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Peptide folding in the presence of interacting protein crowders

Bille, Anna LU ; Mohanty, Sandipan and Irbäck, Anders LU (2016) In Journal of Chemical Physics 144(17).
Abstract

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... (More)

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.

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author
organization
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type
Contribution to journal
publication status
published
subject
in
Journal of Chemical Physics
volume
144
issue
17
publisher
American Institute of Physics
external identifiers
  • Scopus:84973640757
  • WOS:000377711300043
ISSN
0021-9606
DOI
10.1063/1.4948462
language
English
LU publication?
yes
id
bcdd0877-27aa-4226-b23a-4ca76eac6201
date added to LUP
2016-08-16 18:15:53
date last changed
2017-02-01 11:16:53
@article{bcdd0877-27aa-4226-b23a-4ca76eac6201,
  abstract     = {<p>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.</p>},
  articleno    = {175105},
  author       = {Bille, Anna and Mohanty, Sandipan and Irbäck, Anders},
  issn         = {0021-9606},
  language     = {eng},
  month        = {05},
  number       = {17},
  publisher    = {American Institute of Physics},
  series       = {Journal of Chemical Physics},
  title        = {Peptide folding in the presence of interacting protein crowders},
  url          = {http://dx.doi.org/10.1063/1.4948462},
  volume       = {144},
  year         = {2016},
}