In membrane-bound proteins

Alpha helices are sufficiently versatile to produce many very different classes of structures. In membrane-bound proteins, the regions inside the membranes are frequently a helices whose surfaces are covered by hydrophobic side chains suitable for the hydrophobic environment inside the membranes. Membrane-bound proteins are described in Chapter 12. Alpha helices are also frequently used to produce structural and motile proteins with various different properties and functions. These can be typical fibrous proteins such as keratin, which is present in skin, hair, and feathers, or parts of the cellular machinery such as fibrinogen or the muscle proteins myosin and dystrophin. These a-helical proteins will be discussed in Chapter 14. 

The first approach has successfully been applied to the study of amorphous as well as to macroscopically ordered solids. Examples of applications include the determination of backbone geometries in fibrous proteins [4] or the determination of protein-backbone, side-chain, and bound-ligand orientation with respect to the membrane normal in membrane-bound proteins [5-8]. Membranes, bilayers, bicelles, or liposomes are neither solid nor liquid systems but have aspects of both and are sometimes liquid crystalline. In most of these systems, time-independent anisotropic interactions play an important role,... 

The mitochondrion is bounded by two pho-spholipid membranes. The outer membrane is freely permeable to molecules, including water, with a molecular weight of up to about 5000. The inner membrane is rich in membrane-bound proteins and consists, in terms of membrane area, of 50% phospholipid and 50% protein (Lenaz, 1988). Pyruvate dehydn>genase, a mitochondrial enzyme, is water soluble. The proteins of the respiratory chain, as well as ATP synthase, are all bound to the inner mitochondrial membrane. The enzymes of the Krebs cycle are water soluble, with the exception of succinate dehydrogenase. This enzyme is bound to the mitochondrial membrane, where it directly funnels electrons, via HAD, to the respiratory chain. 

Adeleoth, P., Bezezinski, P., Surface-mediated proton-transfer reactions in membrane-bound proteins, Biochim. Biophys. Acta, 2004, 1655, 102-115. 

D. vulgaris and two ionizable centers in D. desulfuricans ATCC27774 that result in concerted two-electron/two-proton transfer steps has been called proton-thrusting, because it is akin to the redox-linked proton-transfer mechanisms seen in membrane-bound protein complexes involved in proton pumping. 

As with the Biuret assays it may be necessaty to remove soluble materials that interfere with the assay. Common interfering agents include a number of common buffers (e.g. HEPES) and neutral detergents (e.g. Triton XiOO). Indeed the Folin method is notorious for the number of compounds that interfere (5, 6). One of the easiest approaches is to precipitate the protein using icecold trichloroacetic add (TCA) as described above under the Biuret assay. A number of variations on the original method have been developed to overcome interference, particularly by detergents in membrane-bound proteins (9). 

The line width of the EPR spectrum of a radical such as a nitroxide in solution is sensitive to motion in the range of correlation times 10 -10" s. This is due to the anisotropy of the hyperfine splitting. If the motion is rapid enough to average this anisotropy, the spectrum shows narrow lines. For slower motion the spectrum broadens out. The rate of motion is determined by simulation, or by comparison with labelled molecules of known correlation time. By means of an experimental technique known as saturation-transfer EPR the spectra may be made to be sensitive to correlation times up to 10 s, as found, for example, in membrane-bound proteins. 

The modem era of biochemistry and molecular biology has been shaped not least by the isolation and characterization of individual molecules. Recently, however, more and more polyfunctional macromolecular complexes are being discovered, including nonrandomly codistributed membrane-bound proteins [41], These are made up of several individual proteins, which can assemble spontaneously, possibly in the presence of a lipid membrane or an element of the cytoskeleton [42] which are themselves supramolecular complexes. Some of these complexes, e.g. snail haemocyanin [4o], are merely assembled from a very large number of identical subunits vimses are much larger and more elaborate and we are still some way from understanding the processes controlling the assembly of the wonderfully intricate and beautiful stmctures responsible for the iridescent colours of butterflies and moths [44]. 

In this chapter we describe some examples of structures of membrane-bound proteins known to high resolution, and outline how the elucidation of these structures has contributed to understanding the specific function of these proteins, as well as some general principles for the construction of membrane-bound proteins. In Chapter 13 we describe some examples of the domain organization of receptor families and their associated proteins involved in signal transduction through the membrane. 

The reaction center is built up from four polypeptide chains, three of which are called L, M, and H because they were thought to have light, medium, and heavy molecular masses as deduced from their electrophoretic mobility on SDS-PAGE. Subsequent amino acid sequence determinations showed, however, that the H chain is in fact the smallest with 258 amino acids, followed by the L chain with 273 amino acids. The M chain is the largest polypeptide with 323 amino acids. This discrepancy between apparent relative masses and real molecular weights illustrates the uncertainty in deducing molecular masses of membrane-bound proteins from their mobility in electrophoretic gels. 

