Skip to main content
  • Oral presentation
  • Open access
  • Published:

Balancing selectivity vs stability using molecular dynamics and umbrella sampling

Coiled coils are highly represented in biologically relevant macromolecules involved in important biological functions, such as gene expression regulation. The coiled coil environment has the great advantage to provide two very well defined intermolecular recognition surfaces. The peptide system VPE-VPK is a rationally designed heterodimeric coiled coil structure [1, 2]. The characteristic structure of the α-helical coiled coil allows randomizing the interaction partners of this dimeric system. Using a pool of VPE mutants that contains every possible combinations of the 20 canonical amino acids, specific binders could be searched empirically [1, 3]. In this work, three key positions in the hydrophobic core were randomized in a VPE phage displayed library (Figure 1).

Figure 1
figure 1

VPE-VPK represented as (a) a helical wheel diagram and (b) a ribbon diagram, with randomized positions in yellow, and the directly interacting position in green.

This screen led to the identification of a novel core packing between VPE and VPK. One single consensus sequence was selected by the system, bearing a tyrosine in the hydrophobic core. Surprisingly, the dimer selected by phage display has a lower stability compared to the mother system. This important result raises the central question of selectivity vs stability. In order to address both aspects, theoretical investigations were conducted using molecular dynamics within the Gomacs suite. Pulling apart the two helices up to 3.00 nm from each other, potentials of mean force were calculated by umbrella sampling with a view to compare the energy barriers of the mother dimer to the phage display variant.


  1. Nyakatura EK, Reimann O, Vagt T, Salwiczek M, Koksch B: Accommodating fluorinated amino acids in a helical peptide environment. Rsc Adv. 2013, 3: 6319-6322. 10.1039/c3ra41110a.

    Article  CAS  Google Scholar 

  2. Salwiczek M, Samsonov S, Vagt T, Nyakatura E, Fleige E, Numata J, et al: Position-dependent effects of fluorinated amino acids on the hydrophobic core formation of a heterodimeric coiled coil. Chemistry. 2009, 15: 7628-7636. 10.1002/chem.200802136.

    Article  CAS  Google Scholar 

  3. Vagt T, Nyakatura E, Salwiczek M, Jäckel C, Koksch B: Towards identifying preferred interaction partners of fluorinated amino acids within the hydrophobic environment of a dimeric coiled coil peptide. Organic & biomolecular chemistry. 2010, 8: 1382-1386. 10.1039/b917205j.

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations


Corresponding author

Correspondence to Jeremie Mortier.

Additional information

Jeremie Mortier, Elisabeth K Nyakatura contributed equally to this work.

Rights and permissions

Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits use, duplication, adaptation, distribution, and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Reprints and permissions

About this article

Cite this article

Mortier, J., Nyakatura, E.K., Miettinen, M. et al. Balancing selectivity vs stability using molecular dynamics and umbrella sampling. J Cheminform 6 (Suppl 1), O22 (2014).

Download citation

  • Published:

  • DOI: