Alpha-Domain Structures

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. 

Coiled-coil a helices contain a repetitive heptad amino acid sequence pattern 

In the heptad sequence ate close to the hydrophobic core and can form salt bridges between the two a helices of a colled-coll structure, the e-resldue In one helix with the g-resldue In the second and vice versa. 

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The most frequent of the domain structures are the alpha/beta (a/P) domains, which consist of a central parallel or mixed P sheet surrounded by a helices. All the glycolytic enzymes are a/p structures as are many other enzymes as well as proteins that bind and transport metabolites. In a/p domains, binding crevices are formed by loop regions. These regions do not contribute to the structural stability of the fold but participate in binding and catalytic action. 

It can be assumed that the amino acids following this hinge region (Val 93 to Leu 447) are part of the head domain. The point of papain cleavage is at amino acid 82 27. TTie core part of the polypeptide chain is mainly folded in )3-sheets (34 %) and to a lesser extent (15 %) arranged in alpha-helical structures 7. In contrast with CBH I the core of CBH II possesses only 2 disulfide bridges (176-235 368-415) and four free sulfhydryl groups. Similarly to CBH I carboxyl functions are involved in the active center (Asp 175 and Glu 184) 28. 

Wiche, G., Becker, B., Luber, K., Weitzer, G., Castanon, M. J., Hauptmann, R., Stratowa, C., and Stewart, M. (1991). Cloning and sequencing of rat plectin indicates a 466-kD polypeptide chain with a three-domain structure based on a central alpha-helical coiled coil. /. Biol. Chem. 114, 83-99. 

Fig. 1 Structure of the neuronal SNAREs. Upper panel domain structure of the three neuronal SNARE proteins involved in synaptic vesicle fusion. Syntaxin 1A and SNAP-25 (contains two SNARE motifs) are associated with the presynaptic membrane, whereas synaptobrevin 2 is synaptic vesicle associated. The SNARE motifs form a stable complex (core complex) whose crystal structure has been analyzed (lower panel). In the complex, each of the SNARE motifs adopts an alpha-helical structure, and the four alpha-helices are aligned in parallel forming a twisted bundle (modified from Sutton et al. 1998). Stability of the complex is mediated by layers of interaction (—7 to +8) in which amino acids from each of the four alpha-helices participate (see text).

Figure 7.9 Topological structures of a-amylase A. Two-dimensional representation of the secondary and domain structures of porcine pancreatic a-amylase. Alpha helices are represented as circles and (3-strands in the up-direction as squares, and in the down direction as double squares. The (a/(3)g—TIM barrel comprises domain A. Hydrogen bonds between (3-strands are shown by dashed lines. The a-helices and (3-strands are identified in the various domains by A, B and C. (Reprinted by permission ofthe authors M. Qian et al.120) Two-dimensional representation ofthe secondary and domain structures of barley malt a-amylase (AMY2-2). Alpha helices are represented as cylinders and (3-strands as arrows. The (a/(3)g—TIM barrel comprises domain A, with eight (3-strands and an equivalent of eight a-helices. The active-site is composed ofthe loops that connect the C-termini ofthe (3-strands to the N-termini ofthe peripheral a-helices. (Adapted from A. Kadziola et al.121)...

Li-Smerin, Y, Hackos, D. H., and Swartz, K. J. (2000). Alpha-helical structural elements within the voltage-sensing domains of a K+ channel./ Gen. Physiol. 115, 33-50. 

In addition to Pgp-mediated MDR, there is also a non-Pgp-mediated MDR phenomenon. This comprises another ABC transporter subfamily that is called the MRP-family. At least seven members have been identified, and five (MRP 1, -3, -4, -5, and -6) of them are expressed at the BBB [(44,91) reviewed by Borst (92,93)]. The MRPs are membrane-fixed systems that vary in size from 1325 to 1545 amino acids (92). They comprise two transmembrane domains of six alpha hehces, a cytoplasmic linker region, and two intracellular ABCs. The linker region is essential for its transport function (94,95). In addition, MRP1, -2, -3, and -6 have an extra domain structure comprising five additional transmembrane-segments at the animo-end (92,96). Today, MRPs are considered amphipatic anion efflux pumps. 

