Tag Archives: Protein design

Maybe the backbone is more important than the side chains

I’m really embarrassed that I was unaware of the following work on protein design from Japan. Apparently, they were able to design proteins stable at 100 Centigrade using a methodology of which I was completely in the dark (N. Koga et al., Principles for designing ideal protein structures. Nature 491, 222–227 (2012), Y. R. Lin et al., Control over overall shape and size in de novo designed proteins. Proc. Natl. Acad. Sci. U.S.A. 112, E5478–E5485 (2015)). I read those journals but must have skipped the articles — I’ll have to go back and have a look.

A recent article (PNAS 117 31149 – 31156 ’20) brought it to my attention. Here’s what they say they’ve done.

“We proposed principles for designing ideal protein structures stabilized by completely consistent local and nonlocal interactions , based on a set of rules relating local backbone structures to preferred tertiary motifs (7, 10 — given above). These design rules describe the relation of the lengths or torsion patterns of two secondary structure elements and the connecting loop to favorable packing geometries . The design principles enable to encode strongly funneled energy landscapes into amino acid sequences, by the stabilization of folded structures (positive design) and by the destabilization of nonnative conformations (negative design) due to the restriction of folding conformational space by the rules”

Hard to believe but it works apparently. The paper also stands an idea about protein structure and stability on its head — the hydrophobic core of a compact protein, in this case a designed protein with a Rossmann fold (two pairs of alpha helices sandwiching a beta sheet is absolutely crucial to the ultimate 3 dimensional conformation of the protein backbone.

The protein is quite stable, not denaturing at 100 C. So then they mutated 10 of the large hydrophobic amino acids (leucine, isoleucine) to a small one (valine) so that 30 of the 34 amino acids in the core were valine and watched what happened.

What’s your guess? Mine would have been that the core was in a molten globule state and that backbone structure was lost.

That’s not what happened at all. The resulting protein was still stable over 100 C (although not quite as much by 5 KCal/mole)

To quote the authors again — “This result indicates that hydrophobic tight core packing may not be quite important for designed proteins: The folding ability and extremely high stability may arise from the restriction of conformational space to be searched during folding by the local backbone structures. This can lead to an exceptionally stable protein even in the absence of precise core packing.”

Astounding. However, this may not be true for proteins ‘designed’ by natural selection.
It’s time to try the same trick on some of them.