One of Eric Drexler earliest papers discussed using proteins for molecular nanotechnology.
A major milestone would be to make a version 2.0 of a ribosome
A ribosome can be thought of as a factory that builds a protein from a set of genetic instructions. A ribosome has 2.3 million base pairs.
This article points to surveys of DNA and protein related technologies that could lead to molecular nanotechnology
Freitas and Merkle has details on various approaches to positional assembly using Proteins
This was mentioned in an early post on this site