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Membrane proteins Membrane protein structure Editorial overview John E Walker* and Matti Sarastet Addresses *The Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB9 2OH, UK; e-mail:
[email protected] -European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, Germany; e-mail:
[email protected] Current Opinion in Structural Biology 1996, 6:45?-459 © Current Biology Ltd ISSN 0959-440X Abbreviations 2D two-dimensional LH light-harvesting complex
T h e ~;enome of baker's yeast cncodes more than 6000 proteins, and in excess of a third of them are predicted to be integral m e m b r a n e proteins containing one to fourteen m e m b r a n e spans. This large proportion reflects the importance of membranes in the life of a unicellular eukaryote. Cell--cell communication increases with biological complexity and, therefore, in muhicellular urganisms, the fraction of m e m b r a n e proteins is likely to be even higher. In the light of these numbers, the paucity of atomic structural data oil men, b r a n t proteins is a lacuna in our knowled,~c that is only lacing filled slowlv. "Fo date, dctaited structures of only seven families of m e m b r a n e proteins are known, and five of them :ire involved in photo)synthesis and respiration. Particularly conspicuous i)\ choir ab,,,eilcc tire the structures of active-transport t>rotc~t~s, receptors and ion channels. 'l'hc present state of affairs aNscs from two major practical problems. First, it is difficult or impossiblc to isolate many nacmbrane proteins in the quantities d e m a n d e d by structural analysis, a situation made worse by tim ditificult\ of{)vercxpressing them. Second. it is notoriously (tiflictllt to obtain crystals of n'Jcnqbranc proteins t h a t ctrc suitable for strticttirat anat',,-sis t)v X-rot\- diffraction, t+]lcctr(m diffraction ut" two-dimcn~ioncll (2[)) crystals, whicll seem t(, form morc readily than three-dimensional crystals [11, is an alternative approach of growing importance, ~.iS t h e s t r t l c t u r c s ()f bactcriorhodopsh~ I21 :ind o f plant light-harvesting COml,lex LI-I II 13] demonstrate. fli~h-rcsolution structural analysis of m e m b r a n e proteins by single-particle analysis is also theoretically possible 141 but, tit present, it is a m o r t distant prospect. Anothcr alternative for small m c m b r a n c proteins is NNIR analysis in organic solvents such :is chlorotk)rm. This method was used in the structural study of the c subunit of the I:~)membrane domain of bacterial F i F o - A T P a s c s , us discussed in Fillinvame's review (pp 491-498). f-towcver, it remains to be established that the structure in the organic
soh'ent is an accurate representation of the protein's structure in a phospholipid bilayer. Despite these difficulties, the high-resolution structural database for m e m b r a n e proteins has grown significantly during the last year with the publication of the crystal structures of cytochrome oxidase and of a bacterial light-harvesting complex. T h e structure of a bacterial c y t o c h m m e c oxidase is discussed in this issue by Ostermeier, Iwata and Michel (pp 460~166). It: should be compared with the structure of the bovine mitochondrial enzyme, which was determined in parallel by Tsukihara et a/. [5]. Recently, it has been described in a more c o m p l e t e form than previously at 2.8/~, resolution [6]. T h e b o t t l e n e c k of co'stallization has been addressed by Michel's group, who have introduced a novel approach in which monoclonal antibody fragments are bound to the m e m b r a n e complex with the idea of e x t e n d i n g the hydrophilic domains of the m e m b r a n e protein. T h e i r antibody recognizes a discontinuous e p i t o p e on the m e m b r a n e - e x p o s e d domain of cytochrome c oxidase, and it can be assumed to stabilize one conformation of the complex. This work has d e m a n d e d considerable effort. In particular, the cloning of tke correct c D N A from a hvbridoma cell line and the production of the Fv fragment is critical for crystal formation. All p r o t e i n - p r o t e i n contacts in one plane of the crystal latticc :ire formed by the fragment. In contrast, the crystals grown by Yoshikawa's group were produced by conventional means in a long-term effort that took twenty years. It is comfl~rtin< to workers in the cvtochrome oxidase field that most of their prcdictions made on the basis of spcctn)scop'~: mutagencsis and topological studies have bccn borne out by the atomic strticturcs. [-]o~xevcr, several interesting ncw features have cnlcr,
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bacteriochlorophyll B molecules and two carotenoids. T h e mode of chlorophyll binding divides them into two groups that absorb light at different wavelengths. Somewhat surprisingly, the structure of the related L H 2 complex from Rps. motischianum, which was also published recently, revealed an octameric ring. This variation in the ring may indicate that other arrangements may also be possible. T h e structure of LH1 has been determined at a lower resolution by the electron diffraction of 2D crystals. T h e oligomer also has a ring structure, but with sixteen subunits. As Fyfe and Cogdell point out, the basic structural motif of purple bacterial LHs has now been established, and it is a ring. T h e y also note that one intriguing problem that arises is the coassembly of otigomers with different pigment contents. T h e long march to the high-resolution structure of photosystem I (PSI) is the topic of Fromme's review (pp 473-484). Many laboratories share the effort, bt, t the Berlin group seems to hold the lead. T h e current refinement of the PSI structure is being published at 4 resolution. This structure now allows the assignment of most of the transmembrane helices and several prosthetic groups and metal centres. It has taken three years of tedious work to improve the resolution from 6 ~ to 4 ~ . If progress follows a linear course, the first high-resolution structure will be ready in 1998. More than 15 years ago, long before the structure of any membrane protein had been determined to atomic resolution, crystals of an Eschetichia coli porin were shown to be suitable for X-ray analysis, but, alas, the structure has defied solution until this year. In the meantime, the structures of several other porins have been determined, starting with that of a Rhodobacter porin published in 1990 [7]. As discussed by Schulz (pp 485-490), one of the authors of this landmark publication, the porins are a special class of membrane protein that contain an antiparallel [3-barrel structure with a channel running through the middle. T h r e e barrels associate to form a trimeric assembly. T h e porins fall into two classes: 'general' pores with 16 [3 strands forming the barrel, and 'specific' pores, which contain a wider barrel of 18 strands, but, paradoxically, with a narrower channel. T h e structure of the specific pore, maltoporin, and the translocation pathway of malto-oligosaccharides along a helical staircase •of aromatic amino acids have been elucidated during the past year. Whether structures similar to those of the porins are found in eukaryotes has been a controversial issue, but there is a growing body of evidence that the porins found in mitochondrial membranes may be [3 structures. One feature of the bacterial porins that has helped their structural analysis is their stability. T h e importance of this property is underlined by recent experiments in which native porins have been refolded from inclusion bodies, thus opening the way to mutagenesis and protein-engineering experiments.
