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Salk scientists add new bond to protein engineering toolbox

Haiyan Ren, Lei Wang and Zheng Xiang

From left: Scientists Haiyan Ren, Lei Wang and Zheng Xiang

Proteins are the workhorses of cells, adopting conformations that allow them to set off chemical reactions, send signals and transport materials. But when scientists are designing a new drug, trying to visualize the processes inside cells or probe how molecules interact with each other, they can't always find a protein that will do the job they want. Instead, they often engineer their own novel proteins to use in experiments, either from scratch or by altering existing molecules.

As reported in Nature Methods, researchers in the lab of Lei Wang have developed a new tool for protein engineering: a way to add strong, unbreakable bonds between two points in a protein or between two proteins.

When a protein folds from a loose chain of amino acid building blocks into its active three-dimensional structure, bonds and chemical interactions naturally form between different parts of the chain to keep the structure assembled. Most are relatively weak, driven by the electrochemical charges of different amino acids. Stronger bonds, called disulfide bridges, occur between pairs of cysteines, one particular amino acid. But for protein engineers, either type of bond has had its own deficiencies. So linking two parts of a protein in a predictable and permanent way has been notoriously hard.

Wang and his team wanted to be able to add strong, irreversible bonds—called covalent bonds—to proteins to alter their shape, make them more stable or attach them to one another. So they began trying to create a new amino acid, different from the 20 that exist naturally.

They created dozens of possible amino acids and tested each one to see if it bound with just the right strength. After a series of tests, they settled on a newly created amino acid called p-2-fluoroacetyl-phenylalanine, or Fact, then designed three proteins using it in their sequences. Tests of the proteins showed that they formed a covalent bond with Fact.

"I think anyone who is working on proteins, or anything related to proteins, could make use of this new technology," says Wang. "It can provide a novel way to control proteins or design proteins to study basic biology."