A WRAP for biology’s greasiest problem

By mimicking cell membrane environments, new custom-designed proteins make water-repelling proteins soluble without detergents.

IPD WRAPs researcher Ljubica Mihaljevic works at a lab bench at the Institute for Protein Design.

Embedded in the boundary between the inside and outside of each cell are membrane proteins. They act as first responders by sensing signals, regulating which molecules enter and leave the cell, and enabling cells to quickly adapt to changes in their environment. 

The membrane protein surface repels water. Its hydrophobic nature has complicated the development of therapies and vaccines to target membrane proteins.

“Membrane proteins are notoriously difficult to work with. We needed to find a way to keep them intact in water,” said David Baker, professor of biochemistry at the University of Washington School of Medicine and director, UW Medicine Institute for Protein Design. 

After taking on this challenge, researchers report, for the first time, that membrane protein structures can be distinguished by using computationally designed protein coverings.

The discovery could overcome some cell biology obstacles in biomedical research. Work on syphilis vaccines, for example, has been stalled by difficulties in studying antigens from the outer membranes of the bacteria that cause this infection. Antigens are chemical warning signs that can provoke an immune system attack on a cell.

To extract membrane proteins, scientists have conventionally used detergents, which contain surface-acting molecules to bridge oily and watery substances. This approach is often a tedious, multistep endeavor and can limit application of the findings. 

The project led by the UW Medicine Institute for Protein Design developed a new solution: custom-designed proteins that can surround membrane proteins. These WRAPs (Water-soluble Rosetta Fold-diffused Amphipathic Proteins) shield the hydrophobic surfaces and allow them to remain soluble and stable in water — without detergents.

Pooja Bandawane (left) and David E. Kim at computers used in protein design.

The researchers describe this advance in the July 2 issue of Science. 

Because WRAPs are genetically fused to their membrane-protein targets, and purified directly from the soluble fraction, they allow researchers to bypass the membrane altogether without having to modify native sequence. The protein designers showed that WRAPs can make a wide range of membrane proteins water-soluble while preserving their native structure. The scientists validated the finding by obtaining a high-resolution (2.95 Å) image of the structure of a WRAPed Mycobacterial porin, a cell transmembrane channel on this bacterium through which dissolved nutrients flow.

“The capability provided by WRAPs opens many new possibilities for both research and therapeutic application,” said Baker, the senior author of the paper.

He explained that WRAPs unlock broad applications across efforts to develop vaccines, diagnostics and drugs by making membrane proteins experimentally accessible without compromising structural and functional features.

One example, the researchers said, is the outer membrane proteins of Treponema pallidum, the bacterium that causes syphilis. These proteins are prime antigens that have long resisted production and structural characterization. WRAPs changed that by enabling stable, soluble antigens that can be finally characterized. This vital information may lead to vaccines and new diagnostics.

“I’m excited to finally release our WRAP approach to the broader scientific community and to see how it accelerates discovery in the membrane protein field,” said Ljubica Mihaljevic, lead author of the paper. She is a Howard Hughes Medical Institute Helen Hay Whitney Postdoctoral Fellow at the Institute for Protein Design. David E. Kim, a research scientist in biochemistry, and Pooja Bandawane, a Ph.D. student in biochemistry, both at the UW School of Medicine, are co-lead authors. 

This work was supported Coefficient Giving (GV673605158); Gates Foundation (INV-043758, INV-040928, INV-051483); National Institute of Allergy and Infectious Disease, National Institutes of Health (U19AI144177); Howard Hughes Medical Institute, including a HHMI Helen Hay Whitney postdoctoral fellowship; Curci Foundation Ph.D. Fellows Program; and an Erwin Schrödinger Postdoctoral Fellowship (J- 4663).

Baker is an investigator of the Howard Hughes Medical Institute. 

A patent application has been filed for the new methods and proteins described in this work. 

Written by Ljubica Mihaljevic.