Parameterization of the proline analogue Aze (azetidine-2-carboxylic acid) for molecular dynamics simulations and evaluation of its effect on homo-pentapeptide conformations.
Bessonov, Kyrylo; Vassall, Kenrick A.; Harauz, George
2013 • In Journal of Molecular Graphics and Modelling, 39, p. 118-25
[en] We have parameterized and evaluated the proline homologue Aze (azetidine-2-carboxylic acid) for the gromos56a3 force-field for use in molecular dynamics simulations using GROMACS. Using bi-phasic cyclohexane/water simulation systems and homo-pentapeptides, we measured the Aze solute interaction potential energies, ability to hydrogen bond with water, and overall compaction, for comparison to Pro, Gly, and Lys. Compared to Pro, Aze has a slightly higher H-bonding potential, and stronger electrostatic but weaker non-electrostatic interactions with water. The 20-ns simulations revealed the preferential positioning of Aze and Pro at the interface of the water and cyclohexane layers, with Aze spending more time in the aqueous layer. We also demonstrated through simulations of the homo-pentapeptides that Aze has a greater propensity than Pro to undergo trans-->cis peptide bond isomerization, which results in a severe 180 degrees bend in the polypeptide chain. The results provide evidence for the hypothesis that the misincorporation of Aze within proline-rich regions of proteins could disrupt the formation of poly-proline type II structures and compromise events such as recognition and binding by SH3-domains.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Bessonov, Kyrylo ; Université de Liège - ULiège > Dép. d'électric., électron. et informat. (Inst.Montefiore) > Bioinformatique
Vassall, Kenrick A.
Harauz, George
Language :
English
Title :
Parameterization of the proline analogue Aze (azetidine-2-carboxylic acid) for molecular dynamics simulations and evaluation of its effect on homo-pentapeptide conformations.
Publication date :
2013
Journal title :
Journal of Molecular Graphics and Modelling
ISSN :
1093-3263
eISSN :
1873-4243
Publisher :
Elsevier, Netherlands
Volume :
39
Pages :
118-25
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
Copyright (c) 2012 Elsevier Inc. All rights reserved.
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