Helix bending in alamethicin: molecular dynamics simulations and amide hydrogen exchange in methanol

Biophysical Journal
N GibbsC E Dempsey

Abstract

Molecular dynamics simulations of alamethicin in methanol were carried out with either a regular alpha-helical conformation or the x-ray crystal structure as starting structures. The structures rapidly converged to a well-defined hydrogen-bonding pattern with mixed alpha-helical and 3(10)-helical hydrogen bonds, consistent with NMR structural characterization, and did not unfold throughout the 1-ns simulation, despite some sizable backbone fluctuations involving reversible breaking of helical hydrogen bonds. Bending of the helical structure around residues Aib10-Aib13 was associated with reversible flips of the peptide bonds involving G11 (Aib10-G11 or G11-L12 peptide bonds), yielding discrete structural states in which the Aib10 carbonyl or (rarely) the G11 carbonyl was oriented away from the peptide helix. These peptide bond reversals could be accommodated without greatly perturbing the adjacent helical structure, and intramolecular hydrogen bonding was generally maintained in bent states through the formation of new (non-alpha or 3[10]) hydrogen bonds with good geometries: G11 NH-V9 CO (inverse gamma turn), Aib13 NH-Aib8 CO (pi-helix) and, rarely, L12 NH- Q7 NH (pi-helix). These observations may reconcile potentially conflic...Continue Reading

Citations

Nov 6, 2002·Journal of Molecular Biology·Frank S CordesMark S P Sansom
Dec 21, 2000·Trends in Pharmacological Sciences·M S Sansom, H Weinstein
Apr 8, 2000·Current Opinion in Structural Biology·L R Forrest, M S Sansom
Jun 19, 1998·Current Opinion in Structural Biology·M S Sansom
Aug 7, 2010·Bioinorganic Chemistry and Applications·Spyridon PapazachariasPaul Cordopatis
Oct 21, 2010·Biophysical Journal·Stefan QuintChristina Scharnagl
Nov 16, 2004·Biochemical and Biophysical Research Communications·Zakhar O ShenkarevAlexander S Arseniev
Nov 5, 2002·Biophysical Journal·D Peter TielemanMark S P Sansom
Sep 12, 2007·Journal of Peptide Science : an Official Publication of the European Peptide Society·Francesc J CorchoJuan J Perez
Apr 23, 2014·Biochimica Et Biophysica Acta·Asif Rahaman, Themis Lazaridis
Sep 28, 2013·Biochimica Et Biophysica Acta·Asif Rahaman, Themis Lazaridis
Jan 14, 2000·Journal of Structural Biology·D K ChangK L Lin
Jul 12, 2005·Acta Microbiologica Et Immunologica Hungarica·A SzekeresCs Vágvölgyi
May 24, 2005·Biophysical Journal·Ana Caballero-HerreraLennart Nilsson
Jan 6, 1999·Biophysical Journal·D P TielemanH J Berendsen
Jan 25, 2002·Biophysical Journal·Z O ShenkarevA S Arseniev
May 30, 2002·Protein Engineering·M N Fodje, Salam Al-Karadaghi
Aug 31, 2000·Proteins·A GrossfieldT B Woolf
Mar 31, 2007·Physical Chemistry Chemical Physics : PCCP·Martin F Jarrold
Jun 26, 2007·Chemistry & Biodiversity·Balázs LeitgebLászló Kredics
Sep 5, 2019·International Journal of Molecular Sciences·Chetna TyagiFerenc Ötvös
Sep 21, 2013·The Journal of Biological Chemistry·Hairat SabitPeter W Swaan
Feb 13, 2021·The Journal of Physical Chemistry Letters·Erin R BirdsallMartin T Zanni
Mar 13, 1999·Biophysical Chemistry·P C Biggin, M S Sansom
Sep 18, 2018·Organic Letters·Mohammed H Al-HunitiMitchell P Croatt
Mar 5, 2004·Journal of the American Chemical Society·Rajagopalan SudhaMartin F Jarrold
Feb 2, 2006·Journal of the American Chemical Society·Gabriel A CookGeorge W Gokel
Feb 28, 2002·Journal of the American Chemical Society·Paul H SchlesingerGeorge W Gokel

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