Digging out structural changes of surrounded proteins

Time-resolved X-ray solution scattering (TXSS) allows researchers to study changes in protein structure. To use TXSS on integral membrane proteins — which are important to many biological functions and common drug targets — the proteins must be removed from the membrane with detergent.

Detergent forms a micelle around the protein. This micelle is disordered and larger than the protein, making it more difficult to pick out changes in protein structure and hindering TXSS’s application to membrane proteins. Sarabi et al. modeled micelle fluctuations during TXSS data analysis to solve this problem.

Their theoretical framework revealed that above a protein- and detergent-dependent scattering angle, ignoring the micelle’s fluctuations does not affect the data.

“We’ve addressed a long-standing theoretical issue,” said author Richard Neutze. “In the past, we made an assumption that above a certain scattering angle we could ignore this problem, and these formulas have shown that that’s true.”

For data below a certain scattering angle, the micelle’s effect can be canceled with a switcheroo. The authors simulated the protein of interest in a micelle and simulated this same protein with structural changes in another micelle, then swapped the simulated micelles.

“That trick — of taking the detergent’s trajectory and artificially writing it into the other detergent’s trajectory — guarantees most of these problems cancel,” Neutze said.

This work’s protein of interest was bacteriorhodopsin, whose structure changes in responses to light. Next, the researchers will expand their theoretical framework to other light-sensitive proteins as well as membrane proteins that are not light driven, including drug-sensitive proteins.

Source: “Modelling difference X-ray scattering observations from an integral membrane protein within a detergent micelle,” by Daniel Sarabi, Lucija Ostojić, Robert Bosman, Adams Vallejos, Johanna-Barbara Linse, Michael Wulff, Matteo Levantino, and Richard Neutze, Structural Dynamics (2022). The article can be accessed at https://doi.org/10.1063/4.0000157 .