PMID: 8953214Oct 1, 1996Paper

Molecular dynamics simulations of peptides from BPTI: a closer look at amide-aromatic interactions

Journal of Biomolecular NMR
D van der SpoelH J Berendsen

Abstract

Molecular dynamics (MD) simulations of short peptides in water were performed to establish whether it is possible to reproduce experimental data from chemical shift measurements by nuclear magnetic resonance spectroscopy. Three different tetrapeptides were studied. The first, YTGP (Tyr-Thr-Gly-Pro), shows an electrostatic interaction between the aromatic ring of Tyr and the backbone amide hydrogen atom of Gly. The second, YTAP (Tyr-Thr-Ala-Pro), cannot make such an interaction because of steric hindrance of the Ala side chain and hence does not show a well-defined conformation. The third, FTGP (Phe-Thr-Gly-Pro), is shown to alternate between two different conformations. It is demonstrated that small differences in chemical shift, corresponding to these slightly different conformations, can be quantitatively modeled in MD simulations when using the proper force-field parameters and water model Explicit inclusion of hydrogen atoms o the aromatic rings is essential for a proper description of electrostatic interactions, but the choice of the water model is equally important. We found that a combination of the SPC/E water model and a revised GROMOS87 force field gives close agreement with experiment, while the same and other force ...Continue Reading

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Citations

Oct 1, 1996·Protein Science : a Publication of the Protein Society·D van der SpoelH J Vogel
Sep 29, 2011·Journal of Molecular Modeling·Naser AlijabbariBoris Gelmont
Oct 22, 2005·Physical Chemistry Chemical Physics : PCCP·Kirsi TappuraTapio T Rantala
Oct 3, 2013·Physical Chemistry Chemical Physics : PCCP·Rashmi Tambe Shukla, Yellamraju U Sasidhar
Apr 27, 2004·Journal of Biomolecular Structure & Dynamics·I Stoica
May 23, 2012·Acta Crystallographica. Section B, Structural Science·Qiang ZhuHarold T Stokes
Nov 5, 1999·Protein Science : a Publication of the Protein Society·D RoccatanoH J Berendsen
Jul 21, 2004·The Journal of Chemical Physics·Qiang HuangCheng-Lung Chen
May 3, 2014·The Journal of Physical Chemistry. B·Gaobo YuJian Zhou
Dec 17, 2014·The Journal of Chemical Physics·Liming QiuMark W Vaughn
Jan 31, 2009·Journal of Chemical Theory and Computation·David S CeruttiTerry P Lybrand
Jul 17, 2007·Progress in Biophysics and Molecular Biology·Pinak Chakrabarti, Rajasri Bhattacharyya
May 12, 2005·Angewandte Chemie·Paolo RaiteriMichele Parrinello
Jun 10, 2015·The Journal of Membrane Biology·Arockiasamy Petrishia, Mohan Sasikala
Jul 4, 2006·Protein Science : a Publication of the Protein Society·David S CeruttiJ Andrew McCammon
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Apr 7, 2011·Journal of Computational Chemistry·Mark J Abraham, Jill E Gready
Oct 21, 2005·Journal of Molecular Biology·M Marvin SeibertDavid van der Spoel
Dec 3, 2014·Computational Biology and Chemistry·Márcio DornLuis C Lamb
May 27, 2015·Journal of Chemical Information and Modeling·Jin ZhangDavid van der Spoel
Feb 13, 2001·Biophysical Journal·C M ShepherdA H Juffer
May 30, 1998·The Journal of Biological Chemistry·M PellegriniD F Mierke

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