
Anders Irbäck
Professor

Markov modeling of peptide folding in the presence of protein crowders
Author
Summary, in English
We use Markov state models (MSMs) to analyze the dynamics of a β-hairpin-forming peptide in Monte Carlo (MC) simulations with interacting protein crowders, for two different types of crowder proteins [bovine pancreatic trypsin inhibitor (BPTI) and GB1]. In these systems, at the temperature used, the peptide can be folded or unfolded and bound or unbound to crowder molecules. Four or five major free-energy minima can be identified. To estimate the dominant MC relaxation times of the peptide, we build MSMs using a range of different time resolutions or lag times. We show that stable relaxation-time estimates can be obtained from the MSM eigenfunctions through fits to autocorrelation data. The eigenfunctions remain sufficiently accurate to permit stable relaxation-time estimation down to small lag times, at which point simple estimates based on the corresponding eigenvalues have large systematic uncertainties. The presence of the crowders has a stabilizing effect on the peptide, especially with BPTI crowders, which can be attributed to a reduced unfolding rate ku, while the folding rate kf is left largely unchanged.
Department/s
- Computational Biology and Biological Physics - Undergoing reorganization
- eSSENCE: The e-Science Collaboration
Publishing year
2018-02-07
Language
English
Publication/Series
Journal of Chemical Physics
Volume
148
Issue
5
Document type
Journal article
Publisher
American Institute of Physics (AIP)
Topic
- Other Physics Topics
- Biophysics
Status
Published
ISBN/ISSN/Other
- ISSN: 0021-9606