Hi, R., Osada, S., Yumoto, N., and Osumi, T. Characterization of the amino-terminal activation domain of peroxisome proliferator-activated receptor alpha. Importance of alpha-helical structure in the transactivating function. J Biol Chem 274 (1999) 35152-35158. 

The structure of the kinesin monomer is classified into the three subdomains—head, neck-linker, and tail (see Figure I.IA). The head domain (residue 1-323) contains a nucleotide-binding pocket, a catalytic site, which controls the conformational state of the neck-linker (residue 324-338) made of 15 amino acids. The neck-helix domain (residues from 339 to the C-terminus), extended from the neck-linker, forms an alpha-helical structure dimeric kinesins are made via coiled-coil interactions between the neck-helices from two monomers (see Figure I.IA). 

The domain of a protein is determined by its secondary structure. There are four main types of domain structures alpha-helix, beta sheet, beta-turn, and random coil. 

CATH includes four classes (C) alpha, beta, alpha and beta, and few secondary structure (ESS). The alpha-beta class includes both alternating alpha/beta structures and alpha -I- beta structures, originally defined by Levitt and Chothia. The class of a protein domain is determined according to its secondary structure composition and packing. Ninety percent of the protein domains were automatically assigned to their class in CATH 2.5.1, using the method developed by Michie et The remaining 10% of domains... 

A number of design principles are not specific to magainin-related peptides, but are shared with many peptides, or domains of proteins, which disrupt membrane function. Common features of working models include an abundance of basic amino acids to provide an electrostatic attraction to negatively-charged membranes the adoption of an alpha-helical structure in hydrophobic environments and the assembly of peptide monomers into a multimeric structure that can span a membrane and form a hydrophilic pore (e.g. 13-16),... 

Figure 1.1 The amino acid sequence of a protein s polypeptide chain is called Its primary structure. Different regions of the sequence form local regular secondary structures, such as alpha (a) helices or beta (P) strands. The tertiary structure is formed by packing such structural elements into one or several compact globular units called domains. The final protein may contain several polypeptide chains arranged in a quaternary structure. By formation of such tertiary and quaternary structure amino acids far apart In the sequence are brought close together in three dimensions to form a functional region, an active site.

Figure 4.4 Schematic diagram of the structure of the a/p-barrel domain of the enzyme methylmalonyl-coenzyme A mutase. Alpha helices are red, and p strands are blue. The inside of the barrel is lined by small hydrophilic side chains (serine and threonine) from the p strands, which creates a hole in the middle where one of the substrate molecules, coenzyme A (green), binds along the axis of the barrel from one end to the other. (Adapted from a computer-generated diagram provided by P. Evans.)...

FIGURE 21.11 The structure of UQ-cyt c reductase, also known as the cytochrome hci complex. The alpha helices of cytochrome b (pale green) define the transmembrane domain of the protein. The bottom of the structure as shown extends approximately 75 A into the mitochondrial matrix, and die top of the structure as shown extends about 38 A into the intermembrane space. (Photograph kindly provided by Di Xia and Johann Deismhofer [From Xia, D., Yn, C.-A., Kim, H., Xia,J-Z., Kachnrin, A. M., Zhang, L., Yn,... 

Starting from a collection of samples remarkably well resolved (alpha > 6) on Chiralcel OD (Cellulose tris(3,5-dimethylphenylcarbamate) coated on aminopropyl silica), a putative three-point enantiophore for binding to CSR was derived (Fig. 4-10). This enantiophore query was used to search (CFS 3D search) within a list comprising 4203 compounds tested on Chiralcel OD. From this search domain of CHIRBASE 3D, 191 structures were found to match the enantiophore. 

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

Anand K, Palm GJ, Mesters JR, SiddeU SG, Ziebuhr J, HUgenfeld R (2002) Structure of coron-avirus main proteinase reveals combination of a chymotrypsin fold with an extra alpha-heUcal domain. EMBO J 21 3213-3224... 

The N-terminal domain of the OCP is an orthogonal alpha-helical bundle, subdivided into two four-helix bundles (Figure 1.3a and c). These subdomains are composed of discontinuous segments of the polypeptide chain (gray and white in Figure 1.3c). To date, the OCP N-terminal domain is the only known protein structure with this particular fold (Pfam 09150). The hydroxyl terminus of the 3 -hydroxyechinenone is nestled between the two bundles. The C-terminal domain (dark... 

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