Proteins fold by packing their non-polar (fat-soluble) building blocks into the protein interior and surrounding it by a polar (water-soluble) surface. However, many proteins also have a charged network embedded in their central non-polar core that is essential for the proper biological function, but disturbs the delicate balance in physical forces governing the folding process.


"Nature has achieved an immense complexity in its biomolecules that was optimized during billions of years of evolution", Ville Kaila says. "To understand the basic physical principles behind these charged networks, we wanted to build minimalistic artificial proteins that lack this evolutionary baggage".  


Kaila and his team developed a protein design approach, in which they built new proteins using computational models and then experimentally tested them by combining various biophysical and structural methods. The designed proteins consisted of only four a-helices connected by loop regions, a pattern commonly found in many natural proteins. By inserting charged networks into the protein core, the researchers discovered a highly delicate balance between stabilizing and destabilizing physical forces that keep the proteins together.  


"Understanding such effects is also interesting from a biomedical perspective, as several disease-related mutations may disturb this force balance, and lead to protein dysfunction or aggregation that can have severe physiological effects", Kaila continues.


The researchers discovered specific chemical interactions that help to stabilize the buried charged networks. These micro-environments work by forming contacts with both the charged and non-polar parts of the protein. "It was fascinating to see that these charged-stabilizing motifs were discovered both by our computational design approach, but also when we screened the structure of around 180 000 charged networks in natural occurring proteins", Kaila explains. "This mean that we might have re-discovered some of the physical principles that arose during evolution of complex proteins."


Using the discovered design principles, the researchers could create highly stable artificial proteins that were resistant towards unfolding at extreme temperatures and harsh chemical conditions, which is untypical for naturally occurring proteins.  "This project made us appreciate the remarkable structure of natural proteins and the delicate balance in the physical forces that are tuned to a very high degree, even in the simplest proteins."


The study was funded by the European Research Council (ERC), the Knut and Alice Wallenberg (KAW) foundation, and German Research Foundation (DFG/SFB1035). Computational resources were provided by supercomputers SuperMuc (LRZ) in Garching, Germany and Beskow (SNIC/PDC) in Stockholm.


Reference

Baumgart M., Röpke M., Mühlbauer M.E., Asami S., Mader S.L., Fredriksson K. Gamiz-Hernandez A.P., Kaila V.R.I. Design of buried charged networks in artificial proteins. Nature Communications 12, 1895 (2021).  
doi: 10.1038/s41467-021-21909-7


Web link: https://www.nature.com/articles/s41467-021-21909-7

Lab home page: https:/villekaila.com

Twitter: https://twitter.com/TheKailaLab


Further information:

Prof. Ville R. I. Kaila

Department of Biochemistry and Biophysics
Stockholm University, Sweden

E-mail: ville.kaila AT dbb.su.se

 

Figure. Structures of the designed artificial proteins with various charged networks. Adapted from Baumgart et al. NComms (2021). Figure: Michael Röpke/The Kaila Lab.