Figure 12.14 The three-dimensional structure of a photosynthetic reaction center of a purple bacterium was the first high-resolution structure to be obtained from a membrane-bound protein. The molecule contains four subunits L, M, H, and a cytochrome. Subunits L and M bind the photosynthetic pigments, and the cytochrome binds four heme groups. The L (yellow) and the M (red) subunits each have five transmembrane a helices A-E. The H subunit (green) has one such transmembrane helix, AH, and the cytochrome (blue) has none. Approximate membrane boundaries are shown. The photosynthetic pigments and the heme groups appear in black. (Adapted from L. Stryer, Biochemistry, 3rd ed. New York ...

Important novel information has thus been obtained for the specific biological function of those molecules, but disappointingly few general lessons have been learned that are relevant for other membrane-bound proteins with different biological functions. In that respect the situation is similar to the failure of the structure of myoglobin to provide general principles for the construction of soluble protein molecules as described in Chapter 2. 

From the human genome project it is known, that roughly 30,000 proteins exist in humans. Currently only the 3D-structures of few thousand human pr oteins or protein domains are known. Structures of membrane-bound proteins are several magnitudes rarer. Beside efforts to solve further structures like structural genomics, there is a challenge for computational approaches to predict structures and function for homologous proteins. 

SNAREs is an acronym for soluble NSF acceptor protein receptors. They are a superfamily of small and mostly membrane-bound proteins that are distinguished by the presence of a conserved stretch of 60 amino acids referred to as a SNARE motif. With few exceptions, a single transmembrane domain is located adjacent to the SNARE motif at the C-terminal end. Many SNAREs possess in addition an independently folded N-terminal domain whose structures are more diverse. 

The procedure for purification of Na,K-ATPase in membrane-bound form from the outer renal medulla of mammalian kidney offers the opportunity of exploring the structure of the Na,K-pump proteins in their native membrane environment. The protein remains embedded in the membrane bilayer throughout the purification procedure thus maintaining the asymmetric orientation of the protein in the baso-lateral membrane of the kidney cell in the purified preparation. This preparation has been particularly useful in studies of ultrastructure, protein conformation and for... 

In bacteria, accumulation of substrates against a concentration gradient can occur through two main classes of transport systems (see [30] for a summary). The prototype of the first class of transporters is the /3-galactoside permease of Escherichia coli (see [31]). It is a relatively simple system involving only a single membrane-bound protein. It catalyzes a lactose-H symport. Other transporters... 

Carotenoids are also present in animals, including humans, where they are selectively absorbed from diet (Furr and Clark 1997). Because of their hydrophobic nature, carotenoids are located either in the lipid bilayer portion of membranes or form complexes with specific proteins, usually associated with membranes. In animals and humans, dietary carotenoids are transported in blood plasma as complexes with lipoproteins (Krinsky et al. 1958, Tso 1981) and accumulate in various organs and tissues (Parker 1989, Kaplan et al. 1990, Tanumihardjo et al. 1990, Schmitz et al. 1991, Khachik et al. 1998, Hata et al. 2000). The highest concentration of carotenoids can be found in the eye retina of primates. In the retina of the human eye, where two dipolar carotenoids, lutein and zeaxan-thin, selectively accumulate from blood plasma, this concentration can reach as high as 0.1-1.0mM (Snodderly et al. 1984, Landrum et al. 1999). It has been shown that in the retina, carotenoids are associated with lipid bilayer membranes (Sommerburg et al. 1999, Rapp et al. 2000) although, some macular carotenoids may be connected to specific membrane-bound proteins (Bernstein et al. 1997, Bhosale et al. 2004). 

Protein/peptide hormones are derived from amino acids. These hormones are preformed and stored for future use in membrane-bound secretory granules. When needed, they are released by exocytosis. Protein/peptide hormones are water soluble, circulate in the blood predominantly in an unbound form, and thus tend to have short half-lives. Because these hormones are unable to cross the cell membranes of their target tissues, they bind to receptors... 

Inositol triphosphate (IP3)-gated channels are also associated with membrane-bound receptors for hormones and neurotransmitters. In this case, binding of a given substance to its receptor causes activation of another membrane-bound protein, phospholipase C. This enzyme promotes hydrolysis of phosphatidylinositol 4,5-diphosphate (PIP2) to IP3. The IP3 then diffuses to the sarcoplasmic reticulum and opens its calcium channels to release Ca++ ions from this intracellular storage site. 

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