Establishing effective simulation protocols for beta- and alpha/beta-peptides. II. Molecular mechanical (MM) model for a cyclic beta-residue

The Journal of Physical Chemistry. B
Xiao ZhuQiang Cui

Abstract

All-atom molecular mechanical (MM) force field parameters are developed for a cyclic beta-amino acid, amino-cyclo-pentane-carboxylic acid (ACPC), using a multi-objective evolutionary algorithm. The MM model is benchmarked using several short, ACPC-containing alpha/beta-peptides in water and methanol with SCC-DFTB (self consistent charge-density functional tight binding)/MM simulations as the reference. Satisfactory agreements are found between the MM and SCC-DFTB/MM results regarding the distribution of key dihedral angles for the tetra-alpha/beta-peptide in water. For the octa-alpha/beta-peptide in methanol, the MM and SCC-DFTB/MM simulations predict the 11- and 14/15-helical form as the more stable conformation, respectively; however, the two helical forms are very close in energy (2-4 kcal/mol) at both theoretical levels, which is also the conclusion from recent NMR experiments. As the first application, the MM model is applied to an alpha/beta-pentadeca-peptide in water with both explicit and implicit solvent models. The stability of the peptide is sensitive to the starting configuration in the explicit solvent simulations due to their limited length ( approximately 10-40 ns). Multiple ( approximately 20 x 20 ns) implicit s...Continue Reading

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Citations

Feb 16, 2010·The Journal of Chemical Physics·Jagannath MondalArun Yethiraj
Mar 3, 2012·The Journal of Chemical Physics·Jagannath Mondal, Arun Yethiraj
Oct 7, 2015·The Journal of Physical Chemistry. B·Kai HuangIzabela Szlufarska
Feb 11, 2009·Journal of the American Chemical Society·Soo Hyuk ChoiSamuel H Gellman
Mar 30, 2011·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Weijie HuaShuhua Li
Jul 20, 2011·Chemical Society Reviews·Tamás A Martinek, Ferenc Fülöp
May 23, 2014·Physical Chemistry Chemical Physics : PCCP·Qiang Cui, Marcus Elstner
Jun 24, 2009·The Journal of Physical Chemistry. B·Jagannath MondalArun Yethiraj
Jun 27, 2009·The Journal of Physical Chemistry. B·Fredy SussmanRamón J Estévez
Oct 5, 2010·The Journal of Physical Chemistry. B·Jagannath MondalArun Yethiraj
Nov 30, 2011·The Journal of Physical Chemistry. B·Jagannath MondalArun Yethiraj
Mar 22, 2018·The Journal of Physical Chemistry. a·Karl N BlodgettTimothy S Zwier
Sep 28, 2013·The Journal of Physical Chemistry. a·Ryoji KusakaTimothy S Zwier
Sep 4, 2021·Biophysical Journal·Jaya Krishna KoneruJagannath Mondal

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