NATURE|Vol 438|1 December 2005|doi:10.1038/nature04395 INSIGHT REVIEW 581 Solving the membrane protein folding problem James U. Bowie 1 One of the great challenges for molecular biologists is to learn how a protein sequence defines its three- dimensional structure. For many years, the problem was even more difficult for membrane proteins because so little was known about what they looked like. The situation has improved markedly in recent years, and we now know over 90 unique structures. Our enhanced view of the structure universe, combined with an increasingly quantitative understanding of fold determination, engenders optimism that a solution to the folding problem for membrane proteins can be achieved. (ref. 7). This structure illustrates some of the complexities of mem- brane-protein architecture. Two views of the GlpF monomer (the pro- tein is a tetramer) are shown in Fig. 2, and I will call them front and back. The back side presents a simple picture of TM helices packed together roughly parallel to the membrane normal. Few would have been surprised by this image, even 30 years ago. The front side pre- sents a more complex view, however. Most notable is the pair of helices that penetrate half way into the bilayer, where their amino-ter- mini meet. Such half TM helices are not very common, but are also not particularly unusual (about 1 in 20 of all TM helices) 8 . Also visi- ble in the front view is a common feature of membrane proteins: a highly distorted TM helix. About 60% of TM helices contain signifi- cant bends or other distortions 9 . Finally, loop conformations between In Ilse Aichinger’s famous short story The Bound Man, a man awakes from a coma to find himself bound by ropes 1 . He learns to move grace- fully within these constraints and eventually becomes a circus per- former. Similarly, membrane proteins must perform complex signalling and transport functions within the strict confines of a lipid bilayer. This requires elegant structural adaptations to their environment. Our early views of membrane-protein structure were largely shaped by the pioneering work of Henderson and colleagues, who established a modest resolution view of bacteriorhodopsin in 1975 (ref. 2). Confirming the prescient prediction of Lenard and Singer in 1966 (ref. 3), the structure revealed a bundle of long helical rods tra- versing the membrane. This suggested that membrane proteins could be largely thought of as an assembly of transmembrane (TM) helices. This view was reinforced by the stretches of hydrophobic residues found in membrane-protein sequences that were long enough to form membrane-spanning helices 4 . But recent structures have challenged this simple concept of membrane-protein architecture. In this review, I will briefly illustrate some of the surprising twists and turns that polypeptide chains make in the bilayer and then discuss our current understanding how these structures are built. Finally, I will argue that with concerted effort, practical solutions to the membrane-protein- folding problem are possible. Complex architectures Protein structure within the bilayer can be divided into two general types: ȋ-barrels and bundles of Ȋ-helices. Because the folding problem for ȋ-barrels and helix bundles is very different, and because ȋ-barrel proteins are much less common 5 , I will focus on the helix bundle class. Figure 1 shows our progress with helix bundle protein-structure deter- mination since the first high-resolution membrane protein structure was solved 20 years ago (reviewed in ref. 6). A decade later, the pace of structure determination quickened. We now know 52 unique helix bundle structures, and 38 of these were solved in the past 5 years. As a result, we have a much clearer view of the structural diversity exhib- ited by membrane proteins. Although long TM helices are still consid- ered a fundamental building block, polypeptide chains can be organized into other complex patterns. Perhaps the first dramatic departure from the standard view was the structure of the glycerol/water channel GlpF, determined in 2000 1 Department of Chemistry and Biochemistry, UCLA-DOE Center for Genomics and Proteomics, Molecular Biology Institute, Boyer Hall, UCLA, 611 Charles E. Young Drive E, Los Angeles, California 90095-1570 USA. Number of Helix bundle structures solved Year 0 2 4 6 8 10 12 1985 1986 1987 1988 1989 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 1990 Figure 1 | Progress of helix bundle membrane protein structure determination. Only unique structures are included. The data were obtained from a website maintained by Stephen White (http://blanco.biomol.uci.edu/Membrane_Proteins_xtal.html). For a similar plot including all membrane protein structures, see ref. 6. Nature Publishing Group ©2005