T h e H+-transporting FIF0-ATPases from eubacteria, mitochondria and chloroplasts, and their cousins, the H +transporting V-ATPases found in the membranes of a variety of vesicular structures and in Archaebacteria, are discussed by Fillingame. T h e y are multisubunit enzymes with a globular catalytic domain attached by a stalk to a membrane domain that transports protons. T h e two domains can be separated from each other and studied independently. Unsurprisingly, the globular domain is better understood than the membrane part. An atomic structure containing 2983 of the 3435 amino acids of FI-ATPases from bovine heart mitochondria was described two years ago [8], and a structure of the individual E. coli e-subunit (139 amino acids), which is also part of F1, was determined by N M R more recently [9]. T h e structure of F1-ATPase has reawakened the notion that the enzyme might operate by a rotary mechanism in which the properties of the three catalytic sites of the enzyme are interconverted through a cycle of binding states, described by Boyer in his binding-change mechanism [10], by the rotation of a central o~-helical coiled-coil structure. More recently, the rotary mechanism has received further experimental support [11-13]. An important question that is now emerging is how can a rotary motion be generated by the transport of protons through the F 0 membrane domain? Clearly, an atomic structure of F 0 would help in formulating such a mechanism. Fillingame's review summarizes our current fragmentary knowledge of this domain. A second related issue concerns the transmission of energy from the membrane domain to the catalytic sites, a distance of about 100~. T h e stalk between the F 1 and F 0 domains must participate in this process, and so Fillingame has also summarized our knowledge of this component, and has presented an account of the insights into the mechanism of the F- and V-ATPases that have been gained from high-resolution structural knowledge. Just as the globular and membrane parts of the F-ATPases can be separated biochemically and their structures studied independently, it is also possible to separate intrinsic and extrinsic membrane domains, for example, within the same polypeptide chain by genetic manipulation or by chemical synthesis, and to determine the structures of the component parts. This approach is discussed by Montal (pp 499-510) in his review of protein folds in channel structures. It may be possible, therefore, to build up a repertoire of modular folds that are found in membrane proteins, and then to use this repertoire to build up the structures of other membrane proteins by assembling appropriate modules together. An underlying and controversial assumption of this approach is that complex topologies consisting of mixed o~13 structures remain to be discovered among membrane proteins. T h e well-established membrane protein structures are either all or-helical bundles (as in cytochrome oxidase,
Editorial overview Walker and Saraste
bacteriorhodopsin and bacterial photosynthetic reaction centres, for example) or they are all 13 structures (as in the porins). However, it might be prudent to remember that after the structures of haemoglobin and myoglobin were determined and until the structure of lysozyme was solved, it was thought by some that all globular proteins might be ot helical (so we are told). The model of the membrane part of the acetylcholine receptor channel at 9.~ resolution has been suggested to contain a bundle of five o~ helices surrounded by an outer rim of three-stranded antiparalle113 sheets [14], but this will need to be confirmed by a higher resolution structure. Perutz [15] has written "when in 1953 I discovered that the phase problem of protein crystallography could be solved by isomorphous replacement with heavy atoms, I expected that the structures, not only of haemoglobin, but also of many other (globular) protein structures would presently be solved, but this did not happen. Only three structures had been soh, cd by 1965, and only I1 by 1970. The practical difficulties of crystallization, of preparing isomorphous heavy atom derivatives and of recording the X-ray diffraction data were so great that determination of each new structure took many years." Likewise, from 1985, when the first atomic resolution structure of an integral membrane protein was described [16], to the present da>, a small number of membrane protein structures have been solved, and the rate of determination of new structures in this class of proteins is unlikely to increase significantly until general solutions are found to overcome the severe practical problems of overproduction and crystallization of membrane proteins. Perutz also noted that in the 1950s and 1960s, professional crystallographers were reluctant to enter the risky new field of protein crystallograph,~, and there is a similar general reluctance to enter the tough world of membrane protein structural analysis at present. The reviews here discuss both the problems and possible solutions of membrane protein crystallograp3, and they illustrate vividly that each success has brought its rewards with spectacular leaps forward in understanding of membrane protein function.
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