Designing artificial proteins with spare parts

As part of their work to design new proteins to perform specific functions, Israeli researchers have gone back to nature’s drawing board — evolution. The scientists have now created proteins based on what they call ‘existing natural parts’, which reportedly carry out their intended function with flying colours.

In the lab of Dr Sarel Fleishman, in the Weizmann Institute of Science’s Biomolecular Sciences Department, proteins are designed with computer-based programs that enable them to generate new structures — for example, antibodies or enzymes — that do not exist in nature. If Dr Fleishman’s team want a protein that will perform a specific action — say, bind to another protein or carry out a chemical reaction — they can compute, from beginning to end, the genetic sequence that will line up amino acids in the proper order and cause the protein to fold into the correct three-dimensional shape.

Such proteins could, in theory, usher in a new age of custom-designed drugs and catalysts — but the challenges of planning of large biological molecules are immense. Seeking to solve this problem, the team asked themselves two questions:

1. What does a natural enzyme or antibody have that the artificial proteins don’t?
2. Why are two structures with similar make-up so different when it comes to the way they perform inside a biological system?

The group focused their attention on some parts of natural antibodies or enzymes that don’t make it into their computer designs — particularly structures called ‘loops’, which are inherently unstable and ‘non-ideal’ and therefore challenging when it comes to computational prediction. These non-ideal loops can be often be found at the very centre of the active regions — those that recognise a target or bind to or cleave another molecule.

To incorporate these parts, the researchers decided to design a functioning antibody from existing parts, rather than building one from scratch. They broke the structures found in natural antibodies down into segments, including the loops and other supporting features. In effect, the researchers tinkered with ready-made parts, similar to the way evolution works.

The team then went back to the computerised planning process, this time armed with their new insight. Their new designs were tested experimentally in the lab, a few dozen antibodies at a time. Initially the designs performed poorly, but through five design-build-test cycles, the researchers uncovered some general rules for designing antibodies.

In essence, they created a sort of symbiotic evolution — the design programs evolving along with the experimental tests, each pushing the other forward. To demonstrate the feasibility of this concept, the team created artificial antibodies that targeted insulin and characterised these molecules down to the resolution of single atoms. Their results have been published in the Proceedings of the National Academy of Sciences.

Computer designs (lime green) are compared with experimental structures (purple) at the atomic level, revealing atomic accuracy in overall structure (left) and in loop regions (right).

In future experiments, the scientists plan to design artificial antibodies modelled on those of camels and llamas — creatures whose antibodies have 100 amino acids, as opposed to the 200 in human antibodies. This could make the design and production of artificial antibodies for human conditions more efficient, and might have relevance for designing new diagnostics and therapeutics.

Top image credit: ©stock.adobe.com/au/Drobot Dean