Bulletin of the American Physical Society
APS March Meeting 2024
Monday–Friday, March 4–8, 2024; Minneapolis & Virtual
Session N27: Physics of Proteins: Folding and Function
11:30 AM–2:18 PM,
Wednesday, March 6, 2024
Room: 101H
Sponsoring
Unit:
DBIO
Chair: Wouter Hoff, Oklahoma State University-Stillwater
Abstract: N27.00010 : A rapid transition in the unfolding of ubiquitin at high SDS concentrations
1:42 PM–1:54 PM
Presenter:
Hrachya Ishkhanyan
(King's College London)
Authors:
Hrachya Ishkhanyan
(King's College London)
Armen Poghosyan
(National Academy of Sciences of Armenia)
Jan S Pedersen
(Aarhus Universitet)
Daniel Otzen
(Aarhus Universitet)
This study focuses on ubiquitin (Ubi) as a model protein and employs small-angle X-ray Scattering (SAXS) and molecular dynamics (MD) simulations to investigate its behavior in the presence of SDS. Earlier controversies surrounding the nature of the Ubi-SDS complex have been resolved by these SAXS studies, confirming that Ubi conforms to the canonical core-shell model upon exposure to SDS.
We made the surprising observation that Ubi unfolding rate accelerates rapidly when crossing a certain SDS concentration threshold far above the critical micelle concentration of 5 mM SDS. At room temperature, Ubi unfolds slowly in the presence of SDS at concentrations from the cmc to around 60 mM, showing that it is kinetically stable against denaturation in SDS. However, within the concentration range of 60-70 mM SDS, there is a pronounced acceleration in unfolding, regardless of temperature and independent of ionic strength. A similar trend is observed in all-atom MD simulations performed at elevated temperatures (450K), which reveal the unfolding mechanisms to be the intercalation of SDS molecules inside the protein, resulting in the breakage of the secondary structure from the inside. In the concentration range above 50mM, the unfolding rate increases several times, as with higher concentrations, we observe a higher degree of clustering of SDS molecules inside the protein. It is worth noting that the resulting Ubi-SDS complexes after cooling down to 303.15K, closely resemble that of the canonical core-shell structures shown by previous SAXS studies.
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