Robert Bradbury provides a broad analysis of protein-based assembly He discusses recent capabilities in molecular electronics (rotaxane) and organic chemistry. He describes why the march of progress in computers, computer aided enzyme design and algorithms are lowering the cost necessary to advance protein assembly to be able to manufacture a programmable nano-assembler (PNA).
Probably in 2005 the design of a complete assembly line is a $100 million project and the actual implementation in the range of $1 billion.
Similar costs are reasonable expectations for a mechanosythesis effort.
Some current protein design work:
David Baker, who's team created Top7, the first articial protein in 2003. They are developing improved methods to predict and redesign protein-DNA interaction specificity, and extending their protein design methodology to the design of enzymes that catalyze chemical reactions not catalyzed by naturally occurring proteins.
A discussion of possibilites for creating artificial enzymes These are generally synthetic polymers or oligomers with enzyme-like activities, often called synzymes.