Peptide folding in the presence of interacting protein crowders

Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotata...

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Bibliographic Details
Published in:The Journal of chemical physics 2016-05, Vol.144 (17), p.175105-175105
Main Authors: Bille, Anna, Mohanty, Sandipan, Irbäck, Anders
Format: Article
Language:English
Subjects:
Animals
Annan fysik
Aprotinin - chemistry
Biofysiks
Biologi
Biological Sciences
Biophysics
Cages
Computer Simulation
Folding
Fysik
Humans
INORGANIC, ORGANIC, PHYSICAL AND ANALYTICAL CHEMISTRY
INTERACTIONS
MONTE CARLO METHOD
Monte Carlo simulation
Natural Sciences
Naturvetenskap
Other Physics Topics
PEPTIDES
Peptides - chemistry
Physical Sciences
Physics
Protein Folding
Proteins
Receptors, GABA-B - chemistry
SIMULATION
Thermodynamics
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Summary:Using Monte Carlo methods, we explore and compare the effects of two protein crowders, BPTI and GB1, on the folding thermodynamics of two peptides, the compact helical trp-cage and the β-hairpin-forming GB1m3. The thermally highly stable crowder proteins are modeled using a fixed backbone and rotatable side-chains, whereas the peptides are free to fold and unfold. In the simulations, the crowder proteins tend to distort the trp-cage fold, while having a stabilizing effect on GB1m3. The extent of the effects on a given peptide depends on the crowder type. Due to a sticky patch on its surface, BPTI causes larger changes than GB1 in the melting properties of the peptides. The observed effects on the peptides stem largely from attractive and specific interactions with the crowder surfaces, and differ from those seen in reference simulations with purely steric crowder particles.
ISSN:0021-9606
1089-7690
DOI:10.1063/1.4948462