[graphene]

There is the fact that proteins are constrained to function as part of organisms that are capable of self-replication. This constraint means that proteins (mostly) are not very stable wrt oxidisation and UV degradation, and only work properly in aqueous solution.

It's anyone's guess how significant these constraints will be from the viewpoint of developing artificial protein machines (maybe rapid (bio)degradation is a good thing!), but there's definitely large swathes of chemical design space outside of arbitrary chains of known amino acids, and we might be able to discover entire classes of molecular machines that don't have the drawbacks of bioinspired proteins.

[TeMPOraL]

Probably. But to do that, we need to be able to do work on that level; existing proteins seem to be just about enough for us to run proper experiments and eventually bootstrap production of nanocomponents better suited for our needs.