Novel technique for creating protein nano-machines

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Researchers from University of Washington designed proteins that can bond together in a DNA-like formation of double helix

A team of researchers from University of Washington School of Medicine designed proteins capable of bonding together in a DNA-like fashion to form a double helix. The technique can enable the design of protein nanomachines for potential application in diagnosis and treatment of various diseases. According to Zibo Chen, the lead author of the paper and a UW graduate student in biochemistry, the technique allows to design proteins that can form desired bonds together. The research was conducted at UW Medicine’s Institute of Protein Design, directed by David Baker, professor of biochemistry at the University of Washington School of Medicine and a Howard Hughes Medical Institute investigator. The research was published in the journal Nature on December 19, 2018.

DNA is used as a major component for designing biomolecular nanomachines, owing to the ability of DNA strands to come together and form hydrogen bonds to create DNA’s double helix. However, the bond formation takes place only when sequences of strands are complementary. The researchers developed new protein design algorithms. The algorithms are capable of generating complementary proteins. The proteins use the same chemical language of DNA to accurately pair with each other. According to Chen, the study focuses on computationally designing hydrogen-bond networks to offer each protein pair with a unique complementary sequence.  According to Scott Boyken, another author of the paper and postdoctoral researcher at the Institute for Protein Design, the technique offers a precise, programmable approach to control how protein machines interact.

The team used a computer program developed in the Baker lab called Rosetta. The program leverages that fact that the shape an amino acid chain will assume is controlled by the forces of attraction and repulsion among the fluid in which the chain is immersed and amino acids of the chain. The team calculated the shape that best balances out the forces of attraction and repulsion. This in turn enables the chain to achieve its lowest overall energy level. The program can therefore, predict the shape taken by a given amino acid chain. The research was conducted in collaboration with Ohio State University and University of California, Santa Cruz.

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Latisha Diaz is a general assignment reporter at Plains Gazette. She has covered sports, entertainment and many other beats in his journalism career, and has lived in City Houston for more than 8 years. Latisha has appeared periodically on national television shows and has been published in (among others) The National Post, Politico, The Atlantic, Harper’s, Wired.com, Vice and Salon.com.