Nonstandard abbreviations used: endoplasmic reticulum (ER); phosphoglycerate kinase (PGK); bovine growth hormone (bGH); transthyretin (TTR). urant, many of them exhibiting what are called twostate kinetics, that is, traversing only between the unfolded and native states, usually on the time scale of a few seconds or less. A wealth of studies of such proteins has begun to define the modes by which proteins fold into their native forms. The process does not appear to be random, as the search time required would be impossibly long; rather, the unfolded protein undergoes specific kinetically preferred steps on the way to the native state, albeit that there may be multiple choices at any given point (see Figure 1a). The ability to examine the transition states for two-state folding reactions by mutation analyses, pioneered by Alan Fersht and his colleagues, allows determination of the elements of structure that are present at the transition state and provides information on which structural features of the native protein have formed during folding up to a given point (12). Proteins appear to follow multiple approaches to the transition state. For example, some proteins rapidly acquire secondary structure (which is present already at the transition state) before organizing tertiary structure; for others, a rapid collapse of hydrophobic regions to form a core can occur before or at the same time as secondary and tertiary structure formation. An interesting observation from the recent work of David Baker and coworkers is that proteins whose contiguous amino acid sequences remain in contact with each other via secondary or tertiary structure in the final three-dimensional native state fold faster than those whose local structures are formed from distantly separated sequences (in a parallel β-sheet, for instance), implying an entropic penalty for bringing together the distant segments of polypeptide in the latter proteins (13).