Abstract
Intrinsically disordered proteins are a class of proteins that lack stable folded conformations and instead adopt a range of conformations that determine their biochemical functions. The temperature-dependent behavior of such disordered proteins is complex and can vary depending on the specific protein and environment. Here, we have used molecular dynamics simulations and previously published experimental data to investigate the temperature-dependent behavior of histatin 5, a 24-residue-long polypeptide. We examined the hypothesis that histatin 5 undergoes a loss of polyproline II (PPII) structure with increasing temperature, leading to more compact conformations. We found that the conformational ensembles generated by the simulations generally agree with small-angle X-ray scattering data for histatin 5, but show some discrepancies with the hydrodynamic radius as probed by pulsed-field gradient NMR spectroscopy, and with the secondary structure information derived from circular dichroism. We attempted to reconcile these differences by reweighting the conformational ensembles against the scattering and NMR data. By doing so, we were in part able to capture the temperature-dependent behavior of histatin 5 and to link the observed decrease in hydrodynamic radius with increasing temperature to a loss of PPII structure. We were, however, unable to achieve agreement with both the scattering and NMR data within experimental errors. We discuss different possible reasons for this including inaccuracies in the force field, differences in conditions of the NMR and scattering experiments, and issues related to the calculation of the hydrodynamic radius from conformational ensembles. Our study highlights the importance of integrating multiple types of experimental data when modeling conformational ensembles of disordered proteins and how environmental factors such as the temperature influence them.
Originalsprog | Engelsk |
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Tidsskrift | Journal of Physical Chemistry B |
Vol/bind | 127 |
Udgave nummer | 28 |
Sider (fra-til) | 6277-6286 |
Antal sider | 10 |
ISSN | 1520-6106 |
DOI | |
Status | Udgivet - 2023 |
Bibliografisk note
Funding Information:We thank Marie Skepö and Birthe B. Kragelund for sharing the SAXS, NMR, and CD data and for discussions on disordered proteins and Simone Orioli for discussions about the simulations. This research was funded by the Lundbeck Foundation BRAINSTRUC initiative in structural biology (R155-2015-2666, https://lundbeckfonden.com/ ). We acknowledge access to computational resources from the ROBUST Resource for Biomolecular Simulations (supported by the Novo Nordisk Foundation grant no. NF18OC0032608) and from the Biocomputing Core Facility at the Department of Biology, University of Copenhagen.
Publisher Copyright:
© 2023 American Chemical Society