Consistency Principle for Protein Design

Abstract

Protein design holds promise for applications such as the control of cells, therapeutics, new enzymes and protein-based materials. Recently, there has been progress in rational design of protein molecules, and a lot of attempts have been made to create proteins with functions of our interests. The key to the progress is the development of methods for controlling desired protein tertiary structures with atomic-level accuracy. A theory for protein folding, the consistency principle, proposed by Nobuhiro Go in 1983, was a compass for the development. Anfinsen hypothesized that proteins fold into the free energy minimum structures, but Go further considered that local and non-local interactions in the free energy minimum structures are consistent with each other. Guided by the principle, we proposed a set of rules for designing ideal protein structures stabilized by consistent local and non-local interactions. The rules made possible designs of amino acid sequences with funnel-shaped energy landscapes toward our desired target structures. So far, various protein structures have been created using the rules, which demonstrates significance of our rules as intended. In this review, we briefly describe how the consistency principle impacts on our efforts for developing the design technology.