Skip to ContentSkip to Navigation
About us Latest news News News articles

The effect of environment on peptide and protein folding: a molecular dynamics study

26 March 2010

Promotie: Y. Xue, 16.15 uur, Academiegebouw, Broerstraat 5, Groningen

Proefschrift: The effect of environment on peptide and protein folding: a molecular dynamics study

Promotor(s): prof.dr. A. Mark

Faculteit: Wiskunde en Natuurwetenschappen

Contact: Ying Xue, tel. 00 61 4 239 05086, e-mail:

The effect of environment on peptide and protein folding: a molecular dynamics study

The focus of my PhD has been the investigation of the environmental effects on peptide and protein folding. Specifically, molecular dynamics (MD) simulations using explicit water have been performed to analyze in detail specific conditions that either promote or inhibit protein folding. My initial work focused on the ability of the force field to reproduce the folding dynamics of a series of small peptides in water. It was found that the conformational properties were well reproduced but the folding times derived from the simulations were considerably shorter than those estimated from experiment. As a part of this work I also derived a new set of dihedral potentials that gave a better agreement between the simulations and the available X-ray data. I also investigated in detail an approach, which attempts to mimic the effect of the chaperon GroEL by modifying the polarity of the solvent environment. Within cells, chaperons such as GroEL facilitate the folding of protein and peptides in an energy dependent manner. The simulations showed that mimicking the effect of the chaperon could increase the rate of folding of small peptides as well as a small protein from thermally denatured states. Finally I investigated the effect of interfaces on peptide folding, looking at the effect of polyethylene glycol (PEG) spacers on the conformational properties of small peptides and the interfacial structure of self-assembled switchable peptide surfactants.

Last modified:13 March 2020 01.15 a.m.
printView this page in: Nederlands

More news

  • 01 September 2021

    Sense or nonsense? Young researchers are putting twenty proverbs to the test

    Proverbs. Without thinking about it, we make use of them daily. But our society is constantly changing. Are these ancient wisdoms any use to us still? Young researchers from various disciplines, among whom are many members of the Young Academy...

  • 15 June 2021

    From ‘closed’ science to Open Science

    Vera Heininga is the Open Science coordinator and future programme leader of the upcoming Open Science programme of the University of Groningen. Together with her colleagues, she created the Open Science Community Groningen (OSCG). She explains...

  • 17 May 2021

    ‘Encouraging young people, that’s my most important job’

    Four and a half years ago, he received the Nobel Prize. During the award ceremony in Stockholm, Ben Feringa made a resolution: I will put science on the map. His mission is being given a new boost with the establishment of the Ben Feringa Fund,...