Protein stability: still an unsolved problem

Abstract

This brief review suggests that molecular packing, the efficient filling of space, may be the most generally applicable factor that leads to the unique structures of most globular proteins. While simple in concept, the details of packing can lead to very subtle effects. The mechanical properties of a protein, dynamics and deformations under stress, tend to be asymmetric. In terms of structural alterations and thermostability, responses to genetic mutations are context dependent and remain difficult to predict with any confidence. Through small shifts proteins can frequently accommodate major changes in composition of the core region without substantial alteration in the basic chain conformation. Extending a jigsaw puzzle analogy, all of the pieces (side chains) are convex, varying flexible, and cannot be packed together without leaving cavities. Although large cavities do occasionally occur, a relatively even distribution of empty space is more common, and the overall packing does seem to specify the unique native structure. While it might appear that the translation machinery of the cell could have been designed with any set of α amino acids, the packing requirements, while strong, must be flexible enough to permit nondestructive single site mutations. This flexibility, combined with the need to produce a unique structure, may limit the average number of allowed side chain rotamers per residue. This in turn will reduce the allowable asymmetry of the side chains in order to maintain the largest number of structural motifs. It may be hard to improve on current set of amino acids.