4.5 Article

Parameterization of the proline analogue Aze (azetidine-2-carboxylic acid) for molecular dynamics simulations and evaluation of its effect on homo-pentapeptide conformations

Journal

JOURNAL OF MOLECULAR GRAPHICS & MODELLING
Volume 39, Issue -, Pages 118-125

Publisher

ELSEVIER SCIENCE INC
DOI: 10.1016/j.jmgm.2012.11.006

Keywords

Aze (azetidine-2-carboxylic acid); Poly-proline II; cis-trans Isomerization; Molecular dynamics; GROMACS: myelin basic protein; Intrinsically disordered protein; Multiple sclerosis

Funding

  1. Natural Sciences and Engineering Research Council of Canada [RG121541]
  2. Multiple Sclerosis Society of Canada

Ask authors/readers for more resources

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 cyclohexanefwater simulation sytems 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 bend in the polypeptide chain. The results provide evidence for the hypothesis that the mis-incorporation 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. (C) 2012 Elsevier Inc. All rights reserved.

Authors

I am an author on this paper
Click your name to claim this paper and add it to your profile.

Reviews

Primary Rating

4.5
Not enough ratings

Secondary Ratings

Novelty
-
Significance
-
Scientific rigor
-
Rate this paper

Recommended

No Data Available
No Data Available