1997·Proteins·W A Shirley, C L Brooks

❮ Previous
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Citations

Dec 3, 2005·European Biophysics Journal : EBJ·Alice GlättliWilfred F van Gunsteren
Apr 4, 2006·Journal of the American Society for Mass Spectrometry·Zhongqi Zhang, Joseph Bordas-Nagy
Dec 21, 2000·Trends in Pharmacological Sciences·M S Sansom, H Weinstein
Sep 15, 2011·Journal of the American Chemical Society·Patricio O CraigPeter G Wolynes
Aug 28, 2002·Proceedings of the National Academy of Sciences of the United States of America·Danilo RoccatanoAlan E Mark
Dec 14, 2011·Biochemical and Biophysical Research Communications·Eamonn F Healy, Peter J King
Oct 2, 2007·Biophysical Journal·Seiichiro TanizakiMichael Feig
Sep 13, 2005·Protein Science : a Publication of the Protein Society·Danilo RoccatanoGiorgio Colombo
Oct 21, 2010·Biophysical Journal·Stefan QuintChristina Scharnagl
Jul 25, 2015·The Journal of Physical Chemistry. B·Chenyi LiaoJianing Li
Jul 12, 2005·Acta Microbiologica Et Immunologica Hungarica·A SzekeresCs Vágvölgyi
Jan 6, 1999·Biophysical Journal·D P TielemanH J Berendsen
Jun 22, 2017·Journal of Chemical Theory and Computation·Mee Y ShelleyJohn C Shelley
Aug 31, 2000·Proteins·A GrossfieldT B Woolf
Jun 26, 2007·Chemistry & Biodiversity·Balázs LeitgebLászló Kredics
Dec 21, 2019·Physical Chemistry Chemical Physics : PCCP·Jakub DąbrowskiArkadiusz Ptak
Aug 15, 2000·Annual Review of Nutrition·N Berriot-VaroqueauxJ R Wetterau
Feb 1, 2011·Biopolymers·Ottavia SpigaNeri Niccolai
Oct 28, 2018·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Daniel SethioElfi Kraka
Jan 16, 2021·The Journal of Biological Chemistry·Chloe A N GerakLawrence P McIntosh
Oct 13, 2009·Journal of Chemical Theory and Computation·Willy WriggersDavid E Shaw
Mar 13, 1999·Biophysical Chemistry·P C Biggin, M S Sansom
Jun 10, 2021·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Na Liu, Qingzhong Li
Aug 19, 2004·Journal of the American Chemical Society·Darón I FreedbergRichard W Pastor
Jan 21, 2004·Biochemistry·Debra M FerraroAndrew D Robertson

❮ Previous
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